Contacts of the strand formed by residues 32 - 37 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2C MSE 3.2 33.3 - - - +
3C LYS 2.8 10.3 + - - +
4C ASN* 3.1 29.4 + - - +
5C ILE* 2.8 28.1 + - - +
27C ARG* 4.9 1.5 + - - -
31C ALA* 1.3 74.1 - - - +
33C VAL* 1.3 63.1 + - - +
34C TRP* 4.5 9.0 - - + +
16D HIS* 4.4 14.5 + - - -
267D GLN* 4.8 8.5 + - - +
269D VAL* 3.5 18.0 - - - +
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Residues in contact with VAL 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C ILE* 3.4 5.2 - - + +
7C ALA* 4.0 26.2 - - + -
19C ASN* 5.5 0.4 - - - +
23C GLU* 4.3 18.4 - - + +
26C MSE 3.7 42.6 - - + -
27C ARG* 2.8 52.1 + - + +
31C ALA 3.9 1.5 + - - +
32C ASN* 1.3 79.3 - - - +
34C TRP* 1.3 68.1 + - - +
35C PRO* 3.2 12.2 - - + +
13D VAL 4.6 0.5 - - - +
16D HIS* 5.7 0.2 - - - -
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Residues in contact with TRP 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4C ASN* 3.7 33.8 + - + +
5C ILE 2.8 14.7 + - - +
6C LEU* 3.4 20.9 - - + +
7C ALA 2.9 24.2 + - - -
32C ASN* 4.5 4.9 - - + +
33C VAL* 1.3 79.9 - - - +
35C PRO* 1.3 63.0 - - - +
36C LEU 3.2 5.1 + - - -
67C ILE* 4.1 32.5 - - + -
72C LYS 3.5 10.8 - - - -
73C LEU* 4.5 5.6 - - + -
75C THR* 3.3 27.1 - - - -
76C CYS* 3.6 27.1 - - + -
13D VAL* 3.2 25.1 - - + +
14D TYR* 3.6 27.8 - + - -
15D GLY 5.1 3.3 - - - +
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Residues in contact with PRO 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C ALA 3.6 5.8 - - - +
19C ASN* 3.9 11.0 - - + +
23C GLU* 4.8 8.3 - - + -
27C ARG* 4.1 15.9 - - - +
33C VAL* 3.2 22.9 - - + +
34C TRP* 1.3 79.2 - - - +
36C LEU* 1.3 60.8 + - - +
37C ASN* 3.1 21.2 + - - +
11D HIS* 2.8 44.1 + - + +
12D VAL 4.6 1.1 - - - +
13D VAL* 3.6 15.0 - - - +
20D SER* 6.3 0.2 - - - -
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Residues in contact with LEU 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C LEU* 3.8 18.2 - - + -
7C ALA 2.8 12.2 + - - +
8C ILE* 3.2 43.2 - - + +
9C GLN 3.5 0.5 + - - -
19C ASN* 3.8 0.7 - - - -
34C TRP 3.2 3.6 + - - -
35C PRO* 1.3 67.9 - - - +
37C ASN* 1.3 64.0 + - - +
38C THR 3.4 1.9 + - - -
59C HIS* 4.5 0.2 - - - +
60C LEU* 3.6 52.0 - - + +
63C ILE* 3.9 31.0 - - + -
64C VAL* 4.1 15.0 - - + -
96C ILE* 4.3 0.4 - - + -
13D VAL* 3.8 8.1 - - + -
40D GLN* 3.9 10.8 - - - +
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Residues in contact with ASN 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C GLN 3.3 4.7 - - - -
11C HIS* 3.3 41.0 + - + +
19C ASN* 3.1 24.4 + - - +
35C PRO* 3.1 16.9 + - - +
36C LEU* 1.3 72.0 - - - +
38C THR* 1.3 63.1 + - - +
39C VAL 3.7 5.8 - - - +
40C GLN* 5.9 0.9 - - + +
55C MSE 3.5 7.3 - - - +
60C LEU* 4.2 3.6 - - - +
11D HIS* 3.9 9.7 + - - -
37D ASN* 3.7 18.6 - - - +
40D GLN* 3.1 33.3 + - - +
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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