Contacts of the helix formed by residues 1369 - 1375 (chain A) in PDB entry 3PT6
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 THR1369 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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988A ASN* 3.8 9.0 - - + +
1310A ALA* 3.6 4.9 - - - -
1367A THR* 4.2 9.2 - - + +
1368A ILE* 1.3 75.9 - - - +
1370A VAL* 1.3 61.2 + - - +
1371A ARG* 3.6 7.4 + - - +
1372A ASP* 3.0 31.8 + - - +
1373A THR* 2.9 30.7 + - - -
1521A TRP 3.4 10.3 - - - -
1522A ASP* 3.4 30.0 + - + +
1523A GLY 3.6 4.3 - - - -
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Residues in contact with VAL1370 (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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1310A ALA* 4.0 0.6 - - - +
1369A THR* 1.3 73.6 - - - +
1371A ARG* 1.3 62.0 + - - +
1373A THR* 3.2 15.5 + - - -
1374A MET* 3.2 42.1 + - + +
1519A LEU* 4.3 10.8 - - + -
1520A GLU 3.3 25.4 - - - +
1521A TRP* 3.6 12.0 + - + -
1523A GLY 3.5 3.4 + - - -
1524A PHE* 3.9 25.8 - - - -
1525A PHE* 3.9 21.5 - - + -
1544A PRO* 4.0 9.0 - - + -
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Residues in contact with ARG1371 (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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1038A TYR* 3.4 58.4 + - - -
1369A THR* 3.7 5.3 + - - +
1370A VAL* 1.3 78.4 - - - +
1372A ASP* 1.3 65.2 + - - +
1373A THR 3.0 1.4 + - - -
1375A SER* 3.0 41.0 + - - +
1521A TRP* 2.9 58.0 + - + +
1522A ASP* 2.8 30.5 + - - -
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Residues in contact with ASP1372 (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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1038A TYR* 4.0 15.6 - - - +
1366A ARG* 2.6 33.3 + - - -
1367A THR 4.0 1.9 - - - +
1368A ILE* 3.7 19.2 - - + +
1369A THR* 3.0 35.0 + - - +
1371A ARG* 1.3 84.3 - - - +
1373A THR* 1.3 57.8 + - - +
1397A SER* 3.4 19.1 - - - -
1398A TRP 5.7 0.4 + - - -
1399A PHE* 3.5 16.0 - - + +
1400A GLN* 3.2 19.0 + - - +
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Residues in contact with THR1373 (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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1310A ALA* 3.4 18.2 + - - +
1368A ILE* 4.3 0.7 - - - +
1369A THR 2.9 15.5 + - - -
1370A VAL* 3.4 9.6 - - - -
1371A ARG 3.0 0.4 - - - -
1372A ASP* 1.3 80.9 - - - +
1374A MET* 1.3 76.2 + - + +
1375A SER 4.0 0.2 - - - -
1399A PHE* 3.8 16.6 - - - -
1400A GLN* 4.1 2.2 - - - +
1525A PHE* 4.2 7.9 - - + -
1554A GLU 4.3 0.4 - - - +
1557A ARG* 2.8 61.5 + - + +
1558A SER* 4.1 3.0 - - - +
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Residues in contact with MET1374 (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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1370A VAL* 3.2 23.3 + - + +
1371A ARG 4.2 0.2 - - - -
1373A THR* 1.3 85.3 - - + +
1375A SER* 1.3 63.8 + - - +
1376A ASP* 3.4 3.4 - - - -
1377A LEU* 3.8 30.1 + - + +
1519A LEU* 4.4 9.2 - - + -
1521A TRP* 4.5 7.8 - - + -
1525A PHE* 3.8 28.7 - - + -
1543A HIS* 3.9 18.6 + - + +
1544A PRO* 3.6 32.5 - - + -
1550A VAL* 4.7 2.2 - - + -
1554A GLU* 4.0 23.4 - - + +
1557A ARG* 3.7 9.2 - - + +
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Residues in contact with SER1375 (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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1371A ARG* 3.0 29.9 + - - +
1374A MET* 1.3 77.3 - - - +
1376A ASP* 1.3 59.8 + - - +
1377A LEU 3.2 8.1 + - - +
1396A LEU* 4.1 22.6 + - - +
1397A SER* 5.1 0.3 - - - -
1400A GLN* 2.9 20.9 + - - +
1521A TRP* 4.4 14.6 - - - -
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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