Contacts of the helix formed by residues 63 - 72 (chain D) in PDB entry 2VUU
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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58D GLY* 4.7 0.8 - - - -
59D PRO* 2.9 48.6 + - + +
60D LEU 3.0 6.9 + - - +
61D LEU 3.9 2.7 - - - +
62D ASN* 1.3 77.2 - - - +
64D VAL* 1.3 62.3 + - - +
65D PRO* 3.5 11.6 - - - +
66D LEU* 3.4 31.0 + - + +
67D MET* 3.3 26.2 + - - +
94D ASP* 5.0 0.2 + - - -
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Residues in contact with VAL 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62D ASN* 3.8 2.5 + - - -
63D ASN* 1.3 74.8 - - - +
65D PRO* 1.3 65.8 - - + +
67D MET* 3.0 8.0 + - + +
68D ASP* 2.7 41.8 + - - +
94D ASP* 4.4 29.2 - - + +
101D ARG* 3.4 29.2 - - - +
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Residues in contact with PRO 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62D ASN 5.3 0.7 - - - +
63D ASN* 3.4 13.9 - - - +
64D VAL* 1.3 96.3 - - + +
66D LEU* 1.3 58.5 + - - +
68D ASP* 3.5 8.2 + - + +
69D THR* 3.0 30.0 + - - -
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Residues in contact with LEU 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35D GLN* 3.4 31.9 - - + -
56D PHE* 3.8 34.3 - - + -
57D GLN 4.9 2.5 - - - +
58D GLY* 4.1 12.1 - - - +
59D PRO 3.6 20.4 - - - +
60D LEU* 4.1 9.4 - - + -
63D ASN* 3.4 26.8 + - - +
64D VAL 3.2 0.2 - - - -
65D PRO* 1.3 77.5 - - - +
67D MET* 1.3 58.1 + - - +
69D THR* 3.2 6.7 + - - -
70D LEU* 2.9 29.9 + - + +
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Residues in contact with MET 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60D LEU* 3.0 41.3 - - + +
63D ASN 3.3 18.3 + - - +
64D VAL* 3.0 13.2 + - - +
66D LEU* 1.3 79.8 - - - +
68D ASP* 1.3 63.0 + - - +
70D LEU* 3.2 8.4 + - + +
71D PHE* 3.0 31.1 + - - -
91D ILE* 4.8 4.3 - - - +
94D ASP* 3.3 44.6 - - + +
95D LEU* 3.5 35.0 - - + -
98D ALA* 3.7 13.7 - - + -
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Residues in contact with ASP 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64D VAL* 2.7 31.0 + - - +
65D PRO* 3.7 8.5 - - + +
67D MET* 1.3 74.2 - - - +
69D THR* 1.3 64.9 + - - +
71D PHE* 3.4 5.0 + - - +
72D GLU* 3.3 23.5 + - + +
98D ALA* 4.2 9.7 - - - +
101D ARG* 3.1 32.7 + - - +
102D ALA* 5.8 0.2 - - - +
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Residues in contact with THR 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D ARG* 2.4 41.0 + - - +
56D PHE* 3.7 24.0 - - + -
65D PRO 3.0 16.4 + - - -
66D LEU* 3.2 6.9 + - - -
68D ASP* 1.3 77.5 - - - +
70D LEU* 1.3 59.8 + - - +
72D GLU* 3.1 27.4 + - - +
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Residues in contact with LEU 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D ALA* 3.9 18.5 - - + +
10D VAL 3.9 5.2 - - - +
11D VAL* 3.7 29.4 - - + -
33D ARG* 2.6 58.2 + - - +
35D GLN* 3.8 20.2 - - + +
56D PHE* 3.7 25.7 - - + -
60D LEU* 5.9 0.4 - - + -
66D LEU* 2.9 16.4 + - + +
67D MET* 3.2 11.6 + - + +
69D THR* 1.3 76.3 - - - +
71D PHE* 1.3 69.5 + - + +
74D ALA* 4.3 0.2 - - - +
79D ILE* 5.1 0.7 - - + -
95D LEU* 4.9 3.6 - - + -
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Residues in contact with PHE 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D ALA* 4.0 22.7 - - + -
67D MET 3.0 24.1 + - - +
68D ASP* 4.1 4.5 - - - +
69D THR 3.2 0.4 - - - -
70D LEU* 1.3 80.5 - - + +
72D GLU* 1.3 65.0 + - - +
73D GLY 3.1 1.2 + - - -
74D ALA* 2.9 19.5 + - - +
77D ALA* 4.1 7.6 - - + -
79D ILE* 4.6 6.1 - - + -
95D LEU* 3.4 35.0 - - + -
98D ALA* 3.3 31.6 - - + +
99D ALA* 3.5 23.8 - - + -
102D ALA* 3.6 27.8 - - + +
104D THR* 4.1 1.4 + - - -
105D ILE* 4.0 11.6 - - + +
108D TYR* 4.0 14.4 - + - -
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Residues in contact with GLU 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D ARG* 3.1 30.0 + - - +
68D ASP* 3.3 17.5 + - - +
69D THR* 3.1 35.8 + - - +
71D PHE* 1.3 74.5 - - - +
73D GLY* 1.3 61.5 + - - +
74D ALA 3.3 0.3 + - - -
102D ALA* 5.5 1.3 - - - -
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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