Contacts of the helix formed by residues 1188 - 1204 (chain B) in PDB entry 2O8C
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 SER1188 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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671A ASN* 3.4 15.0 + - - +
672A MET* 3.2 46.3 - - - +
1189B THR* 1.3 64.6 + - - +
1190B PHE* 3.2 2.3 - - - +
1191B PHE* 3.3 19.9 + - - +
1192B VAL* 2.9 39.3 + - - +
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Residues in contact with THR1189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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671A ASN* 3.3 25.1 - - - +
1188B SER* 1.3 79.6 - - - +
1190B PHE* 1.3 56.8 + - - +
1192B VAL* 3.7 8.6 + - - +
1193B GLU* 3.2 24.3 + - - +
1218B GLY* 4.9 12.0 - - - -
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Residues in contact with PHE1190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
671A ASN* 3.2 19.2 + - + +
827A GLY* 3.6 19.5 - - - -
830A VAL* 4.3 12.3 - - + -
1188B SER 3.2 0.8 - - - +
1189B THR* 1.3 77.5 - - - +
1191B PHE* 1.3 59.4 + - - +
1192B VAL 3.2 0.2 - - - -
1193B GLU* 3.1 25.8 + - + +
1194B LEU* 2.8 62.9 + - + +
1215B LEU* 5.7 1.6 - - + -
1216B GLY* 4.7 4.9 - - - -
1218B GLY 3.3 21.1 - - - +
1219B THR* 3.6 39.3 - - + -
1223B ASP 5.4 0.2 - - - -
1227B ILE* 3.7 21.1 - - + -
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Residues in contact with PHE1191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
830A VAL* 3.8 29.8 - - + +
833A LEU* 4.0 22.2 - - + -
834A ALA* 3.7 28.5 - - + -
578B HIS* 4.4 13.2 - + - -
1188B SER* 3.3 22.8 + - - +
1190B PHE* 1.3 80.7 - - - +
1192B VAL* 1.3 60.1 + - + +
1194B LEU* 3.3 1.8 + - - -
1195B SER* 2.8 50.3 + - - -
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Residues in contact with VAL1192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1176B ARG* 6.3 0.7 - - - +
1188B SER* 2.9 26.6 + - - +
1189B THR* 3.9 8.3 - - - +
1191B PHE* 1.3 81.3 - - + +
1193B GLU* 1.3 64.2 + - - +
1195B SER* 3.5 6.3 + - - -
1196B GLU* 3.3 40.2 + - + +
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Residues in contact with GLU1193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1176B ARG* 3.3 34.9 + - - +
1189B THR 3.2 16.1 + - - +
1190B PHE* 3.1 28.9 + - + +
1192B VAL* 1.3 79.6 - - - +
1194B LEU* 1.3 59.9 + - - +
1196B GLU 3.7 0.5 + - - -
1197B THR* 2.8 26.9 + - - -
1214B GLU 3.6 1.0 - - - +
1215B LEU* 4.2 11.2 - - + -
1216B GLY 3.5 20.4 + - - -
1217B ARG* 3.3 43.2 + - - -
1218B GLY* 3.6 7.2 + - - -
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Residues in contact with LEU1194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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827A GLY 4.4 0.4 - - - +
830A VAL* 3.7 12.8 - - + -
831A ALA* 3.5 31.4 - - + +
834A ALA* 4.1 7.4 - - + -
836A PHE* 3.8 27.0 - - + -
1190B PHE* 2.8 56.5 + - + +
1191B PHE 3.8 3.6 - - - +
1193B GLU* 1.3 75.7 - - - +
1195B SER* 1.3 55.0 + - - +
1196B GLU 3.2 0.2 - - - -
1197B THR* 3.1 4.0 + - - -
1198B ALA* 2.7 36.9 + - - +
1215B LEU* 5.0 10.1 - - + -
1227B ILE* 4.2 15.9 - - + -
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Residues in contact with SER1195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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834A ALA* 3.9 8.3 - - - +
578B HIS* 3.2 38.5 - - - +
1191B PHE* 2.8 38.8 + - - -
1192B VAL* 3.8 7.6 - - - -
1194B LEU* 1.3 75.5 - - - +
1196B GLU* 1.3 61.7 + - - +
1198B ALA* 3.5 4.0 + - - +
1199B SER* 3.1 26.7 + - - -
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Residues in contact with GLU1196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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738B VAL* 3.5 46.0 - - + +
742B ASN* 4.8 0.5 + - - -
1175B THR 4.9 2.9 - - - +
1176B ARG* 3.3 41.9 + - - -
1178B GLY 5.5 1.1 - - - -
1192B VAL* 3.3 30.0 + - + +
1193B GLU 4.0 0.4 - - - +
1194B LEU 3.2 0.4 - - - -
1195B SER* 1.3 78.5 - - - +
1197B THR* 1.3 60.9 + - - +
1199B SER* 3.5 13.3 + - - -
1200B ILE* 3.4 18.4 - - - +
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Residues in contact with THR1197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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836A PHE* 4.5 8.5 - - + -
1176B ARG* 3.9 11.1 - - - +
1193B GLU 2.8 15.8 + - - -
1194B LEU* 3.1 10.2 + - - -
1196B GLU* 1.3 77.4 - - - +
1198B ALA* 1.3 61.8 + - - +
1200B ILE* 3.3 28.7 + - + +
1201B LEU* 3.5 10.2 + - + +
1212B VAL* 5.4 4.9 - - + -
1215B LEU* 3.6 38.3 - - + +
1231B VAL* 4.2 22.2 - - + -
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Residues in contact with ALA1198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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834A ALA 3.5 15.9 - - - +
835A ASN 3.4 25.7 - - - +
836A PHE* 3.7 19.5 - - + +
837A PRO* 5.1 1.9 - - - +
578B HIS* 5.3 1.3 - - + +
1194B LEU 2.7 19.8 + - - +
1195B SER 3.9 3.6 - - - +
1196B GLU 3.3 0.2 - - - -
1197B THR* 1.3 71.7 - - - +
1199B SER* 1.3 64.2 + - - +
1201B LEU* 3.7 8.2 + - - +
1202B MET* 3.4 22.2 + - - +
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Residues in contact with SER1199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576B ASP* 5.8 0.2 + - - -
578B HIS* 4.7 14.2 - - - +
580B SER* 5.2 10.6 - - - -
1172B ARG* 5.6 4.0 - - - -
1174B PHE* 4.4 7.0 - - - -
1195B SER 3.1 13.3 + - - -
1196B GLU* 3.6 11.9 - - - -
1197B THR 3.2 0.4 - - - -
1198B ALA* 1.3 75.8 - - - +
1200B ILE* 1.3 60.8 + - - +
1202B MET* 4.6 1.6 - - - -
1203B HIS* 2.8 48.5 + - - +
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Residues in contact with ILE1200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1174B PHE* 3.7 39.0 - - + -
1175B THR 4.8 8.3 - - - +
1176B ARG* 4.8 2.5 - - + -
1196B GLU 3.4 18.2 - - - +
1197B THR* 3.5 15.9 - - + +
1198B ALA 3.3 0.4 - - - -
1199B SER* 1.3 73.6 - - - +
1201B LEU* 1.3 64.7 + - + +
1204B ALA* 2.8 41.4 + - + +
1210B VAL* 3.8 42.8 - - + -
1212B VAL* 4.1 15.3 - - + -
1235B LEU* 4.9 7.9 - - + -
1239B ILE* 5.2 1.1 - - + -
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Residues in contact with LEU1201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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836A PHE* 3.7 36.6 - - + -
837A PRO* 3.8 27.2 - - + +
840A VAL* 3.9 11.7 - - + -
1197B THR 3.5 13.6 + - - +
1198B ALA* 4.0 4.5 - - - +
1199B SER 3.4 0.4 - - - -
1200B ILE* 1.3 77.8 - - + +
1202B MET* 1.3 58.9 + - - +
1204B ALA 4.8 2.1 + - - +
1231B VAL* 4.0 37.0 - - + +
1234B GLU* 3.5 22.6 - - + +
1235B LEU* 4.6 9.0 - - + +
1239B ILE* 4.1 22.6 - - + +
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Residues in contact with MET1202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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835A ASN* 4.7 20.0 - - - +
837A PRO* 5.3 5.6 - - + -
576B ASP* 4.2 12.3 - - + +
717B VAL* 6.3 0.7 - - + -
1198B ALA 3.4 15.1 + - - +
1199B SER* 3.4 1.5 + - - -
1200B ILE 3.1 0.6 - - - -
1201B LEU* 1.3 82.4 - - - +
1203B HIS* 1.3 93.2 + - + +
1204B ALA 3.8 1.5 - - - +
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Residues in contact with HIS1203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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576B ASP* 2.7 32.8 + - - -
580B SER* 4.9 4.3 - - - -
581B ARG* 6.2 1.1 - - - -
716B THR* 5.5 4.0 - - - +
717B VAL* 3.8 36.9 - - + +
1172B ARG* 4.0 18.0 + - - +
1174B PHE* 3.6 18.0 - - + -
1199B SER* 2.8 36.3 + - - +
1202B MET* 1.3 112.0 + - + +
1204B ALA* 1.3 64.0 + - - +
1205B THR* 3.4 12.1 + - - +
1208B SER* 4.7 0.3 + - - -
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Residues in contact with ALA1204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1174B PHE* 3.6 23.8 - - + -
1200B ILE* 2.8 37.2 + - + +
1201B LEU 5.1 1.6 - - - +
1202B MET 5.1 0.9 - - - +
1203B HIS* 1.3 72.0 + - - +
1205B THR* 1.3 62.9 + - - +
1208B SER* 4.1 7.2 - - - -
1210B VAL* 4.4 6.7 - - + -
1239B ILE* 3.5 25.6 - - + +
1241B CYS* 4.6 1.8 - - - -
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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
------------------------------------------------------------
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