Contacts of the helix formed by residues 21 - 35 (chain K) 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 ASP 21 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12K SER* 3.9 18.9 + - - +
20K PHE* 1.3 73.8 - - - +
22K GLN* 1.3 67.0 + - - +
23K HIS* 2.9 14.3 + - - +
24K GLN* 2.6 45.2 + - + +
25K LEU* 3.0 23.9 + - - +
27K ARG* 4.9 2.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 22 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20K PHE 3.8 3.2 + - - -
21K ASP* 1.3 73.3 + - - +
23K HIS* 1.3 74.5 + - + +
25K LEU* 3.3 5.2 + - - +
26K GLN* 3.0 30.1 + - - +
55K GLY 3.8 13.8 + - - +
56K PRO* 3.2 22.4 - - - +
57K GLU* 3.5 42.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 23 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21K ASP* 2.9 15.5 + - - +
22K GLN* 1.3 80.2 + - + +
24K GLN* 1.3 66.1 + - - +
26K GLN* 2.9 23.3 + - - +
27K ARG* 2.7 41.0 + - + +
198K ASP* 6.1 5.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 24 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11K PHE* 4.9 4.9 - - - -
12K SER* 3.8 20.3 + - - -
21K ASP* 2.6 31.0 + - + +
23K HIS* 1.3 71.4 - - - +
25K LEU* 1.3 55.2 + - + +
27K ARG* 2.8 27.1 + - - +
28K GLY* 2.7 33.4 + - - -
209K GLU* 3.6 28.5 + - - +
210K ASP* 2.7 39.3 + - - +
213K ALA* 3.7 21.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 25 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20K PHE* 3.4 41.3 - - + -
21K ASP 3.0 14.5 + - - +
22K GLN 3.4 7.4 - - - +
24K GLN* 1.3 78.2 - - + +
26K GLN* 1.3 55.5 + - - +
28K GLY* 3.3 1.1 + - - +
29K LEU* 2.9 28.9 + - - +
55K GLY* 3.6 30.3 - - - +
56K PRO* 3.9 14.5 - - + +
213K ALA* 3.2 38.8 - - + +
214K PHE* 3.6 16.1 - - + +
217K TRP* 3.9 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 26 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22K GLN* 3.0 30.3 + - - +
23K HIS* 2.9 30.8 + - - +
25K LEU* 1.3 73.6 - - - +
27K ARG* 1.3 65.6 + - - +
29K LEU* 3.0 19.0 + - + +
30K GLN* 3.1 10.4 + - - +
56K PRO* 2.7 31.3 + - + +
57K GLU 4.5 1.0 + - - -
58K LEU* 3.5 30.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 27 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21K ASP* 4.9 2.4 + - - -
23K HIS* 2.7 38.6 + - + +
24K GLN* 2.8 24.0 + - - +
26K GLN* 1.3 71.3 - - + +
28K GLY* 1.3 66.0 + - - +
30K GLN* 2.8 24.6 + - - +
31K VAL* 3.1 10.2 + - - +
196K TYR* 3.5 50.5 - - + +
198K ASP* 4.8 11.2 + - - +
200K HIS* 3.6 40.2 + - - -
210K ASP* 3.2 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 28 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24K GLN 2.7 16.1 + - - -
25K LEU 3.6 3.8 - - - -
27K ARG* 1.3 72.6 - - - +
29K LEU* 1.3 53.7 + - - +
31K VAL* 2.7 26.7 + - - +
32K TYR* 2.7 13.0 + - - +
210K ASP* 4.2 1.0 - - - +
211K VAL* 3.8 21.0 - - - +
214K PHE* 3.8 20.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 29 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25K LEU 2.9 16.2 + - - +
26K GLN* 3.0 11.9 + - - +
28K GLY* 1.3 71.3 - - - +
30K GLN* 1.3 54.5 + - - +
32K TYR* 3.6 1.7 - - + +
33K THR* 2.6 40.9 + - - +
50K LEU* 3.5 31.4 - - + -
56K PRO* 5.1 5.6 - - + -
58K LEU* 4.0 25.1 - - + -
66K TYR* 3.2 37.7 - - + +
89K PHE* 4.5 4.0 - - + -
214K PHE* 3.8 31.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 30 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26K GLN 3.1 8.9 + - - +
27K ARG* 2.8 15.4 + - - +
29K LEU* 1.3 75.0 - - - +
31K VAL* 1.3 55.6 + - - +
33K THR* 3.7 4.4 - - - -
34K GLU* 2.7 72.9 + - + +
194K VAL* 3.1 25.9 - - - +
195K GLU 3.4 15.9 + - - +
196K TYR* 3.4 21.5 - - + -
197K ALA* 4.3 5.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 31 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27K ARG 3.5 9.6 - - - +
28K GLY* 2.7 14.8 + - - +
30K GLN* 1.3 69.8 - - - +
32K TYR* 1.3 67.5 + - - +
35K VAL* 2.8 34.1 + - + +
36K CYS 3.4 0.3 + - - -
189K LEU* 4.7 1.6 - - + -
194K VAL* 4.5 9.2 - - + -
196K TYR* 3.3 31.4 - - + +
207K MET* 4.4 30.7 - - + +
211K VAL* 3.8 22.0 - - + -
301K HEM 4.3 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 32 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28K GLY 2.7 12.0 + - - +
29K LEU* 3.6 4.9 - - + +
31K VAL* 1.3 76.9 - - - +
33K THR* 1.3 65.3 + - - +
36K CYS* 3.1 24.0 + - + -
37K ALA* 2.6 58.6 + - + +
40K HIS* 3.6 13.0 + - + -
41K GLY* 3.3 29.1 - - - -
42K MET* 3.0 40.9 + - + +
66K TYR* 4.6 1.8 - - - -
70K PHE* 5.8 1.1 - + - -
89K PHE* 3.8 24.6 - + - +
90K PRO* 5.0 1.0 + - - +
100K LEU* 4.7 7.6 - - + -
211K VAL* 3.9 3.7 - - + +
214K PHE* 3.5 22.9 - + + -
215K LEU* 5.1 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 33 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29K LEU* 2.6 26.2 + - - +
30K GLN* 3.7 4.2 - - - -
32K TYR* 1.3 80.9 - - - +
34K GLU* 1.3 65.5 + - + +
35K VAL 3.5 0.5 + - - -
37K ALA* 3.7 18.8 - - + +
38K ALA 4.8 1.6 + - - -
66K TYR* 2.8 31.6 + - + +
69K GLN* 3.4 30.7 - - - +
70K PHE* 5.2 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 34 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30K GLN* 2.7 56.7 + - + +
33K THR* 1.3 79.2 - - + +
35K VAL* 1.3 60.0 + - + +
38K ALA* 5.5 2.1 - - - +
193K LEU 4.4 2.5 - - - +
194K VAL* 3.5 30.8 - - + +
195K GLU 4.4 2.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 35 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31K VAL* 2.8 29.5 + - + +
33K THR 3.3 0.2 - - - -
34K GLU* 1.3 79.5 - - - +
36K CYS* 1.3 67.5 + - - +
37K ALA 3.5 1.1 - - - -
38K ALA* 3.1 24.3 - - - +
188K PRO* 3.4 31.2 - - + +
189K LEU* 4.6 2.0 - - + -
193K LEU* 4.0 19.7 - - + -
194K VAL* 4.0 22.4 - - + -
207K MET* 4.7 2.9 - - + -
301K HEM 3.6 20.4 - - + +
----------------------------------------------------------
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