Contacts of the helix formed by residues 1418 - 1427 (chain A) in PDB entry 3PTA
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 SER1418 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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657A GLU* 3.1 41.2 + - - -
1416A ASP 3.7 1.4 + - - -
1417A MET* 1.3 77.2 - - - +
1419A ALA* 1.3 63.6 + - - +
1420A LEU* 3.3 7.1 + - - +
1421A VAL* 3.0 13.6 + - - +
1422A ALA* 2.8 26.3 + - - +
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Residues in contact with ALA1419 (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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1417A MET 3.7 1.5 + - - -
1418A SER* 1.3 75.0 + - - +
1420A LEU* 1.3 60.1 + - - +
1422A ALA* 3.5 8.8 - - - +
1423A ALA* 3.4 17.5 + - - +
1446A LEU* 4.2 14.3 - - + +
1447A SER* 3.5 17.8 + - - +
1448A ASP* 3.0 35.9 - - + +
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Residues in contact with LEU1420 (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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657A GLU* 3.7 23.8 - - - +
1418A SER* 3.0 4.0 + - - +
1419A ALA* 1.3 77.9 - - - +
1421A VAL* 1.3 65.0 + - - +
1423A ALA* 3.0 20.7 + - + +
1424A ARG* 3.1 41.2 + - + +
1446A LEU* 3.7 28.4 - - + +
1452A ALA* 4.1 17.5 - - + -
1493A ASN* 3.9 32.8 - - - +
1494A THR 4.3 7.6 - - - +
1495A LEU* 4.7 3.1 - - + +
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Residues in contact with VAL1421 (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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657A GLU* 3.6 17.7 - - + +
1417A MET* 3.8 29.4 - - + -
1418A SER* 3.0 33.3 + - - +
1420A LEU* 1.3 72.3 - - - +
1422A ALA* 1.3 66.5 + - - +
1424A ARG* 3.0 8.3 + - - +
1425A MET* 2.9 27.9 + - + +
1514A TYR* 3.2 35.9 - - + +
1532A PRO* 4.3 3.4 - - + -
1533A MET* 5.8 1.3 - - + -
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Residues in contact with ALA1422 (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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1379A ASN* 4.2 15.5 - - + +
1417A MET 4.9 0.4 - - - +
1418A SER 2.8 12.9 + - - +
1419A ALA* 3.5 15.0 - - - +
1420A LEU 3.2 0.2 - - - -
1421A VAL* 1.3 76.4 - - - +
1423A ALA* 1.3 61.5 + - - +
1425A MET* 3.7 15.2 + - + +
1426A ARG* 3.1 24.4 + - - +
1447A SER* 5.7 2.0 - - - +
1545A HIS* 5.3 3.8 - - - +
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Residues in contact with ALA1423 (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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1419A ALA 3.4 2.7 + - - +
1420A LEU* 3.0 12.9 + - + +
1421A VAL 3.0 0.2 - - - -
1422A ALA* 1.3 77.1 - - - +
1424A ARG* 1.3 67.1 + - - +
1426A ARG* 2.9 28.2 + - - +
1427A HIS* 3.0 16.3 - - + +
1444A VAL* 5.8 5.2 - - + -
1446A LEU* 3.4 30.7 - - + -
1495A LEU* 4.6 9.6 - - + -
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Residues in contact with ARG1424 (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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657A GLU* 4.9 6.0 + - - +
660A GLN* 4.2 9.1 + - - +
1420A LEU* 3.5 35.0 - - + +
1421A VAL* 3.0 9.5 + - - +
1423A ALA* 1.3 75.1 - - - +
1425A MET* 1.3 64.1 + - - +
1427A HIS 3.2 8.0 + - - -
1428A ILE* 3.3 17.8 - - - +
1439A LEU* 3.4 15.0 - - + +
1493A ASN* 5.6 1.0 - - - +
1494A THR* 3.3 20.4 + - - +
1495A LEU* 3.2 40.8 + - + +
1497A PRO* 3.4 24.6 - - - +
1514A TYR* 3.0 39.8 + - + -
1533A MET* 3.3 23.8 - - - +
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Residues in contact with MET1425 (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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1379A ASN* 3.7 10.5 - - - +
1417A MET* 3.6 34.1 - - + -
1421A VAL* 2.9 23.0 + - + +
1422A ALA* 3.9 13.0 - - + +
1424A ARG* 1.3 72.7 - - - +
1426A ARG* 1.3 63.7 + - - +
1427A HIS 3.0 6.1 + - - -
1428A ILE* 3.0 20.8 + - - +
1514A TYR* 4.3 5.4 - - + -
1516A ARG* 3.2 17.1 + - - +
1532A PRO* 5.1 0.2 - - - -
1540A LEU* 4.1 22.4 - - + -
1545A HIS* 3.9 25.8 - - - +
1546A ARG* 3.9 26.9 - - - -
1547A VAL* 4.1 12.1 - - - -
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Residues in contact with ARG1426 (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 ALA 3.1 14.2 + - - +
1423A ALA* 2.9 25.3 + - - +
1425A MET* 1.3 77.4 - - - +
1427A HIS* 1.3 88.9 + - + +
1428A ILE 3.3 4.1 + - - +
1545A HIS* 3.4 39.4 + - + +
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Residues in contact with HIS1427 (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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1423A ALA* 3.0 27.5 + - + +
1424A ARG* 3.6 8.5 - - - +
1425A MET 3.0 1.8 + - - -
1426A ARG* 1.3 109.4 + - + +
1428A ILE* 1.3 59.7 + - - +
1429A PRO* 3.6 8.5 - - - +
1438A ASP 4.2 0.2 - - - +
1439A LEU* 3.2 18.9 - - + +
1440A PRO* 3.6 29.5 - - + +
1442A ILE* 4.5 11.7 - - + -
1444A VAL* 3.9 33.0 - - + +
1495A LEU* 4.2 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