Contacts of the helix formed by residues 56 - 65 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55A ILE* 1.3 75.6 - - - +
57A PRO* 1.4 74.2 - - + +
58A VAL* 3.4 26.7 - - + +
59A GLU* 3.2 21.3 + - - +
60A LEU* 2.8 28.4 + - - +
89A ASN* 4.4 10.6 + - - +
95A GLY* 5.5 4.3 - - - -
96A VAL 3.5 14.8 + - - +
97A LEU* 4.1 10.8 - - - +
98A VAL* 5.2 0.4 - - - -
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Residues in contact with PRO 57 (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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55A ILE 3.9 4.7 - - - +
56A THR* 1.4 86.5 - - + +
58A VAL* 1.3 53.6 + - + +
60A LEU* 3.1 8.8 + - + +
61A LYS* 2.8 35.5 + - - +
68A LEU* 4.4 13.5 - - + -
71A LEU* 3.6 4.0 - - + +
72A THR* 5.6 2.9 - - - +
75A LEU* 4.2 27.1 - - + -
86A ARG* 4.8 5.2 - - - +
96A VAL* 3.3 37.2 - - + +
98A VAL* 4.8 7.2 - - + +
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Residues in contact with VAL 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 THR* 3.2 16.3 - - + +
57A PRO* 1.3 76.8 - - + +
59A GLU* 1.3 64.4 + - - +
61A LYS* 3.2 21.6 + - + +
62A LYS* 3.2 36.6 + - + +
68A LEU* 4.5 12.8 - - + +
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Residues in contact with GLU 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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54A CYS 5.4 0.9 - - - +
55A ILE* 3.7 23.2 - - + +
56A THR* 3.2 25.6 + - - +
58A VAL* 1.3 80.9 - - - +
60A LEU* 1.3 58.8 + - - +
62A LYS* 3.5 19.8 + - + +
63A VAL* 3.2 31.0 + - + +
97A LEU* 6.1 0.2 - - - +
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Residues in contact with LEU 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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45A VAL* 4.3 5.6 - - + +
48A SER* 3.6 31.2 - - - -
49A ILE* 4.0 27.6 - - + +
55A ILE* 3.9 28.2 - - + +
56A THR 2.8 16.7 + - - +
57A PRO* 3.1 5.8 + - + +
59A GLU* 1.3 76.0 - - - +
61A LYS* 1.3 63.1 - - - +
62A LYS 3.2 0.4 - - - -
63A VAL* 3.3 3.5 + - + +
64A LEU* 3.1 33.5 + - + +
71A LEU* 3.9 24.9 - - + -
75A LEU* 4.3 11.7 - - + -
98A VAL* 4.6 3.4 - - + -
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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 PRO 2.8 12.7 + - - +
58A VAL* 3.4 12.8 - - + +
60A LEU* 1.3 76.1 - - - +
62A LYS* 1.3 61.1 + - + +
65A SER* 2.8 29.6 + - - -
66A VAL* 3.3 29.4 + - - +
67A ASP* 5.4 0.7 - - - +
68A LEU* 4.0 34.9 - - + +
71A LEU* 3.6 15.3 - - + +
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Residues in contact with LYS 62 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58A VAL* 3.2 34.5 + - + +
59A GLU* 3.6 21.5 - - + +
60A LEU 3.2 0.6 - - - -
61A LYS* 1.3 84.5 - - + +
63A VAL* 1.3 63.4 + - + +
65A SER* 3.5 17.3 + - - +
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Residues in contact with VAL 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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48A SER* 3.9 23.6 - - - +
55A ILE* 4.4 13.2 - - + -
59A GLU* 3.2 21.4 + - + +
60A LEU* 3.3 8.2 + - + +
62A LYS* 1.3 77.1 - - + +
64A LEU* 1.3 61.3 + - + +
65A SER* 5.3 0.2 + - - -
23B GLN* 3.9 17.8 + - - -
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Residues in contact with LEU 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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44A LYS* 4.0 28.9 - - + +
45A VAL* 3.6 28.3 - - + -
48A SER* 3.4 25.1 - - - +
60A LEU* 3.1 35.3 + - + +
63A VAL* 1.3 78.8 - - - +
65A SER* 1.3 70.6 + - - +
66A VAL* 3.1 28.9 + - + +
71A LEU* 4.2 10.1 - - + -
74A MET* 5.4 0.2 - - + -
23B GLN* 5.5 2.8 + - - -
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Residues in contact with SER 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 14.4 + - - -
62A LYS* 3.5 12.0 + - - +
63A VAL 5.3 0.6 + - - -
64A LEU* 1.3 78.3 - - - +
66A VAL* 1.3 58.8 + - - +
23B GLN* 5.6 5.5 + - - -
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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