Contacts of the helix formed by residues 9 - 37 (chain I) in PDB entry 2QJK
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 GLY 9 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10I THR* 1.3 58.5 + - - -
11I ARG* 3.2 27.1 + - - +
12I ARG* 3.3 41.6 + - - +
13I ASP* 3.9 8.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 10 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9I GLY* 1.3 70.9 - - - -
11I ARG* 1.3 59.3 + - - +
12I ARG 3.6 0.7 - - - -
13I ASP* 3.8 16.6 + - + +
14I PHE* 3.2 35.0 + - + +
17I TYR* 6.4 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 11 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250H ARG* 4.5 17.1 + - - +
9I GLY* 3.2 20.4 - - - +
10I THR* 1.3 82.1 - - - +
12I ARG* 1.3 63.7 - - + +
14I PHE* 3.6 9.3 - - - +
15I LEU* 3.6 15.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 12 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250H ARG* 4.7 16.6 - - + +
9I GLY* 3.3 39.3 + - - +
11I ARG* 1.3 78.7 - - + +
13I ASP* 1.3 68.1 + - + +
15I LEU* 3.1 9.4 + - - +
16I TYR* 2.9 57.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 13 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9I GLY 3.9 5.4 - - - +
10I THR* 3.8 27.0 + - + +
11I ARG 3.4 0.4 - - - -
12I ARG* 1.3 84.3 + - + +
14I PHE* 1.3 65.2 + - - +
16I TYR* 3.4 12.6 + - - +
17I TYR* 3.0 57.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 14 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243H LEU* 5.7 3.8 - - + -
10I THR* 3.2 30.0 + - + +
11I ARG* 3.6 9.6 - - - +
12I ARG 3.2 0.4 - - - -
13I ASP* 1.3 75.4 - - - +
15I LEU* 1.3 73.8 + - + +
17I TYR* 2.8 9.0 + - + +
18I ALA* 2.7 57.9 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 15 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243H LEU* 4.0 28.0 - - + +
246H LEU* 4.1 20.6 - - + +
247H THR* 3.6 45.3 - - + +
250H ARG* 4.7 19.7 - - - +
11I ARG 3.6 7.5 + - - +
12I ARG* 3.1 9.4 + - - +
14I PHE* 1.3 96.4 - - + +
16I TYR* 1.3 61.7 + - + +
18I ALA* 2.9 2.8 + - - +
19I THR* 2.7 36.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 16 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250G ILE* 6.0 4.5 - - + -
247H THR* 4.2 27.0 + - + -
250H ARG* 5.8 4.6 - - + +
251H LEU* 4.6 22.7 + - + +
12I ARG* 2.9 51.6 + - + +
13I ASP* 3.6 18.6 - - - +
15I LEU* 1.3 84.6 - - + +
17I TYR* 1.3 59.3 + - + +
19I THR* 3.7 7.6 - - - +
20I ALA* 3.1 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 17 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10I THR* 6.4 0.4 - - + -
13I ASP* 3.0 42.1 + - - +
14I PHE* 2.8 10.5 + - + +
16I TYR* 1.3 76.4 - - + +
18I ALA* 1.3 63.5 + - - +
19I THR 3.2 1.3 - - - -
20I ALA* 4.5 7.1 - - + +
21I GLY* 3.3 17.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 18 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243H LEU* 4.0 18.0 - - + +
14I PHE* 2.7 45.9 + - + -
15I LEU* 3.5 7.9 - - - +
17I TYR* 1.3 71.9 - - - +
19I THR* 1.3 63.0 + - - +
21I GLY* 3.5 1.6 + - - -
22I ALA* 3.2 21.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 19 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240H LEU* 4.6 5.5 - - + +
243H LEU* 3.7 24.7 - - - +
244H LEU* 4.3 20.2 + - + +
247H THR* 3.4 25.4 + - + +
15I LEU* 2.7 15.8 + - - +
16I TYR* 3.7 9.0 - - - +
18I ALA* 1.3 73.6 - - - +
20I ALA* 1.3 70.7 + - + +
21I GLY 2.7 5.3 + - - -
22I ALA* 2.8 15.0 + - - +
23I GLY* 3.0 9.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 20 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16I TYR 3.1 15.4 + - - +
17I TYR* 4.5 9.6 - - + +
19I THR* 1.3 84.0 - - + +
21I GLY* 1.3 62.0 + - - +
23I GLY* 3.4 3.6 + - - +
24I ALA* 3.1 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 21 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17I TYR 3.3 14.3 + - - -
18I ALA* 3.7 5.4 - - - -
19I THR 2.7 3.2 + - - -
20I ALA* 1.3 75.2 - - - +
22I ALA* 1.3 64.0 + - - -
23I GLY 3.2 0.2 + - - -
24I ALA* 3.2 7.0 + - - +
25I VAL* 3.0 26.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 22 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236H PHE* 4.1 8.8 - - + +
239H VAL* 5.6 4.0 - - + -
240H LEU* 3.9 25.8 - - + +
243H LEU* 4.6 9.6 - - + -
18I ALA 3.2 11.3 + - - +
19I THR 2.8 10.6 + - - +
21I GLY* 1.3 70.3 - - - -
23I GLY* 1.3 67.8 + - - +
25I VAL* 3.1 12.4 + - - +
26I ALA* 3.0 21.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 23 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240H LEU* 4.4 12.2 - - - +
19I THR 3.0 12.1 + - - -
20I ALA* 3.7 5.6 - - - -
22I ALA* 1.3 79.2 - - - +
24I ALA* 1.3 64.9 + - - +
26I ALA* 3.0 5.7 + - - +
27I THR* 2.9 25.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 24 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20I ALA 3.1 12.9 + - - +
21I GLY* 3.2 9.8 + - - +
23I GLY* 1.3 73.8 - - - +
25I VAL* 1.3 64.0 + - + +
27I THR* 3.1 10.3 + - - -
28I GLY* 3.0 20.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 25 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236H PHE* 3.2 28.0 - - + -
21I GLY 3.0 19.0 + - - +
22I ALA* 3.3 12.1 - - - +
24I ALA* 1.3 76.3 - - - +
26I ALA* 1.3 65.9 + - - +
28I GLY* 3.3 1.7 + - - -
29I ALA* 3.0 17.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 26 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236H PHE* 3.3 26.4 - - + -
237H LEU* 6.4 1.1 - - + -
240H LEU* 5.0 10.3 - - + -
22I ALA 3.0 6.8 + - - +
23I GLY* 3.0 10.6 + - - +
25I VAL* 1.3 76.4 - - - +
27I THR* 1.3 58.6 + - - +
29I ALA* 2.5 30.8 + - - +
30I ALA* 3.0 9.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 27 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23I GLY 2.9 19.7 + - - -
24I ALA* 3.2 15.0 - - - +
26I ALA* 1.3 73.4 - - - +
28I GLY* 1.3 63.0 + - - +
30I ALA* 3.2 9.2 + - - +
31I VAL* 3.1 33.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 28 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24I ALA 3.0 13.9 + - - -
25I VAL 3.7 2.5 - - - -
26I ALA 2.8 1.0 + - - -
27I THR* 1.3 72.1 - - - +
29I ALA* 1.3 57.5 + - - +
30I ALA 2.9 5.7 + - - -
31I VAL* 3.0 9.6 + - - +
32I TRP* 2.8 33.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 29 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236H PHE* 4.3 17.5 - - + -
25I VAL 3.0 12.8 + - - +
26I ALA* 2.5 22.3 + - - +
28I GLY* 1.3 70.8 - - - +
30I ALA* 1.3 52.3 + - - -
32I TRP* 5.0 2.7 - - - -
33I PRO* 2.9 24.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 30 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26I ALA 3.0 7.2 + - - +
27I THR* 3.2 13.2 - - - +
28I GLY 2.9 0.2 - - - -
29I ALA* 1.3 76.8 - - - +
31I VAL* 1.3 65.2 + - + +
33I PRO* 2.8 25.6 - - - +
34I LEU* 3.4 16.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 31 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27I THR* 3.2 26.0 - - + +
28I GLY* 3.0 10.1 + - - +
30I ALA* 1.3 76.7 - - + +
32I TRP* 1.3 67.5 + - - +
34I LEU* 3.0 23.8 + - + +
35I ILE* 3.1 34.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 32 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28I GLY 2.8 18.2 + - - +
29I ALA* 4.5 2.9 - - - +
31I VAL* 1.3 74.7 - - - +
33I PRO* 1.3 61.9 - - + +
35I ILE* 2.7 36.1 + - + +
36I ASN* 2.6 70.8 + - + +
39I ASN* 4.3 6.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 33 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88G ASN 4.5 5.6 - - - +
89G GLY* 6.0 4.0 - - - -
93G LEU* 4.9 10.8 - - + +
29I ALA 2.9 23.6 - - - +
30I ALA* 2.8 25.8 - - - +
32I TRP* 1.3 93.2 - - + +
34I LEU* 1.3 59.8 + - + -
36I ASN* 3.8 9.4 - - + -
37I GLN* 3.1 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 34 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60G VAL* 4.1 28.9 - - + -
61G THR* 5.1 1.6 - - + +
64G VAL* 3.8 25.4 - - + +
93G LEU* 4.6 16.8 - - + -
30I ALA* 3.6 18.2 - - + +
31I VAL* 3.0 19.1 + - + +
33I PRO* 1.3 79.6 - - + +
35I ILE* 1.3 60.2 + - + +
37I GLN* 3.1 29.3 + - - +
38I MET* 5.4 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 35 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31I VAL* 3.2 33.4 - - + +
32I TRP* 2.7 27.8 + - + +
34I LEU* 1.3 79.5 - - + +
36I ASN* 1.3 67.7 + - - +
37I GLN 3.1 2.0 - - - -
38I MET* 3.0 13.9 + - - +
179J TRP* 3.0 47.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 36 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88G ASN* 3.0 27.8 + - + +
32I TRP* 2.6 52.8 + - + +
33I PRO* 4.1 6.7 - - + -
35I ILE* 1.3 74.5 - - - +
37I GLN* 1.3 53.2 + - - +
39I ASN* 2.6 63.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 37 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64G VAL* 3.7 24.9 - - + +
67G MET* 3.6 16.4 - - - +
68G HIS* 2.7 38.5 + - - -
87G VAL* 3.8 21.4 - - + +
88G ASN* 3.6 25.9 + - - +
93G LEU* 4.3 8.7 - - + -
33I PRO 3.1 14.6 + - - +
34I LEU* 3.1 27.1 + - - +
36I ASN* 1.3 75.0 - - - +
38I MET* 1.3 89.1 + - - +
39I ASN 3.4 7.8 + - - +
----------------------------------------------------------
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