Contacts of the helix formed by residues 1421 - 1430 (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 SER1421 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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660A GLU* 4.6 13.4 - - - +
1419A ASP 3.8 1.6 + - - -
1420A MET* 1.3 77.0 - - - +
1422A PRO* 1.3 67.5 - - - +
1423A LEU* 3.3 16.3 + - - +
1424A VAL* 3.0 20.3 + - - +
1425A ALA* 2.7 32.2 + - - +
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Residues in contact with PRO1422 (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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1420A MET 3.5 2.7 - - - +
1421A SER* 1.3 89.9 - - - +
1423A LEU* 1.3 61.1 + - - +
1425A ALA* 3.4 7.9 + - + +
1426A ALA* 3.0 22.9 + - - +
1449A LEU* 4.2 9.9 - - + +
1450A GLY 4.9 6.2 + - - +
1451A ASP* 3.6 47.8 - - + +
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Residues in contact with LEU1423 (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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660A GLU* 5.6 7.0 - - + -
1421A SER* 3.1 11.0 + - - +
1422A PRO* 1.3 79.1 - - - +
1424A VAL* 1.3 65.2 + - + +
1426A ALA* 3.1 14.5 + - - +
1427A ARG* 3.1 42.2 + - - +
1449A LEU* 3.8 16.9 - - + +
1455A ALA* 3.8 29.2 - - + -
1495A SER* 4.0 23.8 - - - +
1496A THR 4.3 13.2 - - - +
1497A LEU* 4.8 5.8 - - + -
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Residues in contact with VAL1424 (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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660A GLU* 4.3 17.0 - - + +
1420A MET* 3.8 32.1 - - + -
1421A SER* 3.0 23.2 + - - +
1423A LEU* 1.3 72.8 - - + +
1425A ALA* 1.3 64.8 + - - +
1427A ARG* 3.5 17.0 + - - +
1428A MET* 3.1 24.8 + - + +
1516A TYR* 3.7 27.6 - - + +
1533A GLU* 6.1 0.4 - - - +
1534A PRO* 4.2 10.1 - - + -
1535A MET* 6.0 0.2 - - + -
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Residues in contact with ALA1425 (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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1382A ASN* 4.2 21.3 - - + +
1420A MET* 4.2 1.5 - - - +
1421A SER 2.7 19.1 + - - +
1422A PRO* 3.6 10.1 - - + +
1423A LEU 3.2 0.2 - - - -
1424A VAL* 1.3 71.0 - - - +
1426A ALA* 1.3 66.6 + - - +
1428A MET* 3.3 18.0 + - + +
1429A ARG* 3.1 25.0 + - - +
1547A HIS* 5.1 2.6 - - - +
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Residues in contact with ALA1426 (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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1422A PRO 3.0 13.4 + - - +
1423A LEU* 3.1 10.5 + - - +
1425A ALA* 1.3 76.7 - - - +
1427A ARG* 1.3 63.1 + - - +
1429A ARG* 2.9 36.6 + - - +
1430A HIS* 3.1 20.8 - - + -
1447A VAL* 4.8 2.5 - - + -
1449A LEU* 4.1 23.1 - - + -
1497A LEU* 4.4 10.1 - - + -
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Residues in contact with ARG1427 (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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660A GLU* 5.6 3.0 - - - +
663A GLN* 5.8 0.6 + - - -
1423A LEU* 3.1 43.4 + - + +
1424A VAL* 3.6 15.7 - - - +
1426A ALA* 1.3 75.6 - - - +
1428A MET* 1.3 54.7 + - - +
1430A HIS* 2.7 25.7 + - - +
1431A ILE* 3.3 15.8 + - - +
1442A LEU* 3.8 13.4 - - + +
1496A THR* 2.7 27.4 + - - +
1497A LEU* 2.7 35.8 + - + +
1499A PRO* 3.5 28.7 - - - +
1516A TYR* 3.3 42.9 + - + -
1535A MET* 4.1 7.3 - - - +
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Residues in contact with MET1428 (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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1382A ASN* 3.9 20.9 - - - +
1420A MET* 3.9 12.6 - - + -
1424A VAL* 3.1 11.5 + - + +
1425A ALA* 3.7 20.4 - - - +
1427A ARG* 1.3 77.8 - - - +
1429A ARG* 1.3 61.3 + - - +
1430A HIS 3.3 0.3 + - - -
1431A ILE* 3.6 10.4 + - - +
1516A TYR* 4.5 9.9 - - + -
1518A ARG* 3.4 23.9 + - - -
1534A PRO* 4.6 5.2 - - - -
1542A LEU* 3.7 29.4 - - + -
1547A HIS* 3.7 20.0 + - - +
1548A ARG* 3.6 36.1 - - - -
1549A VAL* 3.9 7.9 - - - -
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Residues in contact with ARG1429 (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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1425A ALA* 3.1 12.4 + - - +
1426A ALA* 2.9 35.1 + - - +
1428A MET* 1.3 78.3 - - - +
1430A HIS* 1.3 81.9 + - + +
1431A ILE 3.4 2.8 + - - +
1447A VAL* 4.0 17.4 - - - +
1448A ARG 5.2 3.0 + - - -
1449A LEU* 5.9 1.8 - - - +
1547A HIS* 3.4 42.9 + - + +
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Residues in contact with HIS1430 (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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1426A ALA* 3.1 25.6 - - - -
1427A ARG 2.7 10.3 + - - +
1429A ARG* 1.3 103.9 + - + +
1431A ILE* 1.3 60.6 + - - -
1432A PRO* 3.5 8.3 - - - +
1441A ASP 4.3 0.5 - - - +
1442A LEU* 3.6 21.5 - - + +
1443A PRO* 3.7 28.8 - - + +
1445A ILE* 4.0 19.7 - - + -
1447A VAL* 4.1 12.2 - - + +
1497A LEU* 4.3 14.4 - - + -
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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