Contacts of the strand formed by residues 64 - 70 (chain D) in PDB entry 2V32
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 64 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31D TRP* 3.6 14.8 - - + -
32D GLY* 4.2 3.6 - - - -
33D VAL* 3.6 33.9 - - + +
59D PHE* 3.0 42.7 + - + +
60D LYS* 4.3 3.7 + - - +
62D ARG* 3.9 16.4 - - + +
63D GLY* 1.3 80.3 - - - +
65D LYS* 1.3 71.5 + - - +
66D LEU* 3.7 2.8 + - - +
132D ILE* 6.2 0.4 - - + -
160D ILE* 3.9 31.2 - - + -
164D GLN* 4.3 0.2 - - - +
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Residues in contact with LYS 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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26D TRP* 3.1 64.3 + - + +
27D LEU* 3.7 19.7 + - + +
30D SER* 3.7 14.4 - - - +
31D TRP 3.0 13.3 + - - +
32D GLY* 3.3 2.1 - - - -
33D VAL 2.8 27.9 + - - +
63D GLY 5.2 0.9 - - - +
64D VAL* 1.3 72.3 - - - +
66D LEU* 1.3 62.0 + - - +
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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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26D TRP* 3.3 13.0 - - - -
33D VAL* 3.6 18.2 - - + -
35D PHE* 4.2 11.2 - - + -
52D VAL* 3.7 31.0 - - + +
56D GLU* 4.6 13.2 - - + +
59D PHE* 3.7 54.1 - - + -
64D VAL 3.7 1.3 + - - +
65D LYS* 1.3 76.2 - - - +
67D ILE* 1.3 64.7 + - - +
95D PRO* 6.4 0.2 - - + -
96D TYR* 3.4 33.2 - - + +
97D PRO* 3.4 2.3 - - - +
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Residues in contact with ILE 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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21D LEU* 4.2 16.2 - - + -
23D PHE* 4.0 9.6 - - + -
26D TRP* 3.6 33.7 - - + -
32D GLY* 6.3 0.2 - - - -
33D VAL 2.9 18.6 + - - +
34D LEU* 3.2 25.6 - - + +
35D PHE* 2.9 32.5 + - - +
66D LEU* 1.3 76.0 - - - +
68D ALA* 1.3 69.0 + - - +
96D TYR* 4.5 0.4 - - - -
97D PRO* 3.4 32.3 - - + +
99D ILE* 3.4 27.8 - - + -
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Residues in contact with ALA 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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35D PHE* 3.3 31.1 - - + +
37D HIS* 4.8 2.5 - - + +
49D LEU* 4.1 7.9 - - + -
67D ILE* 1.3 78.3 - - - +
69D LEU* 1.3 65.0 + - - +
96D TYR* 3.8 13.6 - - + -
97D PRO 2.9 14.7 + - - +
98D ILE* 3.3 13.9 - - + -
99D ILE* 2.8 24.0 + - - +
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Residues in contact with LEU 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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34D LEU* 4.3 16.8 - - + -
35D PHE 3.0 10.9 + - - +
36D SER* 3.1 7.6 - - - -
37D HIS* 3.1 31.2 + - - -
68D ALA* 1.3 80.9 - - - +
70D SER* 1.3 73.6 + - - +
98D ILE* 4.1 1.1 - - - +
99D ILE* 3.5 32.8 - - + +
101D ASP* 4.0 9.4 - - + -
106D LEU* 3.6 30.1 - - + -
112D MET* 3.6 31.0 - - + -
126D THR* 3.9 13.0 - - + -
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Residues in contact with SER 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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37D HIS* 3.2 38.8 - - - -
38D PRO 4.3 3.1 - - - -
40D ASP* 3.3 10.0 + - - -
69D LEU* 1.3 81.4 - - - +
71D CYS* 1.3 60.5 + - - +
72D ASP* 2.8 27.5 + - - +
77D HIS* 3.4 9.2 + - - -
99D ILE 2.9 10.5 + - - +
100D ALA* 3.5 1.0 - - - -
101D ASP* 2.8 21.0 + - - +
126D THR* 4.3 1.1 - - - -
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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