Contacts of the helix formed by residues 1358 - 1366 (chain A) in PDB entry 3AVS
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 CYS1358 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1331A CYS* 3.3 6.9 - - - +
1334A CYS* 3.8 5.4 - - - -
1336A VAL* 3.6 21.5 - - + -
1338A VAL* 3.8 15.0 - - + -
1343A PHE* 3.9 2.0 - - - -
1357A HIS* 1.3 78.0 - - - +
1359A GLN* 1.3 66.3 - - - +
1360A ASP* 3.8 12.1 - - - -
1361A CYS* 3.5 16.9 + - - -
1362A ALA* 3.2 20.1 + - - +
1502A ZN 2.3 35.9 - - - -
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Residues in contact with GLN1359 (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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1306A LEU* 3.6 29.8 - - + +
1338A VAL* 5.6 0.2 - - - +
1343A PHE* 3.7 36.9 - - + -
1358A CYS* 1.3 75.7 - - - +
1360A ASP* 1.3 72.1 + - - +
1362A ALA* 3.3 1.9 + - - +
1363A ARG* 2.8 64.0 + - + +
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Residues in contact with ASP1360 (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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1358A CYS* 3.3 10.8 - - - -
1359A GLN* 1.3 91.2 + - - +
1361A CYS* 1.3 63.3 + - - +
1363A ARG* 3.4 8.4 + - - +
1364A LYS* 3.1 37.7 + - - +
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Residues in contact with CYS1361 (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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1331A CYS* 3.8 8.3 - - - -
1333A ILE* 3.6 34.1 - - + +
1334A CYS* 3.9 8.7 - - - -
1357A HIS* 4.6 6.4 - - + -
1358A CYS* 3.5 7.3 - - - +
1359A GLN 3.4 0.4 - - - -
1360A ASP* 1.3 78.4 - - - +
1362A ALA* 1.3 65.6 + - - +
1364A LYS* 3.6 30.1 + - - +
1365A THR* 3.9 10.9 + - - +
1502A ZN 2.4 34.1 - - - -
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Residues in contact with ALA1362 (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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1343A PHE* 3.9 15.5 - - + -
1357A HIS* 4.2 2.4 - - + +
1358A CYS 3.2 14.1 + - - +
1359A GLN 3.5 9.0 - - - +
1361A CYS* 1.3 76.9 - - - +
1363A ARG* 1.3 62.0 + - - +
1365A THR* 2.9 20.8 + - - -
1366A SER 3.0 7.7 + - - +
1369A LEU* 3.9 14.1 - - + -
1372A PHE* 3.4 37.4 - - + -
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Residues in contact with ARG1363 (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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1306A LEU* 5.0 0.8 - - - +
1309A ALA* 6.3 1.4 - - - +
1310A LEU* 4.6 9.9 - - - +
1313A ALA* 5.5 9.1 - - - +
1359A GLN* 2.8 57.7 + - - +
1360A ASP* 3.4 8.0 + - - +
1362A ALA* 1.3 76.0 - - - +
1364A LYS* 1.3 62.8 + - - +
1366A SER 3.1 26.2 - - - +
1367A GLY* 3.3 28.3 + - - +
1368A ASN* 4.9 3.6 - - - +
1369A LEU* 3.7 37.7 - - + +
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Residues in contact with LYS1364 (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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1360A ASP* 3.1 30.7 + - - +
1361A CYS* 3.7 23.6 - - - +
1362A ALA 3.2 0.4 - - - -
1363A ARG* 1.3 76.4 - - - +
1365A THR* 1.3 63.1 + - + +
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Residues in contact with THR1365 (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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1357A HIS* 5.7 1.2 - - + -
1361A CYS 3.9 9.0 + - - +
1362A ALA 2.9 13.9 + - - -
1364A LYS* 1.3 80.6 - - + +
1366A SER* 1.3 64.0 + - - +
1371A ASN* 5.7 1.7 + - - -
1372A PHE* 3.4 19.9 - - - -
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Residues in contact with SER1366 (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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1362A ALA 3.0 5.7 + - - +
1363A ARG* 3.1 19.1 - - - -
1365A THR* 1.3 83.3 + - - +
1367A GLY* 1.3 65.8 + - - +
1368A ASN 3.3 0.7 - - - -
1369A LEU* 3.1 21.8 + - - +
1370A GLU* 4.0 17.5 - - - -
1371A ASN* 3.4 23.6 + - - +
1372A PHE* 3.6 11.7 - - - -
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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