Contacts of the helix formed by residues 1511 - 1516 (chain A) in PDB entry 4C8D
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 LEU1511 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1393A LEU* 4.5 5.4 - - + -
1396A PRO 4.3 2.0 + - - -
1401A ASN* 4.1 11.2 - - + +
1402A TRP* 3.6 40.4 - - + +
1405A PHE* 3.7 37.5 - - + -
1417A VAL* 4.4 11.7 - - + -
1510A PRO* 1.3 71.7 - - + +
1512A PRO* 1.3 67.0 - - - +
1513A GLU 3.2 2.7 - - - -
1514A TYR* 2.9 16.2 + - + +
1515A THR* 2.9 24.1 + - - -
1682A PHE* 3.5 34.3 - - + -
2726A CL 3.7 9.2 - - + -
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Residues in contact with PRO1512 (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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1396A PRO 5.1 3.8 - - - +
1397A SER* 6.3 0.7 - - - -
1509A LEU 3.7 12.3 - - - +
1510A PRO* 3.5 3.8 - - + -
1511A LEU* 1.3 91.5 - - - +
1513A GLU* 1.3 62.2 + - + +
1515A THR* 3.4 9.9 - - - +
1516A LYS* 2.9 61.7 + - + +
1519A GLY* 3.8 2.4 - - - -
2726A CL 3.9 7.2 - - + -
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Residues in contact with GLU1513 (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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1511A LEU 3.2 1.0 - - - -
1512A PRO* 1.3 80.0 - - + +
1514A TYR* 1.3 56.4 + - + +
1519A GLY* 3.2 15.2 - - - -
1520A ARG* 3.1 50.1 + - + +
1521A LEU* 2.8 46.2 + - + +
1522A ASN 3.2 2.4 + - - -
2726A CL 3.4 20.0 - - + -
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Residues in contact with TYR1514 (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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1402A TRP* 4.0 27.8 - - + +
1405A PHE* 4.2 25.1 - + + -
1406A ARG* 3.6 17.5 - - - +
1511A LEU* 2.9 18.0 + - + +
1513A GLU* 1.3 80.3 - - - +
1515A THR* 1.3 62.0 + - + +
1516A LYS 3.7 0.7 - - - -
1521A LEU* 3.7 39.4 - - + +
1522A ASN* 3.3 21.2 - - - +
1682A PHE* 5.6 0.2 - - + -
1704A PHE* 3.3 27.9 - + + +
1706A SER* 4.0 19.7 - - - -
1708A GLU* 3.3 35.9 + - - -
2726A CL 4.1 13.2 - - + -
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Residues in contact with THR1515 (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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1509A LEU* 3.4 21.7 - - - +
1510A PRO 2.9 28.3 + - - +
1511A LEU 2.9 10.8 + - - +
1512A PRO* 3.4 6.8 - - - +
1514A TYR* 1.3 80.8 - - + +
1516A LYS* 1.3 66.4 + - - +
1517A ARG 3.6 0.3 + - - -
1522A ASN* 4.1 4.9 + - - -
1567A VAL* 3.7 17.5 - - + -
1682A PHE* 3.6 26.9 - - + -
1702A GLU* 3.5 23.4 - - - +
1704A PHE* 4.1 13.9 - - + +
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Residues in contact with LYS1516 (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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1506A MET* 3.1 42.8 + - + +
1507A GLU* 4.0 17.2 + - - +
1509A LEU* 4.9 3.3 + - + -
1512A PRO* 2.9 42.8 + - + +
1515A THR* 1.3 79.0 + - - +
1517A ARG* 1.3 59.8 + - - +
1518A ASP* 4.2 2.9 - - + +
1519A GLY* 2.7 30.6 + - - +
1522A ASN* 3.0 12.9 + - - +
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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