Contacts of the helix formed by residues 56 - 65 (chain B) in PDB entry 3VOD
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 THR 56 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B ILE* 1.3 76.2 - - - +
57B PRO* 1.4 62.9 - - - +
58B VAL* 4.0 9.9 + - - +
59B GLU* 2.9 26.8 + - - +
60B LEU* 2.7 35.0 + - - +
89B ASN* 4.1 15.9 - - - +
95B GLY* 5.4 2.5 - - - -
96B VAL 3.4 17.0 - - - +
97B LEU* 3.7 17.7 - - + -
98B VAL* 4.9 0.7 - - - -
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Residues in contact with PRO 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B ILE 4.4 2.0 - - - +
56B THR* 1.4 84.5 - - - +
58B VAL* 1.3 54.7 + - + +
60B LEU* 3.6 8.9 - - + +
61B LYS* 2.8 34.0 + - - +
68B LEU* 4.3 15.0 - - + -
71B LEU* 3.7 6.1 - - + +
72B THR* 5.3 4.0 - - + +
75B LEU* 3.9 29.8 - - + -
86B ARG* 4.4 13.2 - - - +
96B VAL* 3.3 24.0 - - + +
98B VAL* 4.7 5.4 - - + -
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Residues in contact with VAL 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B THR* 3.1 9.4 - - - +
57B PRO* 1.3 81.3 - - + +
59B GLU* 1.3 63.4 + - - +
61B LYS* 3.0 22.4 + - + +
62B LYS* 3.1 33.3 + - + +
68B LEU* 4.8 7.0 - - + -
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Residues in contact with GLU 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B ILE* 3.6 21.1 - - + -
56B THR* 2.9 22.1 + - - +
58B VAL* 1.3 79.6 - - - +
60B LEU* 1.3 60.9 + - - +
62B LYS* 3.5 28.8 + - + +
63B VAL* 3.3 30.5 + - + +
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Residues in contact with LEU 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B VAL* 4.3 5.4 - - + +
48B SER* 3.6 31.0 - - - -
49B ILE* 3.9 18.8 - - + -
55B ILE* 3.8 27.3 - - + +
56B THR 2.7 16.0 + - - +
57B PRO* 3.6 4.9 - - + +
59B GLU* 1.3 75.4 - - - +
61B LYS* 1.3 59.2 + - - +
63B VAL* 4.0 2.1 - - + +
64B LEU* 3.1 41.4 + - + +
71B LEU* 4.1 17.7 - - + -
75B LEU* 4.0 29.4 - - + -
98B VAL* 4.3 5.8 - - + -
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Residues in contact with LYS 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57B PRO 2.8 18.3 + - - +
58B VAL* 3.3 14.6 - - + +
60B LEU* 1.3 71.6 - - - +
62B LYS* 1.3 62.0 + - + +
64B LEU* 5.0 1.3 - - - -
65B SER* 2.9 28.5 + - - -
66B VAL 3.2 25.2 + - - +
67B ASP* 4.9 2.2 - - - +
68B LEU* 3.8 36.5 - - + +
71B LEU* 3.8 13.4 - - + +
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Residues in contact with LYS 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A GLN* 5.1 1.6 + - - -
27A ARG* 6.1 1.2 - - - -
58B VAL* 3.1 25.0 + - + +
59B GLU* 3.5 43.6 + - - +
60B LEU 3.3 0.2 - - - -
61B LYS* 1.3 80.7 - - + +
63B VAL* 1.3 66.9 + - + +
65B SER* 3.5 14.1 + - - +
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Residues in contact with VAL 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A GLN* 3.1 43.7 + - - +
48B SER* 4.5 21.8 - - - +
55B ILE* 4.5 13.0 - - + -
59B GLU* 3.3 20.5 + - + +
60B LEU* 4.0 5.6 - - - +
61B LYS 3.5 0.2 - - - -
62B LYS* 1.3 78.6 - - + +
64B LEU* 1.3 60.3 + - + +
65B SER* 4.3 0.2 + - - -
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Residues in contact with LEU 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A HIS* 5.7 10.7 + - + -
23A GLN* 5.1 2.8 - - - +
44B LYS* 3.7 30.1 - - + +
45B VAL* 3.7 28.0 - - + +
48B SER* 3.3 25.4 - - - +
60B LEU* 3.1 37.7 + - + +
63B VAL* 1.3 77.0 - - + +
65B SER* 1.3 71.3 + - - +
66B VAL* 3.4 22.7 - - + +
71B LEU* 4.1 10.3 - - + -
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Residues in contact with SER 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A GLN* 4.6 11.6 - - - +
26A ASP* 5.2 15.5 - - - +
27A ARG* 5.4 6.9 - - - +
30A ASN* 5.9 0.9 + - - -
61B LYS 2.9 13.8 + - - -
62B LYS* 3.5 11.8 + - - +
63B VAL 3.5 2.7 + - - -
64B LEU* 1.3 80.2 - - - +
66B VAL* 1.3 62.6 + - - +
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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