Contacts of the helix formed by residues 1200 - 1205 (chain M) in PDB entry 2JA7
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 ALA1200 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1198M ASP* 2.9 14.1 + - - +
1199M ARG* 1.3 76.1 - - - +
1201M ALA* 1.3 54.1 + - - +
1203M ASN* 2.7 36.1 + - - +
1204M ASP* 3.1 11.1 + - - +
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Residues in contact with ALA1201 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1145M SER 3.9 21.1 - - - +
1146M VAL* 3.5 18.7 - - + +
1198M ASP* 3.5 25.2 + - + +
1199M ARG 3.3 0.4 - - - -
1200M ALA* 1.3 78.6 - - - +
1202M MET* 1.3 59.1 + - - +
1203M ASN 3.2 0.6 + - - -
1204M ASP* 4.1 10.6 - - - +
1205M LYS* 3.8 18.4 + - - +
49U ILE* 5.8 3.4 - - + -
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Residues in contact with MET1202 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1146M VAL* 3.8 16.4 - - + -
1197M LEU* 4.5 8.7 - - + -
1198M ASP 3.0 21.9 + - - +
1199M ARG* 2.6 22.1 + - + +
1201M ALA* 1.3 73.4 - - - +
1203M ASN* 1.3 60.7 + - - +
1205M LYS 3.2 4.3 - - - +
1206M ASP* 4.0 0.3 - - - -
1207M LEU* 3.2 78.2 + - + +
1208M THR 4.2 0.9 - - - +
1209M MET* 4.1 20.6 - - - +
1212M VAL* 3.7 22.2 - - + -
1231M ASP* 5.7 0.4 - - - +
1236M LEU* 3.8 15.5 - - + -
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Residues in contact with ASN1203 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1199M ARG* 3.4 26.9 + - - +
1200M ALA* 2.7 12.0 + - - +
1202M MET* 1.3 82.5 - - - +
1204M ASP* 1.3 66.7 + - - +
1205M LYS 3.1 2.3 + - - -
1206M ASP* 3.6 13.5 + - - +
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Residues in contact with ASP1204 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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704M ALA 5.2 5.7 - - - +
706M HIS* 3.5 35.4 + - - -
1135M ARG* 5.0 7.6 + - - -
1200M ALA 3.1 11.4 + - - +
1201M ALA* 4.1 10.3 - - - +
1203M ASN* 1.3 79.1 - - - +
1205M LYS* 1.3 72.3 + - + +
1206M ASP 3.9 0.9 + - - -
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Residues in contact with LYS1205 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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706M HIS* 5.3 2.0 - - + -
1136M SER* 6.1 2.2 - - - -
1139M GLU* 4.1 23.2 + - - +
1140M HIS 3.9 17.6 + - - -
1141M THR* 3.4 35.6 + - + +
1145M SER* 3.9 25.9 + - - +
1146M VAL* 5.5 1.8 - - + -
1201M ALA 3.8 9.7 + - - +
1202M MET 3.2 8.7 - - - +
1203M ASN 3.8 1.8 - - - -
1204M ASP* 1.3 92.6 - - + +
1206M ASP* 1.3 70.6 + - - +
1207M LEU* 3.1 12.7 + - + +
1274M ARG* 6.5 0.7 - - - -
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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