Contacts of the helix formed by residues 8 - 36 (chain K) in PDB entry 2DYS
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASP 8 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75D THR* 5.0 10.4 - - - +
6K ALA 3.6 3.6 + - - +
7K PRO* 1.3 70.8 - - - +
9K PHE* 1.3 64.6 + - - +
10K HIS* 3.1 24.8 + - + +
11K ASP* 2.9 36.5 + - - +
12K LYS* 3.0 32.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 9 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
606A PGV 4.0 87.8 + - + +
80D THR* 3.8 26.5 - - + -
8K ASP* 1.3 77.7 - - + +
10K HIS* 1.3 70.6 + + + +
12K LYS* 4.4 7.7 - - - +
13K TYR* 2.7 72.6 + + + +
17K VAL* 4.6 11.2 - - + -
12M PRO* 5.7 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 10 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A THR* 3.6 17.5 + - + -
606A PGV 3.6 33.7 + - + -
75D THR* 5.3 3.6 - - + -
76D ASN* 3.5 34.9 - - + +
77D GLU* 3.6 29.5 - - + +
79D LYS* 5.0 0.3 - - - +
80D THR* 2.9 35.2 + - + +
8K ASP* 3.1 24.8 + - + +
9K PHE* 1.3 74.5 - + + +
11K ASP* 1.3 62.3 + - - +
14K GLY* 2.7 25.7 + - - +
15K ASN* 4.4 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 11 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75D THR* 5.8 0.2 - - - -
76D ASN* 3.0 30.9 + - - +
7K PRO* 3.2 21.4 - - + +
8K ASP* 2.9 34.8 + - - +
10K HIS* 1.3 78.1 - - - +
12K LYS* 1.3 65.2 + - - +
15K ASN* 4.0 14.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 12 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
606A PGV 5.2 5.9 + - - -
7K PRO* 3.5 35.3 + - + +
8K ASP* 3.0 20.6 + - - +
9K PHE* 3.8 5.9 - - - +
11K ASP* 1.3 80.1 - - - +
13K TYR* 1.3 94.0 + - + +
15K ASN* 5.1 3.3 + - - -
16K ALA* 5.5 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 13 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80D THR* 4.9 0.2 - - - -
9K PHE* 2.7 60.7 + + + +
12K LYS* 1.3 104.9 - - + +
14K GLY* 1.3 64.5 + - - +
15K ASN 3.3 2.7 - - - -
16K ALA* 3.0 15.0 + - + +
17K VAL* 2.9 28.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 14 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79D LYS* 3.5 19.6 - - - +
80D THR* 3.7 19.2 + - - -
9K PHE 3.6 0.6 + - - -
10K HIS* 2.7 28.2 + - - +
11K ASP 4.6 0.2 - - - -
12K LYS 3.9 0.4 - - - -
13K TYR* 1.3 72.4 - - - +
15K ASN* 1.3 62.1 + - - +
17K VAL* 3.3 2.2 + - - +
18K LEU* 2.9 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 15 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76D ASN* 6.0 0.6 - - - +
79D LYS* 2.6 37.9 + - - +
10K HIS 5.0 0.8 + - - -
11K ASP 4.0 17.6 + - - -
12K LYS 5.1 2.8 + - - -
13K TYR 3.3 1.0 - - - -
14K GLY* 1.3 74.2 - - - +
16K ALA* 1.3 56.4 + - - +
18K LEU* 3.5 5.5 + - - +
19K ALA* 3.0 31.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 16 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12K LYS 5.5 1.3 - - - +
13K TYR* 3.0 20.4 + - + +
15K ASN* 1.3 76.3 - - - +
17K VAL* 1.3 65.4 + - + +
19K ALA* 3.2 4.5 + - - +
20K SER* 2.9 31.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 17 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
606A PGV 4.4 18.4 - - + -
80D THR* 3.6 34.3 - - + +
83D GLY* 3.4 2.5 - - - -
84D ALA* 3.7 14.1 - - - +
9K PHE* 4.6 15.9 - - + -
13K TYR* 2.9 29.6 + - + +
14K GLY 3.7 2.9 - - - +
16K ALA* 1.3 75.7 - - + +
18K LEU* 1.3 64.9 + - - +
20K SER* 4.2 4.0 - - - -
21K GLY* 3.0 23.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 18 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78D TRP* 3.9 29.6 - - + -
79D LYS* 3.7 25.5 + - + +
82D VAL* 3.8 28.0 - - + -
83D GLY* 3.6 9.0 - - - +
86D MET* 5.3 3.4 - - - -
14K GLY 2.9 16.8 + - - +
15K ASN* 3.6 5.6 - - - +
17K VAL* 1.3 78.2 - - - +
19K ALA* 1.3 64.2 + - - +
21K GLY* 4.0 0.2 - - - -
22K ALA* 3.1 28.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 19 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15K ASN 3.0 16.2 + - - +
16K ALA* 3.8 4.0 - - - +
18K LEU* 1.3 83.2 - - + +
20K SER* 1.3 60.1 + - - +
22K ALA* 3.3 3.6 + - - +
23K THR* 3.0 31.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 20 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87D PHE* 6.2 0.2 - - - -
16K ALA* 2.9 22.5 + - - +
17K VAL* 4.0 3.1 + - - -
19K ALA* 1.3 72.1 - - - +
21K GLY* 1.3 60.8 + - - +
23K THR* 3.8 7.2 - - - +
24K PHE* 3.0 31.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 21 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83D GLY 3.5 13.7 - - - -
86D MET* 3.7 11.2 - - - +
87D PHE* 4.0 14.1 + - - -
17K VAL 3.0 19.5 + - - -
20K SER* 1.3 77.7 + - - +
22K ALA* 1.3 62.8 + - - +
24K PHE* 3.8 2.4 - - - +
25K CYS* 3.1 25.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 22 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86D MET* 3.4 30.7 - - + -
18K LEU* 3.1 20.9 + - + +
19K ALA* 3.7 4.5 - - - +
21K GLY* 1.3 77.6 - - - +
23K THR* 1.3 61.9 + - - +
25K CYS* 3.6 1.4 + - - +
26K VAL* 3.2 30.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 23 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19K ALA 3.0 19.1 + - - -
20K SER* 3.8 8.1 - - - +
21K GLY 3.3 0.2 - - - -
22K ALA* 1.3 74.8 - - - +
24K PHE* 1.3 66.8 + - - +
26K VAL* 3.9 3.6 - - - +
27K ALA* 2.9 28.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 24 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87D PHE* 3.5 55.4 - + + -
90D GLY* 3.6 23.3 - - - -
91D PHE* 3.6 6.5 - + + -
94D LEU* 4.5 20.0 - - + -
20K SER 3.0 18.7 + - - +
21K GLY* 3.8 2.5 - - - +
23K THR* 1.3 76.7 - - - +
25K CYS* 1.3 68.0 + - - +
27K ALA* 3.2 5.4 + - + +
28K VAL* 2.9 37.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 25 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86D MET* 3.1 44.6 - - + +
89D ILE* 3.9 23.8 - - - -
90D GLY* 3.8 13.2 - - - -
201D TGL 5.4 6.1 - - - -
21K GLY 3.1 11.7 + - - +
22K ALA 3.7 4.9 - - - +
24K PHE* 1.3 77.6 - - - +
26K VAL* 1.3 60.0 + - - +
28K VAL* 3.1 1.6 - - - +
29K TRP* 2.9 42.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 26 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86D MET* 4.8 10.1 - - + -
22K ALA* 3.2 18.6 + - + +
23K THR* 3.9 4.3 - - - +
25K CYS* 1.3 77.6 - - + +
27K ALA* 1.3 67.9 + - - +
29K TRP* 4.1 3.9 - - - +
30K VAL* 3.0 38.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 27 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23K THR* 2.9 24.0 + - + +
24K PHE* 3.6 7.0 - - + +
26K VAL* 1.3 79.8 - - - +
28K VAL* 1.3 57.5 + - - +
30K VAL* 3.8 3.9 - - - +
31K TYR* 3.0 29.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 28 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90D GLY* 3.2 32.5 - - - +
93D ALA* 3.6 13.9 - - + +
94D LEU* 3.8 26.2 - - + -
97D ILE* 4.0 10.0 - - + +
24K PHE* 2.9 32.8 + - + +
25K CYS 3.1 10.5 - - - +
27K ALA* 1.3 78.5 - - - +
29K TRP* 1.3 59.2 + - + +
31K TYR* 3.5 5.9 + - + +
32K MET* 3.1 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 29 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A MET* 4.6 13.0 - - + -
456A MET* 4.3 19.3 - - + -
460A ILE* 4.0 31.0 - - + -
89D ILE* 2.7 36.6 + - + +
90D GLY* 3.8 3.4 - - - -
92D THR* 4.4 1.6 - - - -
93D ALA* 3.4 25.9 - - + +
96D LEU* 4.1 15.0 - - + -
25K CYS* 2.9 37.1 + - - +
26K VAL* 4.1 4.5 - - - +
28K VAL* 1.3 77.7 - - + +
30K VAL* 1.3 62.5 + - + +
32K MET* 3.3 30.3 + - + +
33K ALA* 2.9 31.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 30 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26K VAL* 3.0 32.7 + - + +
27K ALA* 3.8 4.3 - - - +
29K TRP* 1.3 76.8 - - + +
31K TYR* 1.3 63.6 + - - +
33K ALA* 3.3 4.6 + - - -
34K THR* 3.0 40.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 31 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97D ILE* 3.6 26.8 - - + +
27K ALA 3.0 17.6 + - - +
28K VAL* 3.8 6.7 - - - +
29K TRP 3.3 0.2 - - - -
30K VAL* 1.3 80.6 - - - +
32K MET* 1.3 58.0 + - - +
35K GLN* 2.8 67.4 + - + +
36K ILE* 3.7 25.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 32 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456A MET* 3.6 33.4 - - + -
93D ALA* 4.3 7.4 - - + +
96D LEU* 3.8 28.5 - - + -
97D ILE* 3.6 29.8 - - + -
28K VAL 3.1 17.3 + - - +
29K TRP* 3.3 31.2 + - + +
31K TYR* 1.3 77.7 - - - +
33K ALA* 1.3 83.7 + - + +
34K THR 3.4 0.7 + - - -
36K ILE* 3.3 31.7 + - + +
38K ILE* 3.6 9.3 - - + +
40K TRP* 4.5 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 33 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29K TRP* 2.9 18.3 + - + +
30K VAL* 3.9 5.6 - - - +
32K MET* 1.3 87.3 - - + +
34K THR* 1.3 65.4 + - + +
36K ILE 5.4 0.2 - - - -
38K ILE* 4.7 5.7 + - - +
40K TRP* 2.9 45.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 34 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30K VAL* 3.0 28.5 + - + +
31K TYR* 4.4 0.2 - - - -
33K ALA* 1.3 88.5 - - + +
35K GLN* 1.3 80.2 + - - +
36K ILE 3.7 1.6 - - - -
37K GLY 5.2 2.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 35 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31K TYR* 2.8 56.3 + - + +
34K THR* 1.3 93.3 + - - +
36K ILE* 1.3 61.6 + - - +
37K GLY 3.7 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 36 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96D LEU 4.4 0.4 - - - +
97D ILE* 3.8 30.7 - - + +
100D LYS* 3.8 39.5 + - + +
31K TYR* 3.7 35.0 - - + +
32K MET* 3.3 30.9 + - + +
33K ALA 5.4 0.2 - - - -
34K THR 3.7 0.4 - - - -
35K GLN* 1.3 84.5 - - - +
37K GLY* 1.3 61.5 + - - +
38K ILE* 4.0 12.8 - - + -
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il