Contacts of the strand formed by residues 32 - 37 (chain D) in PDB entry 1VI9
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 32 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C HIS* 4.6 10.7 + - - -
267C GLN* 5.0 7.7 + - - +
269C VAL* 3.7 16.3 - - - +
2D MSE 3.5 34.4 - - - +
3D LYS 2.8 8.2 + - - +
4D ASN* 2.9 30.4 + - - +
5D ILE* 2.9 27.3 + - - +
27D ARG* 4.9 1.5 + - - -
31D ALA* 1.3 75.4 - - - +
33D VAL* 1.3 62.4 + - - +
34D TRP* 4.2 11.0 - - + +
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Residues in contact with VAL 33 (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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13C VAL 4.5 0.3 - - - +
5D ILE 3.5 3.1 - - - +
7D ALA* 4.1 24.5 - - + -
19D ASN* 4.8 1.3 - - - +
23D GLU* 3.8 29.8 - - + +
26D MSE 3.6 43.1 - - + -
27D ARG* 2.8 47.7 + - + +
31D ALA* 4.0 1.7 + - + +
32D ASN* 1.3 77.6 + - - +
34D TRP* 1.3 65.9 + - - +
35D PRO* 3.1 12.5 - - + +
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Residues in contact with TRP 34 (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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13C VAL* 3.1 26.5 - - + +
14C TYR* 3.5 31.3 - + - -
15C GLY 5.1 3.1 - - - +
4D ASN* 3.8 31.2 + - + +
5D ILE 2.8 15.2 + - - +
6D LEU* 3.6 27.1 - - + +
7D ALA 3.0 22.2 + - - -
32D ASN* 4.4 7.2 - - + +
33D VAL* 1.3 80.2 - - - +
35D PRO* 1.3 62.3 - - - +
36D LEU 3.2 4.3 + - - -
67D ILE* 4.1 22.7 - - + -
72D LYS 3.6 20.4 - - - -
73D LEU* 4.3 8.7 - - + -
75D THR* 3.5 17.0 - - - -
76D CYS* 3.7 28.0 - - + -
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Residues in contact with PRO 35 (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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11C HIS* 2.9 47.2 + - + -
12C VAL 4.6 1.3 - - - +
13C VAL* 3.2 18.8 - - - +
20C SER* 6.5 0.2 - - - -
7D ALA 3.7 4.7 - - - +
19D ASN* 3.8 21.5 - - + +
23D GLU* 4.5 9.9 - - + -
27D ARG* 4.0 14.1 - - - +
33D VAL* 3.1 21.8 - - + +
34D TRP* 1.3 79.3 - - - +
36D LEU* 1.3 60.8 + - - +
37D ASN* 3.6 9.6 + - - +
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Residues in contact with LEU 36 (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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13C VAL* 4.1 4.7 - - + -
40C GLN* 3.7 18.6 - - - +
6D LEU* 3.7 19.3 - - + -
7D ALA 2.8 10.8 + - - +
8D ILE* 3.1 49.2 - - + +
9D GLN 3.1 6.1 + - - -
34D TRP 3.2 1.8 + - - -
35D PRO* 1.3 70.0 - - - +
37D ASN* 1.3 62.7 + - - +
38D THR 3.6 0.3 + - - -
59D HIS* 4.7 0.2 - - - +
60D LEU* 3.8 36.6 - - + +
63D ILE* 3.9 26.9 - - + -
64D VAL* 3.9 18.8 - - + -
96D ILE* 4.4 1.8 - - + -
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Residues in contact with ASN 37 (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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11C HIS* 3.6 15.0 + - - -
37C ASN* 3.7 13.1 - - - +
40C GLN* 2.8 43.8 + - - +
9D GLN 3.2 4.4 - - - +
11D HIS* 3.4 29.0 + - + +
19D ASN* 3.0 30.3 + - - +
35D PRO* 3.9 7.5 - - - +
36D LEU* 1.3 71.0 - - - +
38D THR* 1.3 60.9 + - - +
39D VAL 3.4 16.4 - - - +
40D GLN* 5.3 2.6 + - + +
55D MSE 3.3 11.5 - - + +
60D LEU* 4.0 4.8 - - - +
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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