Contacts of the helix formed by residues 37 - 54 (chain A) in PDB entry 3W31
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 37 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A SER 4.0 1.6 + - - -
36A LEU* 1.3 76.2 - - - +
38A ASP* 1.3 63.3 + - - -
40A ASP* 3.2 22.6 + - - +
41A LYS* 2.8 27.3 + - - +
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Residues in contact with ASP 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A GLY* 1.3 69.4 - - - -
39A MET* 1.3 60.8 + - - +
40A ASP 2.8 7.5 + - - -
41A LYS* 3.4 20.7 + - - +
42A ASP* 3.3 12.5 - - - +
119A ARG* 3.7 21.3 + - - +
155A LYS* 3.2 45.1 - - - +
156A ILE 4.5 0.5 - - - +
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Residues in contact with MET 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A GLY* 4.7 0.2 - - - -
38A ASP* 1.3 78.6 - - - +
40A ASP* 1.3 57.9 + - - +
42A ASP* 3.6 18.5 - - - +
43A SER* 4.3 9.0 + - - -
115A TYR* 4.2 27.8 - - + +
116A SER* 3.6 27.8 - - - +
119A ARG* 3.6 28.9 - - - +
166A GLY* 5.5 0.7 - - - -
167A PHE* 4.2 31.6 - - + +
175A LYS 4.6 9.6 - - - +
177A PRO* 4.2 20.4 - - + -
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Residues in contact with ASP 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A LEU* 3.8 14.1 - - - +
37A GLY* 3.2 31.0 + - - +
38A ASP 2.8 2.0 - - - -
39A MET* 1.3 78.9 - - - +
41A LYS* 1.3 56.6 + - - -
42A ASP 3.1 5.8 + - - -
43A SER* 4.0 5.6 + - - -
44A GLU* 3.7 14.9 + - - +
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Residues in contact with LYS 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A LEU 3.9 3.3 - - - +
32A ASN* 3.0 52.9 + - - +
36A LEU* 3.9 21.8 - - + +
37A GLY 2.8 23.8 + - - +
38A ASP* 3.4 16.6 - - - +
40A ASP* 1.3 70.2 - - - +
42A ASP* 1.3 65.2 + - - +
44A GLU* 2.8 25.2 - - - +
45A LEU* 3.2 9.7 + - - +
155A LYS* 3.0 42.3 - - + +
157A MET* 3.7 23.8 - - + +
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Residues in contact with ASP 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A ASP 3.3 10.8 - - - +
39A MET* 3.6 10.8 - - - +
40A ASP 3.1 0.6 - - - -
41A LYS* 1.3 74.8 - - - +
43A SER* 1.3 57.3 + - - +
44A GLU 2.4 17.6 + - - -
45A LEU* 2.8 15.5 + - - +
46A ALA* 3.2 10.0 + - - +
119A ARG* 2.7 36.5 + - - -
156A ILE 4.3 0.2 - - - +
157A MET* 3.4 35.4 - - - +
158A PHE* 3.4 22.5 + - - +
159A LEU* 5.0 1.6 - - - +
166A GLY* 3.7 11.0 - - - -
167A PHE 4.6 2.0 + - - +
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Residues in contact with SER 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A MET 4.3 7.3 + - - -
40A ASP* 4.0 7.9 + - - -
42A ASP* 1.3 77.4 - - - +
44A GLU* 1.3 58.3 + - - +
47A ALA* 3.2 24.6 + - - +
164A GLY 3.8 2.8 - - - +
165A LYS* 3.6 11.5 - - - +
166A GLY* 2.8 29.8 + - - +
174A GLU* 4.8 11.2 - - - +
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Residues in contact with GLU 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A LEU* 2.9 42.1 - - + +
34A LYS* 5.3 2.6 - - - +
36A LEU* 4.1 22.2 - - + +
40A ASP 3.7 6.2 + - - +
41A LYS* 2.8 27.7 - - - +
42A ASP 2.4 13.3 + - - -
43A SER* 1.3 71.4 - - - +
45A LEU* 1.3 64.8 + - - +
47A ALA* 3.2 12.9 + - - +
48A THR* 3.5 8.5 + - - -
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Residues in contact with LEU 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A LEU 4.9 6.3 - - - +
28A LEU* 4.6 10.5 - - + -
31A LEU* 3.4 33.9 - - + +
41A LYS 4.1 5.6 - - - +
42A ASP 2.8 8.3 + - - +
44A GLU* 1.3 77.8 - - - +
46A ALA* 1.3 54.0 + - - +
48A THR* 2.7 28.8 + - + +
49A LEU* 3.0 26.5 + - + +
73A MET* 4.1 22.2 - - + -
157A MET* 4.0 20.2 - - + -
159A LEU* 3.6 25.1 - - + -
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Residues in contact with ALA 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A ASP 3.2 8.0 + - - +
45A LEU* 1.3 77.5 - - - +
47A ALA* 1.3 55.1 + - - +
48A THR 3.1 0.2 + - - -
49A LEU* 3.3 1.0 + - - +
50A GLN* 2.7 36.6 + - - +
159A LEU* 3.8 15.5 - - + +
160A ASP 4.0 4.3 - - - +
161A VAL* 4.0 18.5 - - - +
164A GLY* 3.7 3.2 - - - -
165A LYS 2.8 38.8 - - - +
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Residues in contact with ALA 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A SER 3.2 20.3 + - - +
44A GLU* 3.2 6.6 + - - +
45A LEU 3.1 0.8 - - - -
46A ALA* 1.3 78.8 - - - +
48A THR* 1.3 57.0 + - - +
50A GLN* 3.2 10.2 + - - +
51A LYS* 3.2 24.3 - - - +
164A GLY* 3.5 19.0 + - - +
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Residues in contact with THR 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A VAL* 5.8 7.6 - - + -
27A LEU* 6.4 1.8 - - + -
31A LEU* 3.2 31.9 - - + +
44A GLU* 3.5 5.9 + - - -
45A LEU* 2.7 17.4 + - + -
47A ALA* 1.3 70.0 - - - +
49A LEU* 1.3 57.8 + - + +
51A LYS* 2.8 34.4 + - + +
52A MET* 3.7 18.5 + - + +
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Residues in contact with LEU 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A LEU* 3.0 20.9 + - + +
46A ALA 3.8 4.9 - - - +
48A THR* 1.3 79.0 - - + +
50A GLN* 1.3 54.4 + - - +
52A MET* 2.8 26.5 + - + -
53A ILE* 2.7 46.2 + - + +
69A ALA* 5.4 3.8 - - + -
72A ALA* 4.6 5.8 - - + -
73A MET* 4.4 17.9 - - + -
78A VAL* 3.6 23.6 - - + -
159A LEU* 4.2 19.3 - - + -
161A VAL* 3.9 22.7 - - + -
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Residues in contact with GLN 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A ALA 2.7 21.4 + - - +
47A ALA* 3.2 12.7 + - - +
48A THR 3.1 0.2 + - - -
49A LEU* 1.3 71.5 - - - +
51A LYS* 1.3 90.0 + - - +
52A MET 3.0 0.2 + - - -
54A ASN 2.8 44.7 + - - +
56A SER* 5.1 3.7 + - - -
57A GLY 5.0 5.2 + - - +
161A VAL* 3.1 27.1 + - - +
162A GLN 3.9 9.5 - - - +
163A THR* 4.2 8.6 - - - +
164A GLY* 3.5 21.7 - - - +
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Residues in contact with LYS 51 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47A ALA 3.2 15.7 - - - +
48A THR* 2.8 14.0 + - - +
50A GLN* 1.3 102.7 - - - +
52A MET* 1.3 61.2 + - + +
55A PRO* 4.3 15.1 - - - +
56A SER 4.8 12.1 - - - +
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Residues in contact with MET 52 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A VAL* 5.8 8.7 - - + -
23A ASN* 5.2 5.8 - - - +
48A THR* 3.8 16.8 - - + +
49A LEU* 2.8 56.3 + - + +
51A LYS* 1.3 85.5 - - + +
53A ILE* 1.3 63.2 + - + +
54A ASN 3.4 1.3 + - - -
55A PRO* 3.8 4.7 - - - +
78A VAL* 4.0 25.4 - - + -
79A ARG 5.1 0.7 - - - -
80A GLU* 3.6 17.2 + - - +
212A CYS* 3.5 28.2 - - - +
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Residues in contact with ILE 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A LEU* 2.7 36.1 + - + +
52A MET* 1.3 75.1 - - - +
54A ASN* 1.3 57.6 + - - +
55A PRO* 3.7 1.7 - - - +
65A CYS* 4.1 10.3 - - + +
68A HIS* 3.6 40.4 - - + +
69A ALA* 4.3 8.3 - - - +
72A ALA* 4.7 0.9 - - + -
78A VAL* 4.3 27.1 - - + -
79A ARG 3.7 12.6 - - - +
81A ALA* 2.8 49.0 + - + +
161A VAL* 4.8 10.8 - - + -
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Residues in contact with ASN 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A GLN* 2.8 18.4 + - + +
53A ILE* 1.3 82.2 + - - +
55A PRO* 1.3 73.3 + - - +
56A SER* 2.7 5.0 + - - -
57A GLY* 2.9 31.3 + - - -
58A GLY 3.6 1.9 + - - -
61A ASN* 3.4 25.2 - - - +
65A CYS* 4.0 6.5 - - - -
81A ALA 5.8 0.8 + - - -
83A VAL* 5.8 4.8 - - - +
161A VAL 3.7 18.6 - - - +
162A GLN* 2.6 26.8 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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