Contacts of the helix formed by residues 30 - 54 (chain B) in PDB entry 2QV8
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 30 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B GLU* 1.3 68.3 + - - +
32B ALA 3.8 0.2 + - - -
33B LYS* 3.2 31.5 + - + +
34B ILE* 3.0 37.2 + - + +
165B GLU* 2.5 37.8 - - - +
167B TRP* 4.2 3.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 31 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B ASP* 1.3 74.9 + - - +
32B ALA* 1.3 58.0 + - - +
34B ILE* 3.4 22.3 + - - +
35B SER* 2.9 30.7 + - - -
94B LYS* 4.8 19.5 - - + +
97B LEU* 3.7 23.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 32 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B ASP* 3.3 1.2 + - - -
31B GLU* 1.3 74.9 - - - +
33B LYS* 1.3 61.5 + - - +
35B SER* 3.7 1.0 - - - -
36B ALA* 2.9 32.2 + - - +
97B LEU* 3.7 21.4 - - + +
156B ILE* 3.9 26.9 - - + +
157B PHE* 4.3 4.5 - - - -
158B PRO* 4.6 0.9 - - + -
165B GLU* 3.7 27.3 + - + +
167B TRP* 4.0 5.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 33 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A LEU 5.1 5.5 + - - -
30B ASP* 3.2 36.3 + - + +
32B ALA* 1.3 79.3 - - - +
34B ILE* 1.3 59.1 + - + +
36B ALA* 3.2 0.7 + - - -
37B GLN* 2.8 66.1 + - - +
167B TRP* 3.5 46.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 34 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B ASP* 3.0 36.7 + - + +
31B GLU* 3.8 21.1 - - - +
33B LYS* 1.3 79.1 - - + +
35B SER* 1.3 60.8 + - - +
37B GLN* 3.9 7.7 - - - +
38B SER* 2.8 39.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 35 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B GLU 2.9 18.2 + - - -
32B ALA 3.7 3.8 - - - -
34B ILE* 1.3 78.0 - - - +
36B ALA* 1.3 56.8 + - - +
38B SER* 3.2 7.0 + - - -
39B PHE* 3.0 29.3 + - - +
42B ARG* 5.3 0.3 + - - -
68B LEU* 5.8 0.3 - - - +
91B THR* 5.5 1.2 - - - +
93B LEU* 2.7 32.5 - - - +
97B LEU* 3.9 15.5 - - - -
156B ILE* 3.5 9.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 36 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B ALA 2.9 19.3 + - - +
33B LYS 3.8 2.5 - - - +
35B SER* 1.3 77.2 - - - +
37B GLN* 1.3 57.4 + - - +
39B PHE* 3.4 1.8 + - - +
40B TYR* 3.0 23.7 + - - +
156B ILE* 3.9 15.7 - - + +
167B TRP* 3.4 30.7 - - + -
168B ARG 5.4 0.2 - - - -
169B VAL* 3.4 16.7 - - + +
179B LEU* 4.1 11.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 37 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A LEU* 3.2 48.6 + - + +
33B LYS* 2.8 55.3 + - + +
34B ILE* 3.9 7.4 - - - +
36B ALA* 1.3 72.3 - - - +
38B SER* 1.3 57.0 + - - +
40B TYR* 3.5 5.6 + - - +
41B GLN* 2.9 38.1 + - - +
167B TRP* 4.4 6.3 - - + -
179B LEU* 3.9 18.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 38 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B ILE* 2.8 31.5 + - - +
35B SER* 3.7 5.6 - - - -
37B GLN* 1.3 72.6 - - - +
39B PHE* 1.3 60.1 + - - +
41B GLN* 3.3 15.2 + - - +
42B ARG* 3.0 62.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 39 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B SER 3.0 15.7 + - - +
36B ALA* 3.8 5.2 - - - +
38B SER* 1.3 74.6 - - - +
40B TYR* 1.3 58.5 + - - +
42B ARG* 3.3 7.9 + - - +
43B LEU* 2.8 41.1 + - + +
59B VAL* 4.1 20.0 - - + -
61B ILE* 5.7 1.3 - - + -
68B LEU* 3.7 31.2 - - + -
70B PHE* 3.8 28.0 - + - -
141B LEU* 4.8 4.9 - - + -
152B PHE* 4.0 22.2 - + - -
154B LEU* 3.8 25.1 - - + -
156B ILE* 5.0 2.0 - - + -
169B VAL* 3.8 31.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 40 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A ASN* 5.0 0.7 + - - -
48A GLU* 4.0 20.6 - - + -
51A ILE* 3.2 46.3 - - + +
52A LEU* 4.0 22.0 - - + -
36B ALA 3.0 17.9 + - - +
37B GLN* 3.6 4.3 - - - +
39B PHE* 1.3 78.2 - - - +
41B GLN* 1.3 60.0 + - - +
43B LEU* 3.8 2.9 - - + +
44B LEU* 2.9 50.7 + - + +
169B VAL* 4.0 21.8 - - + -
177B LEU* 4.1 29.6 + - + -
178B ARG* 4.2 4.4 - - - -
179B LEU* 4.0 25.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 41 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A LEU* 6.2 0.6 - - - +
48A GLU* 3.1 25.9 + - + +
52A LEU* 3.5 29.6 - - + +
86A LYS* 3.9 15.6 - - - +
37B GLN* 2.9 26.9 + - - +
38B SER* 3.6 15.5 + - - +
39B PHE 3.3 0.2 - - - -
40B TYR* 1.3 76.6 - - + +
42B ARG* 1.3 61.2 + - + +
44B LEU* 3.5 2.3 + - - +
45B LEU* 3.0 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 42 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B SER 5.3 0.4 + - - -
38B SER* 3.0 46.3 + - - +
39B PHE* 3.9 5.9 - - - +
41B GLN* 1.3 78.3 - - + +
43B LEU* 1.3 59.3 + - - +
45B LEU* 3.3 3.4 + - - +
46B LEU* 2.9 28.9 + - - +
70B PHE* 3.9 24.4 - - + -
87B MSE 3.8 32.1 - - + +
88B THR* 3.8 33.3 + - - +
91B THR* 3.3 35.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 43 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B PHE* 2.8 32.0 + - + +
40B TYR* 3.9 4.5 - - + +
42B ARG* 1.3 73.4 - - - +
44B LEU* 1.3 61.5 + - - +
46B LEU* 3.3 5.0 + - + +
47B ASN* 3.0 23.6 + - - +
59B VAL* 4.3 14.6 - - + -
70B PHE* 4.5 4.1 - - - -
141B LEU* 5.7 1.3 - - + -
143B VAL* 3.9 27.8 - - + -
149B VAL* 4.6 8.5 - - + -
152B PHE* 3.7 32.8 - - + -
169B VAL* 4.1 16.4 - - + -
177B LEU* 4.2 26.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 44 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A LEU* 4.8 19.1 - - + +
45A LEU 5.8 0.2 - - - +
47A ASN* 5.2 5.6 - - - +
48A GLU* 3.8 46.0 - - + +
40B TYR* 2.9 37.9 + - + +
41B GLN 3.8 3.1 - - - +
43B LEU* 1.3 75.6 - - - +
45B LEU* 1.3 60.3 + - + +
47B ASN* 3.4 4.7 + - - +
48B GLU* 2.9 47.5 + - + +
177B LEU* 4.4 17.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 45 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B GLN 3.0 17.3 + - - +
42B ARG* 3.7 4.5 - - - +
43B LEU 3.3 0.2 - - - -
44B LEU* 1.3 79.3 - - + +
46B LEU* 1.3 52.5 + - - +
48B GLU* 3.2 23.1 + - + +
49B GLU* 2.7 44.1 + - + +
82B TRP* 4.8 9.4 - - + -
86B LYS* 3.9 46.7 - - + -
87B MSE 3.7 28.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 46 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B ARG 2.9 17.0 + - - +
43B LEU* 3.3 6.7 + - + +
45B LEU* 1.3 75.0 - - - +
47B ASN* 1.3 57.7 + - - +
49B GLU* 3.4 4.5 + - - +
50B ALA* 2.9 29.8 + - - +
57B PHE* 3.5 42.5 - - + -
58B GLY 3.8 15.3 - - - +
59B VAL* 3.9 13.2 - - + -
70B PHE* 4.4 9.4 - - + -
71B LEU 4.6 2.9 - - - +
82B TRP* 3.8 23.6 - - + -
87B MSE 4.7 6.9 - - + -
143B VAL* 3.6 31.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 47 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A LEU* 6.0 1.6 - - - +
43B LEU 3.0 16.7 + - - +
44B LEU* 3.6 7.2 - - - +
46B LEU* 1.3 75.3 - - - +
48B GLU* 1.3 63.7 + - - +
50B ALA* 3.3 3.1 + - - +
51B ILE* 3.0 43.9 + - - +
143B VAL* 3.5 15.9 - - + +
144B LEU 5.0 1.2 + - - -
147B GLY* 3.3 28.3 + - - -
149B VAL* 3.8 13.3 - - + +
177B LEU* 4.0 23.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 48 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A TYR* 4.4 2.2 - - + -
41A GLN* 3.4 38.9 - - - +
44A LEU* 3.9 27.7 - - + +
44B LEU* 2.9 32.3 + - - +
45B LEU* 3.4 20.8 - - + +
47B ASN* 1.3 79.7 - - - +
49B GLU* 1.3 58.0 + - - +
51B ILE* 3.3 7.8 + - - +
52B LEU* 3.0 49.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 49 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B LEU* 2.7 26.4 + - + +
46B LEU* 3.8 4.7 - - - +
48B GLU* 1.3 69.7 - - - +
50B ALA* 1.3 56.7 + - - +
52B LEU* 4.6 8.4 - - - +
53B SER* 2.6 55.8 + - - -
57B PHE* 3.9 15.3 - - + -
82B TRP* 3.8 35.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 50 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B LEU 2.9 18.4 + - - +
47B ASN 3.3 5.1 + - - +
49B GLU* 1.3 73.9 - - - +
51B ILE* 1.3 57.9 + - - +
54B GLY* 2.9 26.0 + - - -
55B GLN 3.3 21.2 - - - +
57B PHE* 3.7 6.9 - - + -
143B VAL* 3.7 16.6 - - + +
144B LEU 3.6 19.7 - - - +
145B SER* 3.4 11.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 51 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A TYR* 3.8 26.7 - - + +
177A LEU 6.1 0.7 - - - +
179A LEU* 5.8 5.6 - - + +
47B ASN* 3.0 37.6 + - - +
48B GLU* 3.7 4.7 - - - +
49B GLU 3.3 0.2 - - - -
50B ALA* 1.3 77.0 - - - +
52B LEU* 1.3 71.9 + - + +
54B GLY* 4.0 4.9 + - - -
144B LEU 4.8 0.2 - - - +
145B SER 3.6 15.7 - - - +
146B SER 4.7 0.9 - - - -
147B GLY* 3.7 31.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 52 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A LYS* 5.7 1.9 + - - -
37A GLN* 4.3 27.8 + - + +
40A TYR* 3.9 20.9 - - + -
41A GLN* 3.7 32.3 - - + +
179A LEU* 3.6 31.0 - - + -
48B GLU* 3.0 36.7 + - + +
49B GLU* 4.2 8.7 - - - +
51B ILE* 1.3 82.8 - - + +
53B SER* 1.3 58.6 + - - +
54B GLY 3.6 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 53 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B GLU* 2.6 47.8 + - - -
50B ALA 3.7 0.2 + - - -
52B LEU* 1.3 73.0 - - - +
54B GLY* 1.3 60.2 + - - +
55B GLN* 3.2 34.7 + - - +
57B PHE* 3.9 5.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 54 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B ALA 2.9 10.6 + - - -
51B ILE 4.0 3.6 + - - -
52B LEU 3.6 2.4 - - - -
53B SER* 1.3 76.4 - - - +
55B GLN* 1.3 66.6 + - - +
56B ASP* 4.3 1.4 + - - +
145B SER* 3.4 22.9 + - - -
----------------------------------------------------------
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