Contacts of the helix formed by residues 74 - 86 (chain A) in PDB entry 3VVK
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 VAL 74 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70A SER 3.8 10.1 - - - +
71A THR* 3.0 18.3 + - + +
73A LEU* 1.3 78.4 - - - +
75A PRO* 1.3 66.1 - - + +
77A VAL* 3.4 7.0 + - - +
78A SER* 3.0 24.6 + - - -
130A SER* 4.1 8.0 - - - +
133A MET* 4.0 11.2 - - + -
134A ILE* 3.5 34.8 - - + +
256A LYS* 3.3 47.6 - - + +
259A PHE* 5.8 1.1 - - + -
260A ALA* 5.4 2.0 - - + -
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Residues in contact with PRO 75 (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 ALA* 3.7 11.2 - - - +
48A SER* 4.1 4.7 - - - -
49A ILE* 3.7 21.7 - - + +
52A PHE* 4.1 24.2 - - + -
71A THR 3.3 6.7 - - - +
72A ILE* 3.0 24.7 - - - +
74A VAL* 1.3 89.8 - - + +
76A VAL* 1.3 58.4 + - - -
78A SER* 3.4 9.3 - - - -
79A ILE* 2.8 31.7 + - - +
256A LYS 5.7 0.2 - - - +
257A TYR* 4.1 17.7 - - + -
260A ALA* 5.2 1.8 - - + -
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Residues in contact with VAL 76 (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 ILE* 3.8 21.8 - - + -
72A ILE* 3.5 17.7 + - + +
73A LEU* 3.2 17.8 + - + +
75A PRO* 1.3 73.7 - - - +
77A VAL* 1.3 68.3 + - + +
79A ILE* 3.2 8.6 - - + +
80A ALA* 3.1 22.4 + - + +
155C PHE* 3.9 34.8 - - + -
158C ALA* 4.8 7.4 - - + -
182C ILE* 5.8 3.8 - - + -
186C CYS* 4.9 6.7 - - - -
302C 22B 4.6 8.3 - - + -
304C L3P 4.3 13.5 - - + -
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Residues in contact with VAL 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A LEU* 2.9 28.0 + - + +
74A VAL 3.6 4.5 - - - +
76A VAL* 1.3 76.9 - - + +
78A SER* 1.3 58.4 + - - +
80A ALA* 3.3 1.2 + - - +
81A SER* 2.8 30.4 + - - -
126A THR* 3.5 33.7 - - + +
129A LEU* 3.7 38.6 - - + +
130A SER* 4.0 7.2 - - - -
133A MET* 5.3 1.6 - - + -
304C L3P 3.9 23.9 - - + +
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Residues in contact with SER 78 (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 ALA* 4.2 0.2 - - - -
74A VAL 3.0 15.0 + - - -
75A PRO* 3.4 13.5 - - - -
76A VAL 3.2 0.2 - - - -
77A VAL* 1.3 77.6 - - - +
79A ILE* 1.3 58.1 + - - +
82A TYR* 2.8 52.3 + - - +
126A THR* 4.0 11.2 - - - -
252A ASP* 5.9 0.2 - - - +
256A LYS* 4.5 12.9 - - - -
257A TYR* 2.6 32.0 + - - -
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Residues in contact with ILE 79 (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 ILE* 3.7 33.5 - - + +
45A ALA* 3.7 11.4 - - + +
46A GLY* 4.1 16.4 - - - -
49A ILE* 4.2 7.9 - - + -
75A PRO 2.8 19.5 + - - +
76A VAL* 3.2 17.5 - - + +
78A SER* 1.3 73.5 - - - +
80A ALA* 1.3 61.3 + - + +
82A TYR* 4.2 3.4 - - - +
83A THR* 2.6 36.4 + - - +
178C PHE* 4.3 16.2 - - + -
182C ILE* 4.6 16.2 - - + -
302C 22B 4.3 23.8 - - + -
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Residues in contact with ALA 80 (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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76A VAL 3.1 14.2 + - - +
77A VAL 3.6 0.9 - - - +
79A ILE* 1.3 81.8 - - + +
81A SER* 1.3 67.1 + - - +
83A THR* 3.0 4.2 + - - -
84A GLY 3.0 4.7 + - - -
162C THR* 4.0 17.0 - - + -
179C TRP* 2.9 31.9 - - + -
182C ILE* 4.5 7.0 - - + -
304C L3P 3.6 31.0 - - + -
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Residues in contact with SER 81 (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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77A VAL* 2.8 22.8 + - - -
80A ALA* 1.3 72.5 - - - +
82A TYR* 1.3 54.1 + - - +
84A GLY* 2.6 23.2 + - - +
85A LEU* 3.0 13.4 + - - +
90A THR* 4.4 1.9 + - - +
122A GLY* 3.2 15.1 + - - -
125A LEU* 4.0 7.4 - - - +
126A THR* 2.5 42.3 + - - -
179C TRP* 5.1 0.9 - - - -
304C L3P 4.6 12.6 - - - +
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Residues in contact with TYR 82 (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 SER 4.0 10.8 - - - -
38A LEU* 4.0 20.8 - - + +
41A ASN* 2.8 39.9 + - + -
42A ILE* 3.9 20.4 - - + +
78A SER* 2.8 47.6 + - - +
79A ILE 4.3 0.4 - - - +
81A SER* 1.3 72.5 - - - +
83A THR* 1.3 57.7 + - - +
85A LEU* 3.2 17.9 + - + +
86A ALA* 2.9 28.8 + - - +
123A ARG* 2.9 27.5 + - + -
126A THR* 4.6 9.8 + - + -
249A SER* 3.7 5.4 - - - -
252A ASP* 2.7 31.7 + - - +
257A TYR* 4.2 0.2 - - - -
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Residues in contact with THR 83 (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 ILE* 4.0 13.2 - - + +
79A ILE 2.6 18.8 + - - -
80A ALA* 3.0 13.5 + - - -
82A TYR* 1.3 76.9 - - - +
84A GLY* 1.3 61.9 + - - +
86A ALA* 4.1 1.1 - - - +
87A SER* 3.0 24.3 + - - -
175C MET* 3.9 14.1 - - + -
178C PHE* 3.2 40.5 - - + -
179C TRP* 3.5 28.0 - - + +
182C ILE* 4.1 1.5 - - + +
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Residues in contact with GLY 84 (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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80A ALA 3.0 6.1 + - - -
81A SER* 2.6 12.3 + - - -
83A THR* 1.3 78.2 - - - +
85A LEU* 1.3 55.2 + - - -
87A SER* 3.0 15.0 + - - -
89A LEU* 3.0 22.0 + - - -
90A THR* 3.1 19.1 + - - -
179C TRP* 3.3 19.9 - - - -
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Residues in contact with LEU 85 (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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28A VAL* 4.6 0.9 - - - +
38A LEU* 4.1 21.8 - - + +
81A SER 3.0 10.2 + - - +
82A TYR* 3.6 31.2 - - + +
83A THR 3.2 0.2 - - - -
84A GLY* 1.3 74.5 - - - +
86A ALA* 1.3 60.2 + - - +
88A GLY* 2.9 16.5 + - - -
90A THR* 3.3 25.4 - - - +
91A ILE* 3.1 30.5 - - + +
120A MET* 4.1 13.5 - - + -
122A GLY* 3.5 22.0 - - - +
123A ARG* 3.8 29.2 - - + +
126A THR* 5.1 2.2 - - - +
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Residues in contact with ALA 86 (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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25A PHE* 3.4 23.2 - - - +
28A VAL* 4.8 7.2 - - - +
29A LEU* 6.0 0.2 - - - +
38A LEU* 4.0 15.8 - - + +
39A TYR* 3.8 23.8 + - + -
42A ILE* 3.9 12.6 - - + -
82A TYR 2.9 16.6 + - - +
83A THR 4.1 0.7 - - - +
85A LEU* 1.3 76.2 - - - +
87A SER* 1.3 59.6 - - - +
88A GLY 3.4 0.5 + - - -
175C MET* 3.6 19.3 - - + +
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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