Contacts of the helix formed by residues 57 - 70 (chain A) in PDB entry 3VOC
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 TRP 57 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A VAL* 3.7 20.0 - - + -
47A VAL* 3.6 41.7 - - + -
55A PHE* 3.5 23.3 - + + +
56A ASP* 1.3 72.2 + - - +
58A SER* 1.3 63.9 + - - +
59A TYR 3.4 2.7 - - - -
60A TYR* 3.1 9.1 + + - +
61A LYS* 2.9 35.9 + - - +
78A ILE* 5.5 2.5 - - + -
136A LEU* 3.7 22.7 - - + -
139A SER* 2.9 24.2 + - - -
140A PHE* 3.7 41.5 - + + -
143A ASN* 3.3 26.7 - - - +
144A PHE* 3.5 25.8 - + + -
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Residues in contact with SER 58 (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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56A ASP* 2.8 25.1 + - - -
57A TRP* 1.3 75.9 - - - +
59A TYR* 1.3 65.1 + - - +
61A LYS* 3.3 12.6 + - - +
62A THR* 3.0 27.2 + - - -
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Residues in contact with TYR 59 (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 ALA 4.6 0.7 + - - -
16A LYS* 3.6 35.1 - - + -
17A ILE* 2.9 34.1 + - - +
20A TRP* 3.6 27.8 - + - -
46A TYR* 4.1 16.8 - + + -
56A ASP* 4.6 2.5 + - - +
57A TRP 3.4 0.8 - - - -
58A SER* 1.3 81.2 + - - +
60A TYR* 1.3 99.8 + + + +
62A THR* 3.3 7.7 + - - -
63A TYR* 2.9 38.7 + + - +
503A EDO 4.2 13.9 - - - +
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Residues in contact with TYR 60 (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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40A THR* 3.8 12.1 - - + -
41A ASP 2.8 29.4 + - - -
42A VAL* 3.5 24.7 - - + -
43A TRP* 3.0 25.7 + - - -
46A TYR* 3.4 19.7 - + + -
47A VAL* 3.5 34.5 - - + -
56A ASP 5.4 0.7 - - - -
57A TRP* 3.1 9.1 + - + +
59A TYR* 1.3 97.2 - + + +
61A LYS* 1.3 62.4 + - - +
63A TYR* 3.6 7.0 - + + +
64A ALA* 2.8 30.8 + - - +
74A TRP* 4.2 15.7 - + + -
144A PHE* 3.9 17.9 - - + -
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Residues in contact with LYS 61 (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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57A TRP* 2.9 25.5 + - - +
58A SER* 3.3 10.5 + - - +
60A TYR* 1.3 74.9 - - - +
62A THR* 1.3 58.9 + - - +
64A ALA* 3.4 0.8 + - - +
65A ASN* 2.8 39.8 + - - +
143A ASN* 2.9 52.8 + - - +
144A PHE* 3.8 16.6 - - + -
147A TYR* 3.5 20.2 + - + +
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Residues in contact with THR 62 (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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20A TRP* 3.6 35.0 - - + +
58A SER* 3.0 15.5 + - - -
59A TYR* 3.4 10.0 - - - -
61A LYS* 1.3 76.8 - - - +
63A TYR* 1.3 62.8 + - - +
65A ASN* 3.3 10.7 + - + +
66A ALA* 3.0 22.7 + - - +
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Residues in contact with TYR 63 (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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12A GLY* 3.5 26.0 - - - -
13A PRO* 3.8 8.2 + - + +
17A ILE* 4.3 17.5 - - + -
20A TRP* 3.6 12.7 - - + -
23A PHE* 3.7 15.4 - + - -
38A ILE* 3.8 2.6 - - + +
40A THR* 3.1 42.0 + - + +
59A TYR* 2.9 45.9 + + - +
60A TYR* 3.6 14.1 - + + +
62A THR* 1.3 73.8 - - - +
64A ALA* 1.3 63.1 + - - +
66A ALA* 3.1 5.9 + - - +
67A VAL* 3.1 34.2 + - + +
74A TRP* 3.6 16.2 - - + -
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Residues in contact with ALA 64 (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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60A TYR 2.8 22.7 + - - +
61A LYS 3.8 0.9 - - - +
63A TYR* 1.3 73.9 - - - +
65A ASN* 1.3 58.1 + - - +
67A VAL* 3.3 5.8 + - - +
68A LYS* 2.9 30.0 + - - +
74A TRP* 3.8 35.9 - - + -
144A PHE* 4.3 3.1 - - + -
147A TYR* 3.8 24.2 - - + -
150A ILE* 3.9 5.2 - - + +
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Residues in contact with ASN 65 (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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61A LYS* 2.8 29.2 + - - +
62A THR* 3.4 9.9 - - + +
64A ALA* 1.3 72.6 - - - +
66A ALA* 1.3 56.9 + - - +
68A LYS* 3.4 9.6 + - - +
69A GLU* 2.9 31.5 + - - +
147A TYR* 2.6 32.3 + - - -
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Residues in contact with ALA 66 (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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20A TRP* 4.2 16.6 - - + -
23A PHE* 4.6 1.6 - - + -
24A LYS* 4.2 24.5 - - + +
27A LEU* 3.7 17.2 - - + +
62A THR 3.0 13.7 + - - +
63A TYR 3.1 7.8 + - - +
65A ASN* 1.3 75.0 - - - +
67A VAL* 1.3 63.5 + - - +
69A GLU* 3.3 12.7 + - - +
70A ALA* 3.1 24.1 + - - +
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Residues in contact with VAL 67 (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* 3.9 18.6 - - + -
38A ILE* 4.2 13.9 - - + -
63A TYR* 3.1 41.0 + - + +
64A ALA* 3.7 7.4 - - - +
66A ALA* 1.3 75.5 - - - +
68A LYS* 1.3 61.1 + - - +
70A ALA* 3.3 7.8 + - - +
72A LEU* 3.1 39.4 + - + +
73A LYS 3.2 30.3 - - - +
74A TRP* 4.0 17.3 - - + -
150A ILE* 5.2 0.2 - - + -
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Residues in contact with LYS 68 (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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64A ALA 2.9 18.3 + - - +
65A ASN* 3.6 8.3 - - - +
67A VAL* 1.3 77.6 - - - +
69A GLU* 1.3 57.9 + - - +
71A GLY* 2.9 20.8 + - - -
72A LEU 4.0 9.2 - - - -
147A TYR* 5.0 12.1 - - + -
149A SER* 5.5 2.7 - - - -
150A ILE* 3.9 35.4 - - + +
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Residues in contact with GLU 69 (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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24A LYS* 2.7 43.0 + - - +
65A ASN 2.9 18.8 + - - +
66A ALA* 3.7 5.1 - - - +
68A LYS* 1.3 78.3 - - - +
70A ALA* 1.3 59.8 + - - +
71A GLY 3.3 0.9 + - - -
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Residues in contact with ALA 70 (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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24A LYS* 5.2 0.9 - - - +
27A LEU* 3.7 32.5 - - + -
28A GLN* 4.3 13.9 - - + +
31A LYS* 3.3 25.1 - - - +
66A ALA 3.1 16.1 + - - +
67A VAL 3.7 5.8 - - - +
68A LYS 3.2 0.4 - - - -
69A GLU* 1.3 75.4 - - - +
71A GLY* 1.3 58.9 + - - +
72A LEU* 3.5 7.1 + - + -
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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