Contacts of the helix formed by residues 1142 - 1146 (chain A) in PDB entry 1OFD
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 VAL1142 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1140A ALA* 3.7 20.6 - - + +
1141A ARG* 1.3 83.1 - - - +
1143A CYS* 1.3 59.6 + - - +
1144A HIS* 3.2 8.3 - - + -
1145A THR* 3.0 39.7 + - + +
1146A ASN 3.7 2.1 + - - -
1147A ASN* 4.0 12.2 + - + +
1148A CYS* 4.0 16.0 + - - +
1149A PRO* 4.1 2.0 - - + -
3509A F3S 3.4 17.5 - - - -
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Residues in contact with CYS1143 (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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474A CYS* 3.5 20.7 - - + -
475A MET* 4.3 10.3 - - - -
983A LYS* 2.8 28.4 + - - -
1065A THR 4.4 4.7 - - - -
1066A GLY* 3.4 19.3 - - - +
1132A MET* 5.0 3.6 - - - -
1142A VAL* 1.3 77.8 - - - +
1144A HIS* 1.3 60.1 + - - +
1145A THR 3.1 1.3 + - - -
1146A ASN 3.7 0.7 + - - -
1153A ALA* 3.4 19.2 - - + +
3508A FMN 5.6 1.3 - - + -
3509A F3S 2.3 52.0 - - - -
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Residues in contact with HIS1144 (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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472A THR* 3.6 34.2 + - + -
473A PHE* 3.8 32.4 - + - +
474A CYS* 3.6 12.9 - - - +
980A PRO* 3.5 25.3 - - + +
983A LYS* 4.7 2.9 - - - +
1066A GLY 3.2 18.2 + - - +
1067A ALA* 3.8 16.8 - - + -
1141A ARG 4.0 13.9 - - - -
1142A VAL* 4.3 6.5 - - + -
1143A CYS* 1.3 76.4 + - - +
1145A THR* 1.3 69.0 + - - +
1146A ASN 3.6 0.8 + - - -
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Residues in contact with THR1145 (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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982A LYS* 4.7 13.6 - - - +
1142A VAL* 3.0 34.8 + - + +
1144A HIS* 1.3 87.9 + - - +
1146A ASN* 1.3 67.1 + - - +
1147A ASN* 3.1 45.7 + - + +
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Residues in contact with ASN1146 (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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982A LYS* 3.6 33.0 + - + +
983A LYS* 3.5 24.8 - - + +
1142A VAL 3.7 0.6 + - - -
1143A CYS 3.7 5.3 + - - -
1144A HIS 3.6 2.8 - - - -
1145A THR* 1.3 78.9 - - - +
1147A ASN* 1.3 58.3 + - - +
1148A CYS 3.5 2.9 - - - -
1153A ALA 4.3 5.8 - - - -
1154A THR* 2.6 30.3 + - - -
1155A GLN* 2.8 30.1 + - - +
1156A GLN* 3.1 36.7 + - - +
1159A LEU* 3.7 0.5 - - - +
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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