Contacts of the helix formed by residues 32 - 42 (chain A) in PDB entry 2VSH
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 ILE 32 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A LYS* 3.2 22.2 - - + +
23A GLN* 3.4 10.9 + - - +
25A LEU* 2.8 23.4 + - + +
27A LEU* 3.9 19.3 - - + -
30A ARG 3.6 0.6 + - - -
31A PRO* 1.3 70.7 - - - +
33A LEU* 1.3 63.4 + - - +
35A HIS* 3.1 11.8 + - - +
36A THR* 3.1 24.1 + - - -
113A SER 3.6 16.6 - - - +
114A VAL* 3.9 14.8 - - - -
116A PRO* 3.9 16.8 - - + -
219A ILE* 3.8 33.0 - - + -
225A LEU* 4.5 12.1 - - + -
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Residues in contact with LEU 33 (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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6A ILE* 3.9 8.5 - - + -
8A ALA* 4.0 5.6 - - + -
23A GLN* 2.8 27.4 + - + +
24A PHE* 3.8 26.9 - - + -
31A PRO* 4.9 3.6 - - + -
32A ILE* 1.3 72.3 - - - +
34A ILE* 1.3 61.2 + - + +
36A THR* 3.3 2.1 + - - -
37A ILE* 3.0 43.1 + - + +
51A VAL* 3.9 25.4 - - + -
53A VAL* 4.9 0.4 - - + -
61A ALA* 4.5 16.6 - - + +
64A LEU* 4.7 7.0 - - + -
65A VAL* 6.4 0.2 - - + -
78A ILE* 5.7 1.1 - - + -
113A SER* 3.8 30.3 - - - -
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Residues in contact with ILE 34 (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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30A ARG* 4.2 11.0 - - + +
31A PRO* 2.9 33.9 + - + +
33A LEU* 1.3 78.4 - - + +
35A HIS* 1.3 60.5 + - - +
37A ILE* 3.3 11.4 + - + +
38A GLU* 2.9 49.3 + - - +
64A LEU* 3.8 32.5 - - + +
65A VAL* 4.3 3.6 - - + +
68A TYR* 3.7 23.3 - - + -
69A LEU* 3.8 23.3 - - + -
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Residues in contact with HIS 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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27A LEU* 2.6 48.7 + - + +
28A GLY* 5.4 0.7 - - - -
29A ASP 5.3 0.2 - - - -
30A ARG* 3.1 56.3 + - + +
31A PRO 3.2 14.8 + - - -
32A ILE* 3.1 8.6 + - - +
34A ILE* 1.3 78.3 - - - +
36A THR* 1.3 62.0 + - - +
38A GLU* 3.3 23.2 + - - +
39A LYS* 3.3 27.1 + - - +
116A PRO* 3.7 17.3 - - + -
232A ILE* 5.3 7.5 - - + +
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Residues in contact with THR 36 (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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6A ILE* 4.4 14.1 - - + -
32A ILE 3.1 6.7 + - - -
33A LEU 3.5 7.6 - - - -
34A ILE 3.1 0.2 - - - -
35A HIS* 1.3 76.5 - - - +
37A ILE* 1.3 66.4 + - - +
39A LYS* 3.2 15.2 + - - +
40A PHE* 3.4 14.0 - - + -
111A HIS* 3.7 29.2 - - + -
112A ASP 3.8 9.4 - - - +
113A SER* 2.6 29.9 + - - +
115A ARG 4.0 3.6 - - - +
116A PRO* 3.2 19.7 - - - +
118A ILE* 4.9 0.9 - - + -
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Residues in contact with ILE 37 (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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6A ILE* 4.7 6.5 - - + -
33A LEU* 3.0 44.8 + - + +
34A ILE* 3.8 14.4 - - + +
36A THR* 1.3 74.7 - - - +
38A GLU* 1.3 57.6 + - - +
40A PHE* 2.9 25.8 + - - +
41A VAL* 3.2 15.6 + - + +
49A ILE* 4.2 13.0 - - + -
51A VAL* 3.9 26.5 - - + -
65A VAL* 4.7 13.5 - - + -
69A LEU* 3.7 17.9 - - + -
76A ILE* 3.7 21.8 - - + -
78A ILE* 5.2 0.7 - - + -
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Residues in contact with GLU 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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30A ARG* 2.6 48.1 + - - -
34A ILE* 2.9 24.4 + - - +
35A HIS* 3.3 12.9 - - - +
37A ILE* 1.3 76.6 - - - +
39A LYS* 1.3 66.4 + - + +
40A PHE 3.2 1.0 + - - -
41A VAL* 3.2 28.2 + - + +
42A LEU* 4.0 6.6 + - - +
68A TYR 5.0 1.6 - - - +
69A LEU* 3.6 23.9 - - + +
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Residues in contact with LYS 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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30A ARG* 5.9 0.2 - - - +
35A HIS* 3.4 27.4 + - - +
36A THR 3.2 8.2 + - - +
37A ILE 3.2 1.0 - - - -
38A GLU* 1.3 80.2 + - + +
40A PHE* 1.3 59.8 + - + +
42A LEU* 4.6 2.2 + - - +
116A PRO 3.1 24.8 + - - +
117A PHE* 4.8 6.2 - - - +
118A ILE* 3.4 40.8 - - + +
119A THR* 5.3 2.9 - - - -
120A LEU* 3.6 18.4 + - - +
123A ILE* 3.5 15.7 - - + +
1239A PEG 5.6 3.8 - - - +
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Residues in contact with PHE 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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4A ALA* 3.4 24.7 - - + -
6A ILE* 3.6 23.1 - - + -
36A THR 3.4 16.6 - - - -
37A ILE* 2.9 8.7 + - - +
39A LYS* 1.3 79.4 - - + +
41A VAL* 1.3 63.6 + - - +
42A LEU 3.3 2.5 - - - -
43A GLU* 3.3 20.8 + - - +
46A ILE* 4.1 13.6 - - + +
49A ILE* 3.8 21.2 - - + +
75A ARG* 5.3 0.5 + - - -
109A VAL* 3.9 20.0 - - + -
111A HIS* 3.9 23.3 - + + -
118A ILE* 3.5 33.4 - - + -
123A ILE* 3.8 24.0 - - + -
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Residues in contact with VAL 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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37A ILE* 3.2 25.5 + - + +
38A GLU* 3.2 27.1 - - + +
40A PHE* 1.3 77.6 - - - +
42A LEU* 1.3 66.4 + - + +
43A GLU 3.6 1.6 + - - +
49A ILE* 3.6 18.8 - - + -
69A LEU* 5.1 2.2 - - + -
72A TYR* 3.7 60.2 - - + +
75A ARG* 3.4 20.4 + - - +
76A ILE* 4.6 1.1 - - + -
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Residues in contact with LEU 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 GLU 4.0 6.6 + - - +
39A LYS 4.6 1.3 + - - +
40A PHE* 3.3 1.2 - - - +
41A VAL* 1.3 85.9 - - + +
43A GLU* 1.3 65.3 + - - +
44A PRO* 3.0 12.1 - - - +
72A TYR* 4.9 12.6 - - + +
120A LEU* 4.6 25.1 - - + -
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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