Contacts of the strand formed by residues 1237 - 1242 (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 ILE1237 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1165M GLU* 5.6 4.0 - - + +
1166M ASP* 3.4 16.8 - - - +
1169M ILE* 4.6 11.2 - - + -
1194M ARG* 3.2 55.9 - - + +
1195M LEU 3.3 8.3 - - - +
1196M GLU* 4.9 5.8 - - + -
1209M MET* 3.5 3.2 - - - +
1228M TRP* 3.3 4.7 - - - +
1229M SER* 2.8 33.7 + - - +
1235M LYS* 4.2 21.3 - - + +
1236M LEU* 1.3 85.9 - - - +
1238M ILE* 1.3 71.2 + - - +
1239M ARG* 3.9 19.1 - - + -
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Residues in contact with ILE1238 (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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1143M LEU* 5.0 0.9 - - + -
1193M LEU 3.2 12.6 - - - +
1194M ARG* 3.7 0.3 - - - -
1195M LEU* 3.3 36.9 + - + +
1197M LEU* 3.8 22.4 - - + -
1209M MET* 4.5 3.6 - - + +
1212M VAL* 3.6 31.4 - - + -
1213M GLY* 4.9 2.9 - - - +
1216M ILE* 3.9 18.8 - - + -
1226M VAL* 3.6 27.1 - - + -
1227M ILE 3.5 6.5 - - - +
1228M TRP* 4.2 10.1 - - + -
1237M ILE* 1.3 85.4 - - - +
1239M ARG* 1.3 62.9 + - - +
1240M CYS* 4.0 8.5 - - - -
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Residues in contact with ARG1239 (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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1155M ASP* 4.3 1.0 - - - -
1161M THR* 2.6 31.7 + - - +
1166M ASP* 2.8 35.7 + - - +
1169M ILE* 4.7 21.1 - - + -
1170M ILE* 5.6 7.5 - - - +
1192M LEU* 3.3 34.5 - - + +
1193M LEU 3.6 5.6 - - - -
1194M ARG* 4.7 5.2 - - - +
1226M VAL* 3.3 1.9 - - - +
1227M ILE* 2.9 50.2 + - + +
1228M TRP* 4.9 0.4 - - - +
1237M ILE* 3.9 11.0 - - + -
1238M ILE* 1.3 75.8 - - - +
1240M CYS* 1.3 62.7 + - - +
1241M ARG* 3.1 33.7 - - - +
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Residues in contact with CYS1240 (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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1191M TRP 4.2 1.0 - - - +
1192M LEU* 4.2 4.4 - - - +
1193M LEU* 3.3 55.4 + - - +
1195M LEU* 5.5 0.9 - - - -
1216M ILE* 5.7 0.9 - - - -
1224M LEU* 3.9 12.1 - - + +
1225M PHE* 3.1 17.3 - - - +
1226M VAL* 3.5 22.9 - - + -
1238M ILE* 4.0 10.8 - - - -
1239M ARG* 1.3 80.4 - - - +
1241M ARG* 1.3 64.1 + - - +
1260M LEU* 4.8 2.4 - - - +
1267M MET* 4.8 13.9 - - - -
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Residues in contact with ARG1241 (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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1155M ASP* 3.5 32.1 + - - +
1157M ASP 4.4 1.2 + - - -
1158M PRO* 4.3 26.8 + - - +
1161M THR* 4.5 0.6 + - - -
1188M GLN* 4.3 24.7 + - + +
1189M SER 2.8 29.2 - - - +
1190M PRO 4.4 1.2 + - - -
1191M TRP 3.8 14.4 - - - +
1192M LEU* 3.8 12.9 - - + +
1224M LEU* 2.9 19.8 - - - +
1225M PHE* 3.1 35.5 + - + +
1227M ILE* 5.3 2.2 - - - +
1239M ARG* 3.1 41.0 - - - +
1240M CYS* 1.3 78.3 - - - +
1242M VAL* 1.3 65.0 + - - +
1243M VAL* 4.6 0.4 - - - -
1260M LEU* 5.4 0.2 - - - -
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Residues in contact with VAL1242 (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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1189M SER* 3.3 28.2 + - - -
1191M TRP 4.8 1.0 + - - -
1223M ASP* 4.1 12.8 - - + +
1224M LEU* 4.4 4.7 - - + -
1241M ARG* 1.3 73.9 - - - +
1243M VAL* 1.3 87.9 + - - +
1244M ARG* 5.3 6.5 - - + +
1256M GLU* 4.3 20.0 - - - +
1259M MET* 4.5 17.0 - - - -
1260M LEU* 4.3 28.9 - - + -
1263M ILE* 4.2 25.4 - - + -
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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