Contacts of the helix formed by residues 1079 - 1094 (chain B) 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 PRO1079 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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481B LEU* 4.3 21.5 - - + -
496B LYS* 5.8 0.2 - - + -
735B ILE* 3.3 22.7 - - + -
842B LEU* 3.9 28.0 - - + +
1037B ALA* 3.4 3.0 - - - +
1061B HIS* 3.5 19.7 - - + +
1077B GLY 4.9 0.2 - - - +
1078B SER* 1.3 91.8 - - - +
1080B TRP* 1.3 65.0 - - - +
1081B GLU* 3.5 16.8 - - - +
1082B LEU* 3.2 16.4 + - + +
1083B GLY 3.3 8.5 + - - -
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Residues in contact with TRP1080 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
843B ARG* 3.0 45.2 - - - +
1037B ALA* 4.2 6.5 - - - -
1058B ILE* 4.6 4.0 - - + +
1059B SER 4.5 2.2 - - - -
1060B GLY* 3.8 23.8 - - - +
1062B ASP* 5.4 2.7 - - + -
1078B SER 3.6 2.0 + - - -
1079B PRO* 1.3 70.3 - - - +
1081B GLU* 1.3 89.1 + - + +
1083B GLY* 3.0 0.4 + - - -
1084B VAL* 2.7 44.1 + - + +
1104B ALA* 4.8 3.8 - - + -
1105B ASP 3.6 15.3 - - - +
1106B GLY* 2.9 29.7 + - - -
1108B LEU* 3.7 22.4 - - + +
1113B ASP 4.3 2.7 - - - -
1116B MET* 4.2 4.3 - - + -
1117B ALA* 3.6 39.3 - - + -
1120B MET* 4.0 21.8 - - + -
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Residues in contact with GLU1081 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
841B ALA* 3.7 5.2 - - - +
842B LEU* 4.1 14.4 - - + -
843B ARG* 2.8 65.6 + - + +
1079B PRO* 3.1 14.4 - - - +
1080B TRP* 1.3 90.4 + - + +
1082B LEU* 1.3 59.1 + - - +
1085B THR* 2.8 30.8 + - - +
1120B MET* 3.8 26.9 - - + +
1222B LEU* 3.6 19.6 - - + +
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Residues in contact with LEU1082 (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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733B GLU* 4.2 5.2 - - - +
735B ILE* 4.1 15.9 - - + -
752B ARG* 3.7 44.8 + - + +
753B VAL* 5.5 4.7 - - + -
842B LEU* 3.8 19.3 - - + -
1078B SER* 4.6 2.9 - - - -
1079B PRO* 3.2 34.0 + - + +
1080B TRP 3.1 0.4 - - - -
1081B GLU* 1.3 79.6 - - - +
1083B GLY* 1.3 58.0 + - - +
1085B THR* 3.4 5.2 - - + +
1086B GLU* 3.0 32.0 + - - +
1221B CYS* 3.7 32.5 - - + -
1222B LEU* 4.4 2.5 - - + -
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Residues in contact with GLY1083 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
752B ARG* 5.1 0.6 - - - +
1037B ALA* 3.6 22.3 - - - +
1038B GLU 5.1 0.4 - - - -
1041B ILE* 4.1 13.2 - - - -
1058B ILE* 3.8 8.7 - - - -
1079B PRO 3.3 5.7 + - - -
1080B TRP 3.0 5.2 + - - -
1082B LEU* 1.3 77.3 - - - +
1084B VAL* 1.3 58.2 + - - +
1086B GLU* 3.4 1.4 + - - +
1087B VAL* 2.9 35.4 + - - +
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Residues in contact with VAL1084 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1058B ILE* 3.9 28.0 - - + -
1080B TRP* 2.7 32.5 + - + +
1081B GLU 4.6 0.9 - - - +
1083B GLY* 1.3 71.7 - - - -
1085B THR* 1.3 55.0 + - - +
1087B VAL* 3.4 1.4 + - - +
1088B HIS* 2.8 37.2 + - - +
1102B LEU* 4.4 3.1 - - + +
1104B ALA* 3.6 29.2 - - + -
1117B ALA 4.3 1.8 - - - +
1120B MET* 3.5 28.5 - - + +
1121B GLY 4.2 2.2 - - - -
1122B ALA* 3.9 19.5 - - + +
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Residues in contact with THR1085 (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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752B ARG* 5.6 1.3 - - - +
1081B GLU 2.8 20.4 - - - +
1082B LEU* 3.4 9.2 - - + +
1084B VAL* 1.3 80.0 - - - +
1086B GLU* 1.3 60.7 + - + +
1088B HIS* 3.8 0.3 - - - +
1089B ARG* 3.0 33.7 + - - +
1120B MET* 3.8 23.6 - - - +
1221B CYS* 3.2 26.2 - - + +
1222B LEU* 3.8 16.0 + - + -
1225B LEU* 3.6 26.4 - - + +
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Residues in contact with GLU1086 (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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752B ARG* 2.7 38.6 + - - +
1038B GLU 3.7 2.9 - - - +
1039B ILE* 3.6 13.8 - - - +
1040B GLY* 2.9 20.9 + - - -
1041B ILE* 3.7 5.4 - - + +
1042B GLY* 2.9 31.5 + - - +
1043B THR 4.6 0.3 + - - -
1082B LEU 3.0 19.1 + - - +
1083B GLY 3.8 3.4 - - - +
1085B THR* 1.3 76.3 - - - +
1087B VAL* 1.3 58.9 + - - +
1089B ARG* 3.8 6.8 - - - +
1090B VAL* 3.0 41.7 + - + +
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Residues in contact with VAL1087 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1041B ILE* 3.8 27.8 - - + +
1042B GLY* 4.3 6.3 - - - -
1045B ALA* 3.6 19.5 - - + -
1056B ILE* 4.9 2.9 - - + -
1058B ILE* 3.8 21.8 - - + -
1083B GLY 2.9 20.7 + - - +
1084B VAL 3.8 2.5 - - - +
1086B GLU* 1.3 74.7 - - - +
1088B HIS* 1.3 66.2 + - - +
1090B VAL* 4.2 0.2 - - - +
1091B LEU* 3.0 47.7 + - + +
1102B LEU* 3.9 19.1 - - + -
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Residues in contact with HIS1088 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1084B VAL 2.8 22.5 + - - +
1085B THR 3.8 2.2 - - - +
1087B VAL* 1.3 74.2 - - - +
1089B ARG* 1.3 61.7 + - - +
1091B LEU* 4.0 1.2 - - - +
1092B MET* 2.9 59.1 + - + +
1097B ARG* 3.0 32.6 + - - +
1102B LEU* 4.0 12.8 - - + +
1120B MET 3.8 10.1 - - - +
1121B GLY* 4.0 11.5 - - - -
1198B GLY* 4.1 13.4 + - - -
1225B LEU* 3.9 24.0 - - + -
1226B PRO* 4.7 6.5 + - + +
1228B THR* 4.6 0.6 + - - -
1234B TRP* 3.7 27.3 - + - -
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Residues in contact with ARG1089 (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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1085B THR* 3.0 20.3 + - - +
1086B GLU* 3.8 6.3 - - - +
1088B HIS* 1.3 77.3 - - - +
1090B VAL* 1.3 64.3 + - + +
1092B MET* 3.3 2.4 + - - +
1093B GLU* 3.0 45.4 + - + +
1220B ASP 4.0 0.8 + - - -
1221B CYS* 2.7 40.4 + - - +
1224B ASN* 2.5 37.8 + - - +
1225B LEU* 3.5 13.6 - - + +
1226B PRO* 4.2 19.5 - - + -
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Residues in contact with VAL1090 (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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209B THR 5.5 0.2 - - - +
1042B GLY* 3.4 37.5 - - - +
1043B THR* 4.1 5.4 - - - +
1046B ALA* 4.2 7.2 - - + -
1086B GLU* 3.0 28.2 + - + +
1087B VAL 4.2 0.4 - - - +
1089B ARG* 1.3 82.6 - - + +
1091B LEU* 1.3 62.7 + - - +
1093B GLU* 3.4 4.4 + - - +
1094B ASN* 2.8 45.8 + - - +
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Residues in contact with LEU1091 (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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1045B ALA* 3.8 22.2 - - + +
1046B ALA* 3.8 16.6 - - - +
1049B ALA* 3.9 8.1 - - + -
1056B ILE* 4.5 2.9 - - + -
1087B VAL* 3.0 42.6 + - + +
1090B VAL* 1.3 76.3 - - + +
1092B MET* 1.3 62.2 + - - +
1094B ASN* 3.4 2.3 + - - +
1095B GLN 3.1 2.8 + - - -
1096B LEU* 2.7 48.3 + - + +
1097B ARG* 3.8 22.9 - - - -
1100B VAL* 3.5 26.5 - - + -
1102B LEU* 4.0 6.7 - - + -
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Residues in contact with MET1092 (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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1088B HIS* 2.9 43.2 + - + +
1089B ARG 3.6 4.3 - - - +
1091B LEU* 1.3 77.5 - - - +
1093B GLU* 1.3 64.7 + - - +
1095B GLN* 3.1 18.8 + - - +
1097B ARG* 3.6 30.5 - - + +
1226B PRO* 3.8 31.9 - - + +
1227B ASP 4.8 0.4 - - - +
1228B THR* 3.6 24.2 - - - +
1231B ASN* 4.6 10.3 - - - +
1234B TRP* 3.9 20.6 - - + +
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Residues in contact with GLU1093 (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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211B THR* 5.3 0.2 - - - +
212B MET* 3.1 27.2 - - + +
1089B ARG* 3.0 33.2 + - + +
1090B VAL* 3.4 6.0 + - - +
1091B LEU 3.3 0.2 - - - -
1092B MET* 1.3 79.8 - - - +
1094B ASN* 1.3 58.7 + - - +
1095B GLN* 3.3 5.5 + - - +
1226B PRO* 3.6 25.1 - - + +
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Residues in contact with ASN1094 (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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36B ALA* 4.2 1.0 - - - +
209B THR 4.7 0.6 + - - -
210B ASN* 3.3 17.6 - - - +
211B THR* 2.7 60.5 + - - +
212B MET* 3.9 10.6 - - - +
1046B ALA* 4.3 5.1 - - - +
1090B VAL* 2.8 44.2 + - - +
1091B LEU 3.4 1.1 + - - +
1092B MET 3.2 0.2 - - - -
1093B GLU* 1.3 78.0 - - - +
1095B GLN* 1.3 66.6 - - - +
1096B LEU* 3.3 23.3 + - + +
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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