Contacts of the strand formed by residues 1117 - 1134 (chain B) in PDB entry 2QOM
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 ALA1117 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1033B ARG* 3.9 1.6 + - - -
1113B PHE* 2.8 42.6 + - + +
1115B SER* 3.5 14.2 + - - +
1116B GLY* 1.3 79.8 - - - +
1118B TYR* 1.3 58.9 + - - +
1119B ILE* 6.4 0.2 - - + -
1156B GLY 3.4 10.8 - - - +
1157B TYR* 3.4 22.8 - - + -
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Residues in contact with TYR1118 (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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1025B LEU* 3.7 23.6 - - + -
1033B ARG* 3.7 20.4 - - - +
1111B ALA 3.2 13.9 - - - +
1112B MET* 3.9 16.2 - - + -
1113B PHE* 4.1 1.6 - - - -
1117B ALA* 1.3 76.0 - - - +
1119B ILE* 1.3 72.2 + - - +
1154B GLU* 2.6 43.3 + - + +
1155B ALA* 3.3 4.0 - - - +
1156B GLY* 3.0 62.0 + - - +
1157B TYR 4.4 0.2 - - - -
1168B GLU* 3.7 24.3 + - - -
1170B GLN* 3.3 24.3 - - - +
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Residues in contact with ILE1119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1025B LEU* 5.3 0.5 - - - +
1109B ALA 4.1 0.7 - - - +
1110B SER* 3.7 0.3 - - - -
1111B ALA* 2.8 39.9 + - + +
1113B PHE* 4.0 24.3 - - + -
1117B ALA* 6.4 0.2 - - + -
1118B TYR* 1.3 80.6 - - - +
1120B ASP* 1.3 62.2 + - - +
1121B LEU* 4.2 25.8 - - + -
1153B ALA* 5.9 0.4 - - + -
1154B GLU 3.2 10.5 - - - +
1155B ALA* 4.6 10.3 - - + -
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Residues in contact with ASP1120 (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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1024B ASN 4.7 4.2 + - - -
1025B LEU* 3.9 34.2 + - + +
1028B ARG* 2.8 27.6 + - - -
1108B TYR* 4.9 0.2 - - - +
1109B ALA 3.6 3.6 - - - +
1110B SER* 2.7 24.0 + - - +
1118B TYR* 4.5 0.9 - - + -
1119B ILE* 1.3 74.7 - - - +
1121B LEU* 1.3 69.5 + - - +
1122B ILE* 4.3 4.9 + - - +
1152B GLY 3.9 0.9 - - - +
1153B ALA* 3.4 4.0 + - - -
1154B GLU* 2.7 48.9 + - + +
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Residues in contact with LEU1121 (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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1108B TYR* 3.3 3.5 - - - +
1109B ALA* 2.7 52.9 + - + +
1119B ILE* 4.2 18.2 - - + -
1120B ASP* 1.3 77.7 + - - +
1122B ILE* 1.3 60.0 + - - +
1152B GLY 3.5 4.3 - - - +
1153B ALA* 3.6 29.8 - - + -
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Residues in contact with ILE1122 (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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1028B ARG* 3.6 37.0 - - - +
1064B GLN* 5.3 1.1 - - - +
1083B THR* 4.9 10.5 - - + -
1107B LEU 3.5 12.8 - - - +
1108B TYR* 4.0 9.4 - - + -
1120B ASP* 4.3 5.8 - - - +
1121B LEU* 1.3 74.3 - - - +
1123B GLY* 1.3 66.7 + - - +
1124B LYS* 4.2 27.4 - - + -
1150B TYR 4.1 0.6 - - - +
1151B ALA* 3.5 2.3 - - - +
1152B GLY* 2.7 50.9 + - - +
1172B GLU* 6.1 0.9 - - - +
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Residues in contact with GLY1123 (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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1106B GLY* 3.2 1.4 - - - -
1107B LEU* 2.8 39.6 + - - +
1122B ILE* 1.3 73.0 - - - +
1124B LYS* 1.3 59.6 + - - -
1149B TRP* 6.3 0.9 - - - -
1150B TYR 3.3 9.0 - - - -
1151B ALA* 4.4 4.0 - - - -
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Residues in contact with LYS1124 (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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1044B ARG* 6.4 0.4 - - - +
1064B GLN* 6.0 1.8 - - - +
1083B THR* 5.6 1.8 - - + -
1085B THR* 5.6 11.4 - - + -
1105B ALA 3.2 14.6 - - - +
1106B GLY* 3.7 5.8 - - - -
1122B ILE* 4.2 27.6 - - + -
1123B GLY* 1.3 74.2 - - - +
1125B TYR* 1.3 61.0 + - - +
1126B VAL* 3.9 23.7 - - + +
1148B SER 4.2 0.2 - - - +
1149B TRP* 3.7 9.9 - - - -
1150B TYR* 2.9 63.3 + - + +
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Residues in contact with TYR1125 (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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1103B VAL 5.3 1.3 - - - -
1104B GLY* 3.1 4.6 - - - -
1105B ALA* 2.7 40.8 + - + +
1124B LYS* 1.3 73.6 - - - +
1126B VAL* 1.3 65.9 + - - +
1127B HIS* 4.1 26.1 + - + -
1147B HIS* 3.5 40.3 - + + +
1148B SER 3.5 13.2 - - - -
1149B TRP* 3.6 48.5 - + + -
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Residues in contact with VAL1126 (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* 5.0 5.2 - - - +
1087B THR* 5.9 1.1 - - - +
1102B SER* 4.3 6.3 - - - -
1103B VAL 3.7 9.4 - - - +
1104B GLY* 4.6 6.1 - - - -
1124B LYS* 3.9 30.1 - - + +
1125B TYR* 1.3 82.5 - - - +
1127B HIS* 1.3 63.2 + - - +
1128B HIS* 3.2 35.2 - - + +
1147B HIS* 3.2 7.3 - - - +
1148B SER* 2.9 47.2 + - - +
1150B TYR* 5.3 2.2 - - + -
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Residues in contact with HIS1127 (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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1102B SER* 3.2 3.8 - - - -
1103B VAL* 2.9 45.6 + - + +
1125B TYR* 4.1 25.1 + - + -
1126B VAL* 1.3 73.7 - - - +
1128B HIS* 1.3 61.7 + - - +
1129B ASP* 2.9 34.5 + - - -
1145B SER* 4.1 20.9 - - - -
1146B THR 3.8 7.3 + - - -
1147B HIS* 4.4 3.3 - - - +
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Residues in contact with HIS1128 (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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1087B THR* 6.0 1.3 - - + -
1100B THR* 3.8 3.7 - - + +
1101B LYS 4.0 2.5 - - - -
1102B SER* 2.9 25.0 + - - -
1126B VAL* 3.2 27.6 - - + +
1127B HIS* 1.3 72.4 + - - +
1129B ASP* 1.3 60.8 + - - +
1130B ASN* 3.5 11.4 + - - +
1145B SER* 3.3 5.4 - - - -
1146B THR* 2.7 68.5 + - + +
1147B HIS* 4.8 2.9 - - - -
1148B SER* 4.2 4.0 + - - -
1245B SER* 3.6 21.7 + - - -
1247B GLU* 2.7 37.8 + - + +
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Residues in contact with ASP1129 (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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1100B THR* 3.2 4.3 - - - +
1101B LYS* 3.0 43.9 + - + +
1127B HIS* 2.9 29.9 + - - -
1128B HIS* 1.3 71.0 - - - +
1130B ASN* 1.3 60.6 + - - +
1144B TYR 3.8 3.3 - - - +
1145B SER* 3.3 20.3 - - - -
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Residues in contact with ASN1130 (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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1099B LYS 3.7 2.9 - - - -
1100B THR* 2.6 35.0 + - - +
1128B HIS* 3.5 11.6 + - - +
1129B ASP* 1.3 73.1 - - - +
1131B GLU* 1.3 63.0 + - - +
1143B ASP* 3.5 6.2 - - - +
1144B TYR* 3.0 63.3 + - + +
1146B THR* 2.8 40.8 - - - +
1243B ASP* 4.2 7.3 + - - +
1245B SER* 4.0 5.2 - - - -
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Residues in contact with GLU1131 (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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1098B GLY* 3.1 7.1 - - - -
1099B LYS* 2.9 60.6 + - + +
1100B THR* 4.6 0.2 + - - -
1130B ASN* 1.3 75.7 - - - +
1132B TYR* 1.3 64.7 + - - +
1133B THR* 5.4 4.4 + - - +
1141B THR* 3.7 17.1 + - - +
1142B ARG 3.3 4.0 - - - -
1143B ASP* 3.7 16.5 - - - +
1144B TYR* 4.4 1.0 + - - -
1243B ASP* 5.2 4.6 - - - +
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Residues in contact with TYR1132 (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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1095B VAL* 4.1 11.8 + - - +
1096B PHE* 3.3 50.4 - + + +
1097B SER 3.8 2.9 - - - -
1131B GLU* 1.3 76.6 - - - +
1133B THR* 1.3 54.4 + - - +
1134B ALA* 4.1 19.3 - - + -
1141B THR* 2.7 4.6 - - - +
1142B ARG* 2.3 41.8 + - + +
1144B TYR* 3.6 20.9 - - + +
1183B PHE* 3.6 27.7 - + - -
1192B LEU* 5.3 0.8 - - + +
1194B MET* 4.2 12.1 - - + -
1241B LEU* 3.5 21.2 - - + +
1242B ARG 3.5 13.9 + - - -
1243B ASP* 4.0 13.2 - - + -
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Residues in contact with THR1133 (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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1096B PHE* 3.3 0.9 - - - -
1097B SER* 2.8 47.8 + - - -
1098B GLY* 5.0 0.9 - - - -
1131B GLU* 5.4 4.7 + - - +
1132B TYR* 1.3 73.4 + - - +
1134B ALA* 1.3 68.2 + - - +
1135B THR* 3.5 0.7 + - - -
1141B THR* 2.9 32.7 + - - +
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Residues in contact with ALA1134 (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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1095B VAL 3.4 10.3 - - - +
1132B TYR* 4.1 14.8 + - + -
1133B THR* 1.3 76.9 - - - +
1135B THR* 1.3 66.5 + - - +
1136B PHE* 3.1 20.8 + - - +
1137B ALA 4.0 15.6 - - - -
1141B THR 4.3 2.2 + - - -
1192B LEU* 4.3 18.6 - - + -
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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