Contacts of the helix formed by residues 1504 - 1511 (chain A) in PDB entry 4YOC
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 GLY1504 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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974A ARG* 3.5 14.1 - - - -
1500A LEU 2.9 20.0 + - - -
1501A PRO 3.6 2.2 + - - -
1502A HIS 3.4 3.2 - - - -
1503A THR* 1.3 77.3 - - - +
1505A ASN* 1.3 61.7 + - - +
1507A HIS 3.0 8.8 + - - -
1509A HIS* 2.9 31.3 + - - -
1510A TRP* 3.9 8.7 - - - -
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Residues in contact with ASN1505 (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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974A ARG* 3.1 11.3 + - - +
1461A ASP* 3.3 17.2 + - - -
1463A LYS* 4.8 13.3 - - + +
1464A ASN* 2.5 40.7 + - - +
1479A VAL* 5.1 6.9 - - - +
1501A PRO 5.1 2.2 + - - -
1502A HIS 5.5 0.6 + - - -
1503A THR 3.5 0.4 - - - -
1504A GLY* 1.3 74.6 - - - +
1506A ARG* 1.3 68.8 + - + +
1508A ASN* 4.4 4.9 + - - -
1509A HIS* 3.7 12.2 + - - -
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Residues in contact with ARG1506 (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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1503A THR* 3.4 6.3 + - - +
1504A GLY 3.1 1.0 - - - -
1505A ASN* 1.3 87.2 - - + +
1507A HIS* 1.3 81.2 + - + +
1508A ASN 3.6 2.0 + - - -
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Residues in contact with HIS1507 (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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1503A THR* 2.8 39.6 + - + +
1504A GLY 3.0 3.2 + - - +
1506A ARG* 1.3 92.7 - - + +
1508A ASN* 1.3 69.9 + - - +
1509A HIS 3.1 1.6 - - - -
1510A TRP* 3.0 57.4 + + + +
1511A ALA 4.6 0.2 + - - -
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Residues in contact with ASN1508 (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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977A SER* 5.7 0.5 + - - -
978A ASP* 4.9 11.2 + - - +
1437A ARG* 4.9 0.5 + - - -
1504A GLY 3.6 1.4 + - - -
1505A ASN 4.4 4.0 + - - -
1506A ARG 3.6 3.2 + - - -
1507A HIS* 1.3 76.9 - - - +
1509A HIS* 1.3 77.2 + - - +
1510A TRP 3.0 1.4 + - - -
1511A ALA* 3.4 23.7 + - - +
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Residues in contact with HIS1509 (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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973A TYR* 5.4 1.1 - + - -
974A ARG* 3.0 58.8 + - + +
977A SER* 3.4 27.1 + - - -
978A ASP* 5.9 0.7 - - - -
1436A TRP* 3.2 19.0 + - - -
1437A ARG* 3.9 8.2 - - - +
1464A ASN* 4.2 11.0 - - - -
1504A GLY* 2.9 19.1 + - - -
1505A ASN* 3.7 25.8 - - - -
1508A ASN* 1.3 81.8 - - - +
1510A TRP* 1.3 71.9 + - - +
1511A ALA 3.3 0.5 + - - -
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Residues in contact with TRP1510 (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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1436A TRP* 2.9 23.8 + + + +
1499A CYS 4.2 0.6 + - - -
1500A LEU* 3.4 43.5 + - + +
1503A THR* 2.7 28.6 + - - -
1504A GLY* 3.9 6.7 - - - -
1507A HIS* 3.0 53.1 + + + -
1509A HIS* 1.3 76.7 - - - +
1511A ALA* 1.3 66.5 + - - +
1512A GLY 3.3 2.1 + - - -
1513A LEU* 3.4 41.7 + - + -
1533A MET 5.5 1.3 - - - -
1534A GLY 5.9 0.4 - - - -
1535A LYS* 5.4 11.7 - - + -
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Residues in contact with ALA1511 (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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978A ASP* 3.9 11.0 - - - +
1437A ARG* 3.4 27.8 - - - +
1507A HIS 4.6 0.4 + - - -
1508A ASN* 3.4 21.5 + - - +
1509A HIS 3.3 2.0 - - - -
1510A TRP* 1.3 75.6 - - - +
1512A GLY* 1.3 58.8 + - - +
1513A LEU* 3.4 7.2 + - - +
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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