Contacts of the helix formed by residues 1076 - 1094 (chain B) in PDB entry 5JPM
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 THR1076 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1074B SER 4.1 1.4 + - - -
1075B SER* 1.3 71.9 - - - +
1077B TRP* 1.3 63.3 + - - +
1079B THR 3.4 0.7 + - - -
1080B ALA* 3.1 19.1 + - - +
1106B TRP* 3.5 22.2 - - + -
1107B LEU* 3.6 18.9 - - + +
1110B GLN* 3.8 14.6 - - + +
1117B PHE* 4.8 6.1 - - + -
1118B GLN 3.0 26.1 + - - +
1119B ASP* 2.9 21.9 + - - -
1120B PRO* 4.0 5.0 - - - +
1141B LEU* 4.7 4.7 - - + -
1145B VAL* 4.4 15.0 - - + -
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Residues in contact with TRP1077 (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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1012B GLU* 3.6 23.1 - - + -
1075B SER* 4.0 2.7 - - - +
1076B THR* 1.3 74.5 - - - +
1078B LEU* 1.3 89.9 + - + +
1080B ALA* 3.1 7.5 + - - +
1081B PHE* 3.0 24.7 + + - -
1119B ASP* 2.7 18.8 + - - +
1122B PRO* 4.9 4.7 - - + -
1123B VAL* 4.0 22.9 - - + +
1124B LEU* 3.6 33.6 - - + +
1141B LEU* 4.0 25.9 - - + +
1144B PHE* 3.3 41.8 - + + +
1303B GLN* 3.3 43.3 - - - -
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Residues in contact with LEU1078 (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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1011B GLY* 4.6 3.6 - - - -
1012B GLU* 3.8 39.5 - - + +
1015B MET* 4.1 15.3 - - + -
1056B ILE* 5.3 2.7 - - + -
1059B PHE* 5.6 0.4 - - + -
1066B TYR* 4.2 10.8 - - + +
1067B ALA 3.3 37.9 - - - +
1068B ALA* 3.7 11.2 - - + -
1075B SER* 3.4 17.8 + - - +
1077B TRP* 1.3 93.5 - - + +
1079B THR* 1.3 63.3 + - - +
1081B PHE* 3.2 2.5 + - + +
1082B VAL* 3.0 32.2 + - + +
1123B VAL* 4.2 5.6 - - + -
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Residues in contact with THR1079 (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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1065B SER* 3.7 14.8 - - - -
1066B TYR* 2.9 30.6 + - + +
1075B SER 2.8 22.2 + - - -
1076B THR 3.7 5.2 - - - -
1077B TRP 3.3 0.2 - - - -
1078B LEU* 1.3 77.3 - - - +
1080B ALA* 1.3 61.7 + - - +
1082B VAL* 3.5 2.6 + - - +
1083B LEU* 3.2 21.0 + - - +
1103B THR* 3.6 25.3 - - + +
1106B TRP* 3.9 13.7 - - + -
1107B LEU* 3.7 18.8 - - + +
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Residues in contact with ALA1080 (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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1076B THR 3.1 12.7 + - - +
1077B TRP* 3.1 10.3 + - - +
1079B THR* 1.3 76.5 - - - +
1081B PHE* 1.3 65.2 + - - +
1083B LEU* 3.2 1.7 + - - +
1084B LYS 2.9 19.2 + - - -
1107B LEU* 3.8 15.6 - - + +
1144B PHE* 4.1 11.0 - - + -
1145B VAL* 4.0 22.2 - - + -
1148B ALA* 3.1 25.5 - - + +
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Residues in contact with PHE1081 (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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1012B GLU* 3.6 18.6 - - + -
1015B MET* 3.5 45.5 - - + -
1019B ALA* 4.9 1.3 - - + -
1077B TRP* 3.0 13.8 + + + +
1078B LEU* 3.2 11.2 + - + +
1080B ALA* 1.3 76.5 - - - +
1082B VAL* 1.3 61.9 + - - +
1084B LYS* 3.4 17.7 + - + +
1085B VAL* 3.3 36.5 + - + +
1144B PHE* 3.7 29.8 - + + -
1303B GLN* 3.2 29.2 - - - -
1306B VAL* 3.8 21.3 - - + -
1307B ILE* 5.9 2.2 - - + -
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Residues in contact with VAL1082 (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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1015B MET* 4.0 26.7 - - + -
1056B ILE* 4.1 13.7 - - + -
1066B TYR* 3.5 47.6 - - + +
1078B LEU* 3.0 21.0 + - + +
1079B THR 3.8 4.7 - - - +
1081B PHE* 1.3 76.4 - - - +
1083B LEU* 1.3 56.9 + - - +
1085B VAL 3.3 0.3 + - - -
1086B LEU* 2.8 52.9 + - + +
1100B LEU* 5.6 1.8 - - + -
1103B THR* 5.7 0.7 - - + -
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Residues in contact with LEU1083 (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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1079B THR 3.2 10.7 + - - +
1080B ALA 3.2 8.1 + - - +
1082B VAL* 1.3 79.3 - - - +
1084B LYS* 1.3 62.5 + - - +
1086B LEU* 5.1 1.1 - - - -
1087B SER* 3.1 27.8 + - - +
1100B LEU* 4.0 38.6 - - + +
1103B THR* 4.3 10.3 - - + +
1104B SER* 3.8 22.4 - - - +
1107B LEU* 3.8 22.2 - - + -
1148B ALA 3.8 19.9 - - - +
1149B LEU* 4.0 9.6 - - + -
1152B GLY* 4.2 16.8 - - - -
1155B VAL* 5.3 0.7 - - + -
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Residues in contact with LYS1084 (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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1019B ALA* 5.1 7.5 - - - +
1080B ALA 2.9 16.3 + - - +
1081B PHE* 3.7 22.6 - - + +
1082B VAL 3.3 0.4 - - - -
1083B LEU* 1.3 77.1 - - - +
1085B VAL* 1.3 71.7 + - + +
1087B SER* 3.3 11.1 + - - -
1088B LEU* 4.2 8.8 - - - +
1144B PHE* 5.6 7.2 - - + -
1147B ILE* 4.5 9.6 - - + +
1148B ALA* 3.9 15.7 - - + +
1151B HIS* 3.8 50.0 - - + +
1198B TYR* 6.3 0.9 - - - -
1306B VAL* 5.2 3.0 + - - +
1307B ILE* 5.6 7.7 - - - +
1310B ASP* 3.2 27.5 + - - +
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Residues in contact with VAL1085 (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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1015B MET* 3.7 15.7 - - + -
1018B LEU* 3.5 35.4 - - + -
1019B ALA* 3.8 17.9 - - + +
1022B LEU* 3.7 17.3 - - + +
1081B PHE* 3.3 42.2 + - + +
1082B VAL 4.2 0.9 - - - +
1084B LYS* 1.3 86.2 - - + +
1086B LEU* 1.3 65.2 + - + +
1087B SER 3.1 2.5 - - - -
1088B LEU* 3.2 14.3 + - - +
1089B ALA* 3.4 7.6 + - - +
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Residues in contact with LEU1086 (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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1015B MET* 5.8 0.4 - - - -
1018B LEU* 3.9 29.2 - - + -
1053B TYR* 4.2 29.8 - - + -
1056B ILE* 4.0 18.2 - - + -
1057B GLN* 4.5 3.8 - - - +
1066B TYR* 4.3 9.4 - - - +
1082B VAL* 2.8 43.0 + - + +
1085B VAL* 1.3 72.7 - - + +
1087B SER* 1.3 63.5 + - - +
1088B LEU 3.2 0.2 - - - -
1089B ALA* 3.8 15.3 - - + +
1090B GLN* 3.1 28.8 + - + +
1100B LEU* 3.6 20.2 - - + +
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Residues in contact with SER1087 (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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1083B LEU* 3.1 21.9 + - - -
1084B LYS 3.3 11.8 + - - -
1086B LEU* 1.3 78.7 - - - +
1088B LEU* 1.3 63.2 + - - +
1090B GLN* 3.1 26.0 + - - -
1100B LEU* 3.9 12.0 - - - +
1151B HIS* 3.3 30.7 + - - +
1152B GLY* 4.3 1.6 - - - -
1154B ALA* 5.5 5.6 - - - +
1155B VAL* 3.7 17.7 - - - +
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Residues in contact with LEU1088 (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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1022B LEU* 3.6 29.2 - - + -
1026B ARG* 4.9 21.1 - - - +
1084B LYS* 4.2 13.0 - - - +
1085B VAL* 3.2 4.3 + - - +
1087B SER* 1.3 88.7 - - - +
1089B ALA* 1.3 59.5 + - - +
1090B GLN* 3.5 2.1 + - - -
1091B GLU* 4.4 8.1 + - - +
1092B GLN* 4.0 10.7 + - - +
1151B HIS* 4.5 21.3 - - + +
1154B ALA* 5.8 6.3 - - + -
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Residues in contact with ALA1089 (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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1018B LEU* 4.7 2.5 - - + -
1022B LEU* 4.1 11.2 - - + -
1049B ILE* 3.6 25.8 - - + -
1085B VAL 3.4 11.3 + - - +
1086B LEU* 3.4 19.3 + - + +
1088B LEU* 1.3 75.5 - - - +
1090B GLN* 1.3 64.5 + - - +
1091B GLU 3.2 4.1 + - - -
1092B GLN* 3.3 19.5 + - - +
1093B VAL* 3.2 17.9 + - + +
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Residues in contact with GLN1090 (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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1053B TYR* 5.9 2.2 - - + -
1086B LEU* 3.1 20.9 + - + +
1087B SER 3.1 18.8 + - - +
1088B LEU 3.5 1.0 + - - -
1089B ALA* 1.3 77.7 - - - +
1091B GLU* 1.3 96.5 + - - +
1093B VAL* 3.7 8.7 - - - -
1094B GLY* 3.4 2.8 + - - -
1095B GLY* 3.0 40.4 + - - +
1096B SER 5.0 2.0 - - - +
1097B PRO* 4.5 15.5 - - + +
1100B LEU* 3.7 19.5 - - + -
1154B ALA 5.6 1.6 + - - -
1155B VAL* 5.0 15.2 - - + +
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Residues in contact with GLU1091 (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 LEU 4.4 7.2 + - - +
1089B ALA 3.2 1.4 + - - -
1090B GLN* 1.3 105.2 + - - +
1092B GLN* 1.3 62.5 + - + +
1093B VAL 3.7 0.2 + - - -
1094B GLY* 3.9 5.5 + - - -
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Residues in contact with GLN1092 (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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1022B LEU* 4.9 6.9 - - - +
1025B SER* 5.6 3.6 + - - -
1046B VAL* 4.3 23.8 - - + +
1049B ILE* 3.4 30.1 - - + +
1050B GLN* 5.3 2.4 + - - +
1088B LEU 4.0 15.1 + - - +
1089B ALA* 3.4 17.7 - - - +
1091B GLU* 1.3 76.3 - - + +
1093B VAL* 1.3 64.9 + - + +
1094B GLY 3.5 0.6 + - - -
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Residues in contact with VAL1093 (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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187A ARG* 4.9 0.5 - - - -
188A LYS 4.1 9.1 + - - +
1046B VAL 5.5 0.7 - - - +
1049B ILE* 3.6 31.4 - - + +
1050B GLN* 3.6 42.7 + - + +
1053B TYR* 3.8 39.8 - - + -
1089B ALA* 3.2 22.2 - - + +
1090B GLN* 3.7 7.4 - - - -
1092B GLN* 1.3 80.3 - - + +
1094B GLY* 1.3 61.1 + - - +
1095B GLY 3.6 12.3 - - - +
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Residues in contact with GLY1094 (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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185A ARG* 2.9 27.0 + - - -
187A ARG 5.2 0.2 - - - -
188A LYS* 3.4 35.0 + - - +
1053B TYR* 4.5 2.0 + - - -
1090B GLN 3.4 3.9 + - - -
1091B GLU 3.9 4.8 + - - -
1092B GLN 3.5 3.0 - - - -
1093B VAL* 1.3 80.1 - - - +
1095B GLY* 1.3 62.1 + - - +
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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