Contacts of the helix formed by residues 1431 - 1442 (chain A) in PDB entry 5D9Y
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 SER1431 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1426A VAL* 3.6 2.0 - - - -
1427A ASP* 2.9 26.5 + - - +
1429A PHE* 3.5 3.3 - - - -
1430A GLY* 1.3 76.9 - - - +
1432A VAL* 1.3 62.5 + - - +
1433A GLU* 3.2 7.1 + - - +
1434A ALA* 2.9 32.7 + - - +
1435A GLN 3.6 6.9 + - - -
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Residues in contact with VAL1432 (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 ASP* 3.6 22.4 - - + +
1426A VAL* 3.7 17.9 - - + -
1430A GLY 3.7 1.1 + - - +
1431A SER* 1.3 71.0 + - - +
1433A GLU* 1.3 68.9 + - + +
1435A GLN* 3.2 5.2 + - - +
1436A GLU* 3.0 34.0 + - + +
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Residues in contact with GLU1433 (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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1431A SER* 3.2 5.0 + - - +
1432A VAL* 1.3 83.0 - - + +
1434A ALA* 1.3 61.8 + - - +
1436A GLU* 3.0 8.9 + - - +
1437A GLU* 2.9 29.9 + - + +
1440A ARG* 3.3 32.3 + - - -
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Residues in contact with ALA1434 (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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1427A ASP* 3.4 29.6 - - - +
1431A SER* 2.9 19.3 + - - +
1433A GLU* 1.3 78.8 - - - +
1435A GLN* 1.3 59.7 + - - +
1437A GLU* 3.4 8.3 + - - +
1438A LYS* 3.3 27.6 + - - +
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Residues in contact with GLN1435 (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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1178A GLU* 3.8 4.7 + - - +
1179A ARG 5.3 0.8 + - - +
1423A VAL* 4.5 5.3 - - - +
1424A SER* 2.9 29.1 + - - +
1425A ASP 3.5 22.0 - - - +
1426A VAL 3.3 16.6 + - - +
1427A ASP* 3.5 12.7 - - - +
1431A SER 3.6 2.4 + - - +
1432A VAL 3.2 10.0 + - - +
1433A GLU 3.1 0.6 - - - -
1434A ALA* 1.3 81.1 - - - +
1436A GLU* 1.3 60.4 + - - +
1438A LYS* 2.8 35.5 + - - +
1439A LYS* 3.3 33.4 + - - +
1444A ILE* 3.6 21.4 - - - +
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Residues in contact with GLU1436 (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 ASP* 4.7 6.4 - - - +
1432A VAL* 3.0 24.6 + - + +
1433A GLU* 3.0 14.6 + - - +
1435A GLN* 1.3 74.3 - - - +
1437A GLU* 1.3 66.3 + - - +
1439A LYS* 2.7 39.0 + - - +
1440A ARG* 3.1 43.4 + - + +
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Residues in contact with GLU1437 (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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1433A GLU* 2.9 15.9 + - - +
1434A ALA* 3.5 13.0 - - - +
1435A GLN 3.3 0.2 - - - -
1436A GLU* 1.3 77.0 - - - +
1438A LYS* 1.3 53.2 + - + +
1440A ARG* 2.9 35.9 + - - +
1441A SER* 2.7 46.0 + - - -
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Residues in contact with LYS1438 (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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1176A ARG* 4.2 14.3 - - - +
1177A ILE 4.8 2.2 + - - -
1178A GLU* 2.6 35.5 + - - +
1203A SER* 6.3 0.4 - - - -
1427A ASP* 3.9 23.0 - - - +
1428A GLU 4.7 2.2 - - - +
1434A ALA* 3.3 13.1 + - - +
1435A GLN* 2.8 34.3 + - - +
1436A GLU 3.3 0.4 - - - -
1437A GLU* 1.3 77.3 - - + +
1439A LYS* 1.3 57.8 + - - +
1441A SER* 3.4 8.5 - - - +
1442A GLY 3.0 23.0 + - - -
1443A ALA* 3.0 24.0 + - + -
1444A ILE* 3.1 13.5 + - + +
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Residues in contact with LYS1439 (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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1198A TRP* 6.3 0.2 - - - -
1423A VAL* 5.2 8.7 - - - -
1424A SER 4.9 8.2 + - - -
1425A ASP* 5.2 5.3 - - - +
1435A GLN* 3.3 28.9 + - + +
1436A GLU* 2.7 43.8 + - - +
1437A GLU 3.2 0.6 - - - -
1438A LYS* 1.3 78.1 - - - +
1440A ARG* 1.3 62.8 + - + +
1442A GLY* 3.6 5.4 + - - -
1444A ILE* 3.2 31.1 - - + +
1445A GLN* 5.1 1.2 - - - -
1446A VAL* 4.1 24.8 + - + +
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Residues in contact with ARG1440 (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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1433A GLU* 3.3 24.4 + - - -
1436A GLU* 3.2 37.0 - - + +
1437A GLU* 2.9 39.4 + - - +
1439A LYS* 1.3 76.5 - - + +
1441A SER* 1.3 63.3 + - - +
1442A GLY* 3.1 2.3 + - - -
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Residues in contact with SER1441 (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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1437A GLU* 2.7 29.8 + - - -
1438A LYS* 3.0 19.2 + - - +
1440A ARG* 1.3 74.5 - - - +
1442A GLY* 1.3 57.4 + - - +
1443A ALA* 3.3 12.0 + - - +
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Residues in contact with GLY1442 (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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1201A ARG* 3.7 23.1 - - - +
1438A LYS 3.0 5.8 + - - -
1439A LYS 3.6 6.7 + - - -
1440A ARG 3.1 4.4 - - - -
1441A SER* 1.3 79.1 - - - +
1443A ALA* 1.3 64.2 + - - +
1444A ILE 3.0 7.0 + - - -
1445A GLN* 3.8 12.3 + - - +
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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