Contacts of the helix formed by residues 63 - 72 (chain A) in PDB entry 2VUT
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 ASN 63 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59A PRO* 2.5 40.3 + - + +
60A LEU* 3.3 11.5 + - - +
61A LEU 3.2 4.2 - - - +
62A ASN* 1.3 78.0 - - - +
64A VAL* 1.3 64.3 + - - +
65A PRO* 3.2 8.3 - - - +
66A LEU* 3.1 17.2 + - - +
67A MET* 3.5 15.5 + - - +
94A ASP* 5.3 1.0 + - - -
701K LEU* 4.2 8.3 - - - +
702K LYS 5.4 0.3 - - - +
705K GLY* 2.9 44.7 + - - -
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Residues in contact with VAL 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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62A ASN* 4.0 2.0 - - - -
63A ASN* 1.3 73.9 - - - +
65A PRO* 1.4 73.8 - - + +
67A MET* 3.0 10.8 + - + +
68A ASP* 2.9 28.7 + - - +
94A ASP* 4.4 27.1 - - + +
101A ARG* 3.0 35.2 - - - +
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Residues in contact with PRO 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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63A ASN* 3.2 13.5 - - - +
64A VAL* 1.4 93.9 - - + +
66A LEU* 1.3 58.0 + - - +
68A ASP* 3.6 8.7 + - + +
69A THR* 3.0 28.2 + - - -
5C LYS* 4.8 1.0 + - - -
702K LYS 4.0 19.5 - - - +
703K LEU 4.2 7.6 - - - +
704K HIS 3.9 6.0 - - - +
705K GLY* 3.9 20.0 - - - +
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Residues in contact with LEU 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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35A GLN* 4.0 18.6 - - + -
56A PHE* 3.6 34.8 - - + +
58A GLY* 3.6 18.8 - - - +
59A PRO 3.3 11.7 - - - +
60A LEU* 4.6 6.5 - - + -
63A ASN* 3.1 37.5 + - - +
64A VAL 3.1 0.6 - - - -
65A PRO* 1.3 76.6 - - - +
67A MET* 1.3 66.8 + - - +
69A THR* 3.3 5.0 + - - -
70A LEU* 3.0 25.6 + - + +
704K HIS 4.9 0.7 - - - -
705K GLY* 3.3 18.4 - - - +
706K VAL* 4.0 9.4 - - + -
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Residues in contact with MET 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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60A LEU* 3.5 35.9 - - + +
63A ASN 3.5 10.3 + - - +
64A VAL* 3.0 13.3 + - - +
66A LEU* 1.3 78.8 - - + +
68A ASP* 1.3 62.3 + - - +
70A LEU* 3.3 7.7 + - + +
71A PHE* 3.1 30.9 + - + -
91A ILE* 3.7 20.6 - - + +
94A ASP* 3.5 37.7 - - + +
95A LEU* 3.2 36.6 - - + -
98A ALA* 3.7 14.8 - - + -
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Residues in contact with ASP 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 VAL* 2.9 21.5 + - - +
65A PRO* 3.8 7.7 - - + +
67A MET* 1.3 74.2 - - - +
69A THR* 1.3 69.6 + - - +
71A PHE* 3.3 6.2 + - - +
72A GLU* 3.3 23.9 + - + +
98A ALA* 3.8 7.9 - - - +
101A ARG* 2.8 43.6 + - - +
102A ALA* 5.7 0.9 - - - +
3C GLN* 4.8 18.5 + - + +
5C LYS* 5.5 2.2 - - - +
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Residues in contact with THR 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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33A ARG* 2.8 29.0 + - - +
56A PHE* 3.4 28.0 - - + -
65A PRO 3.0 13.2 + - - -
66A LEU* 3.7 9.6 - - - -
68A ASP* 1.3 77.3 - - - +
70A LEU* 1.3 62.2 + - - +
72A GLU* 2.9 20.2 + - - +
5C LYS* 2.9 33.4 + - + -
28C VAL 3.3 23.3 + - - +
29C GLY* 4.3 0.2 - - - -
704K HIS 4.7 4.3 + - - -
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Residues in contact with LEU 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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9A ALA* 3.8 17.1 - - + +
10A VAL 3.8 6.3 - - - +
11A VAL* 3.5 32.1 - - + -
33A ARG* 3.0 67.2 + - + +
34A ALA* 3.7 11.9 - - - +
35A GLN* 4.0 9.0 - - + +
56A PHE* 4.2 10.7 - - + -
60A LEU* 5.7 0.7 - - + -
66A LEU* 3.0 19.6 + - + +
67A MET* 3.4 7.2 - - + +
69A THR* 1.3 77.5 - - - +
71A PHE* 1.3 63.9 + - + +
74A ALA* 4.1 0.2 - - - +
79A ILE* 5.4 0.2 - - + -
95A LEU* 4.8 9.9 - - + -
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Residues in contact with PHE 71 (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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9A ALA* 3.6 26.0 - - + -
67A MET* 3.1 24.8 + - - +
68A ASP* 3.3 4.2 + - - +
69A THR 3.2 0.8 - - - -
70A LEU* 1.3 79.6 - - + +
72A GLU* 1.3 63.9 + - - +
73A GLY 3.1 1.2 + - - -
74A ALA* 3.0 17.8 + - + +
77A ALA* 3.9 16.6 - - + -
79A ILE* 4.5 8.5 - - + -
95A LEU* 3.3 47.6 - - + -
98A ALA* 3.8 8.7 - - + +
99A ALA* 3.7 24.5 - - + -
102A ALA* 3.8 28.4 - - + +
104A THR* 4.0 2.4 + - - -
105A ILE* 4.0 14.8 - - + -
108A TYR* 4.0 6.7 - + - -
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Residues in contact with GLU 72 (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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33A ARG* 3.2 29.3 + - - +
68A ASP* 3.3 12.6 + - - +
69A THR* 2.9 20.8 + - - +
70A LEU 3.3 0.2 - - - -
71A PHE* 1.3 74.7 - - - +
73A GLY* 1.3 61.5 + - - +
74A ALA 3.1 0.6 + - - -
102A ALA* 5.6 1.1 - - - -
3C GLN 3.0 8.9 - - - +
4C GLN* 3.2 30.2 + - - +
5C LYS* 2.7 66.6 + - - +
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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