Contacts of the helix formed by residues 31 - 52 (chain A) in PDB entry 2VM6
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 SER 31 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A TYR* 5.5 0.9 + - - -
12A LEU* 5.2 1.4 - - - +
15A ASP* 5.0 3.9 + - - -
32A LYS* 1.3 54.0 + - - +
33A THR* 3.7 7.4 + - - -
34A SER* 3.2 27.7 + - - -
35A ARG* 2.8 49.4 + - - +
141A GLU* 5.6 0.3 + - - -
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Residues in contact with LYS 32 (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 SER* 1.3 68.3 - - - +
33A THR* 1.3 64.4 + - - +
35A ARG* 3.0 25.9 + - - +
36A VAL* 2.9 39.9 + - + +
141A GLU* 5.8 1.3 - - - +
145A VAL* 3.7 31.0 - - + -
146A LYS* 5.3 6.3 - - - +
149A GLU* 3.9 15.2 + - - -
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Residues in contact with THR 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A TYR* 3.4 21.8 - - - +
12A LEU* 4.3 8.3 - - + -
31A SER* 3.5 5.8 + - - -
32A LYS* 1.3 77.8 - - - +
34A SER* 1.3 58.0 + - - +
36A VAL* 3.4 3.7 + - - +
37A LEU* 2.9 28.8 + - + +
140A TRP* 3.9 20.4 - - + -
141A GLU* 2.9 29.6 + - - -
144A PHE* 3.8 11.5 - - + -
145A VAL* 3.0 27.2 - - + +
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Residues in contact with SER 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A LEU* 3.8 21.3 + - - +
15A ASP* 2.5 33.9 + - - +
31A SER* 3.2 23.4 + - - -
32A LYS 3.2 0.4 - - - -
33A THR* 1.3 80.5 - - - +
35A ARG* 1.3 56.1 + - - +
37A LEU* 3.3 3.7 + - - +
38A GLN* 2.8 53.5 + - - +
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Residues in contact with ARG 35 (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 SER* 2.8 29.8 + - - +
32A LYS* 3.0 30.6 + - - +
34A SER* 1.3 69.5 - - - +
36A VAL* 1.3 66.6 + - + +
38A GLN* 3.4 16.5 + - - +
39A ASN* 3.0 34.9 + - - +
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Residues in contact with VAL 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A LYS* 2.9 31.3 + - + +
33A THR* 3.6 5.6 - - - +
35A ARG* 1.3 77.3 - - + +
37A LEU* 1.3 62.9 + - - +
39A ASN* 3.3 10.1 + - - +
40A VAL* 3.1 22.3 + - - +
144A PHE* 3.8 10.5 - - + -
145A VAL* 4.6 7.2 - - + +
148A PHE* 3.6 42.2 - - + +
149A GLU* 3.8 21.8 - - + +
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Residues in contact with LEU 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A LEU* 4.1 27.4 - - + +
16A TYR* 5.3 3.8 - - + -
33A THR 2.9 21.2 + - - +
34A SER* 3.6 5.6 - - - +
36A VAL* 1.3 72.6 - - - +
38A GLN* 1.3 59.6 + - + +
40A VAL* 4.1 0.2 - - - -
41A ALA* 2.8 47.3 + - + +
89A ILE* 6.2 0.2 - - + -
90A VAL* 4.1 13.5 - - + -
93A PHE* 3.7 55.6 - - + -
140A TRP* 4.4 3.8 - - + -
144A PHE* 3.6 26.7 - - + -
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Residues in contact with GLN 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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15A ASP* 3.5 17.2 + - - +
16A TYR* 4.0 22.6 - - + +
19A CYS* 3.7 36.0 - - + +
34A SER* 2.8 50.9 + - - +
35A ARG* 3.6 14.7 - - - +
37A LEU* 1.3 73.9 - - + +
39A ASN* 1.3 64.7 + - - +
42A PHE* 3.1 29.6 + - - +
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Residues in contact with ASN 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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35A ARG* 3.0 24.4 + - - +
36A VAL* 3.3 8.7 + - - +
38A GLN* 1.3 80.3 - - - +
40A VAL* 1.3 61.8 + - - +
42A PHE* 3.9 4.2 - - - +
43A SER* 3.4 18.4 + - - -
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Residues in contact with VAL 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 VAL 3.1 17.2 + - - +
37A LEU 3.6 4.3 - - - +
39A ASN* 1.3 74.8 - - - +
41A ALA* 1.3 62.9 + - - +
43A SER* 3.2 6.5 + - - -
44A VAL* 2.9 25.8 + - - +
90A VAL* 3.8 26.2 - - + -
144A PHE* 4.0 12.8 - - + -
148A PHE* 3.7 29.6 - - + +
159B PHE* 3.7 29.2 - - + -
163B TYR* 4.2 12.3 - - + +
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Residues in contact with ALA 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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16A TYR* 3.3 23.0 + - + -
37A LEU* 2.8 26.1 + - + +
40A VAL* 1.3 74.1 - - - +
42A PHE* 1.3 52.6 + - - +
44A VAL* 3.6 1.7 - - - +
45A GLN* 2.7 36.4 + - - +
90A VAL* 3.5 30.1 - - + +
93A PHE* 4.1 11.4 - - + -
94A ALA* 3.6 3.2 - - - +
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Residues in contact with PHE 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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16A TYR* 3.3 14.2 + - - +
19A CYS* 4.3 29.6 - - - -
20A VAL* 5.0 12.3 - - + -
22A GLN* 6.3 2.9 - - + -
38A GLN 3.1 19.7 + - - +
39A ASN* 3.9 5.4 - - - +
41A ALA* 1.3 77.7 - - - +
43A SER* 1.3 58.6 + - - +
45A GLN* 3.4 4.6 + - + +
46A LYS* 3.0 64.3 + - + +
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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 ASN 3.4 10.7 + - - -
40A VAL* 3.2 13.8 + - - -
42A PHE* 1.3 78.4 - - - +
44A VAL* 1.3 66.4 + - - +
46A LYS* 4.0 6.2 - - - +
47A GLU* 3.3 21.5 + - - +
159B PHE* 3.9 19.0 - - - -
163B TYR* 5.1 2.8 + - - -
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Residues in contact with VAL 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A VAL 2.9 19.0 + - - +
41A ALA 3.6 7.0 - - - +
43A SER* 1.3 75.9 - - - +
45A GLN* 1.3 62.4 + - - +
47A GLU* 3.3 4.3 + - - +
48A VAL* 2.9 25.8 + - + +
87A GLY 5.6 0.4 - - - +
90A VAL* 3.6 17.3 - - + -
91A THR* 4.0 15.5 - - + -
94A ALA* 3.5 17.9 - - + -
155B ILE* 3.9 28.0 - - + -
159B PHE* 3.6 34.5 - - + -
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Residues in contact with GLN 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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16A TYR* 2.7 36.6 + - - +
20A VAL* 3.7 8.2 - - - +
41A ALA 2.7 20.1 + - - +
42A PHE* 3.7 8.3 - - + +
44A VAL* 1.3 74.5 - - - +
46A LYS* 1.3 58.7 + - + +
48A VAL* 3.4 4.5 + - - +
49A GLU* 2.9 56.0 + - - +
94A ALA* 3.4 27.5 - - + +
97A GLY* 3.4 21.1 - - - -
98A ILE* 3.6 5.8 - - + +
101A LYS* 3.5 13.1 - - - +
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Residues in contact with LYS 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 PHE* 3.0 52.4 + - + +
43A SER* 4.0 7.2 - - - +
44A VAL 3.3 0.2 - - - -
45A GLN* 1.3 73.6 - - + +
47A GLU* 1.3 65.7 + - - +
49A GLU* 3.5 13.4 + - - +
50A LYS* 3.3 22.9 + - - +
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Residues in contact with GLU 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 3.3 8.7 + - - +
44A VAL 3.3 3.2 + - - +
46A LYS* 1.3 80.0 - - - +
48A VAL* 1.3 57.5 + - - +
50A LYS* 3.2 11.4 + - + +
51A ASN* 2.9 43.4 + - - +
154B ARG* 3.3 22.3 + - - -
155B ILE* 3.5 25.3 - - + +
158B GLU* 4.1 4.7 - - - +
159B PHE* 4.2 12.4 - - - -
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Residues in contact with VAL 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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44A VAL* 2.9 24.1 + - + +
45A GLN* 3.8 4.5 - - - +
47A GLU* 1.3 76.5 - - - +
49A GLU* 1.3 55.4 + - - +
51A ASN 3.3 0.5 + - - -
52A LEU* 3.0 51.3 + - + +
94A ALA* 5.4 0.9 - - + -
98A ILE* 3.5 26.0 - - + -
151B GLU* 4.1 14.1 - - + -
152B LEU* 3.9 22.4 - - + -
155B ILE* 3.7 30.3 - - + -
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Residues in contact with GLU 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 GLN* 2.9 39.7 + - - +
46A LYS* 3.8 15.1 - - - +
47A GLU 3.3 0.2 - - - -
48A VAL* 1.3 76.5 - - - +
50A LYS* 1.3 57.3 + - - +
52A LEU 3.9 0.3 - - - -
53A LYS* 3.3 26.0 + - - +
56A LEU* 4.4 13.2 - - + +
98A ILE* 3.7 20.5 - - + +
101A LYS* 2.6 37.3 + - - +
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Residues in contact with LYS 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 LYS 3.3 11.0 + - - +
47A GLU* 3.2 15.7 + - + +
49A GLU* 1.3 77.6 - - - +
51A ASN* 1.3 76.2 + - - +
52A LEU 3.1 2.4 + - - -
53A LYS* 3.6 14.1 + - - +
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Residues in contact with ASN 51 (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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47A GLU* 2.9 27.5 + - - +
48A VAL 4.0 1.6 - - - +
50A LYS* 1.3 87.9 - - - +
52A LEU* 1.3 64.7 + - + +
53A LYS 3.7 0.4 + - - -
54A SER* 5.4 0.7 + - - -
147B TRP* 4.7 5.2 + - - -
151B GLU* 2.6 39.9 + - - +
154B ARG* 2.9 17.8 - - - +
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Residues in contact with LEU 52 (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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48A VAL* 3.0 38.4 + - + +
49A GLU 3.9 2.0 - - - -
50A LYS 3.1 0.2 - - - -
51A ASN* 1.3 82.5 - - - +
53A LYS* 1.3 53.9 + - - +
54A SER 3.2 3.1 - - - -
55A CYS* 3.1 7.9 + - + +
56A LEU* 2.7 50.3 + - + +
98A ILE* 5.7 0.2 - - + -
147B TRP* 3.4 35.4 - - + +
148B ILE* 3.8 35.4 - - + +
151B GLU* 3.6 26.0 - - + -
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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