Contacts of the helix formed by residues 1117 - 1137 (chain B) in PDB entry 1XTB
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 VAL1117 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1098B LEU* 4.5 1.8 - - + -
1101B ALA* 4.1 21.1 - - + -
1110B ILE* 3.0 32.4 + - + +
1112B VAL* 3.9 29.8 - - + +
1115B LYS* 4.0 2.5 - - + +
1116B ASP* 1.3 75.7 + - - +
1118B MET* 1.3 67.1 + - - +
1119B PRO 3.3 1.6 - - - -
1120B GLU* 2.8 46.2 - - - +
1121B VAL* 3.0 7.4 + - + +
1268B TRP* 3.8 19.3 - - + +
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Residues in contact with MET1118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1101B ALA* 3.3 32.1 - - - +
1102B LEU 5.6 0.2 - - - +
1104B ASN* 3.6 36.3 - - - +
1107B ASN* 3.6 22.2 - - + +
1108B THR 3.8 17.3 - - - +
1109B PRO* 4.6 0.2 - - + -
1110B ILE* 4.2 11.7 - - - +
1116B ASP* 3.7 14.1 - - - +
1117B VAL* 1.3 79.4 - - - +
1119B PRO* 1.3 71.4 - - + +
1121B VAL* 3.0 16.0 + - + +
1122B ASN* 2.8 39.2 + - - +
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Residues in contact with PRO1119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1116B ASP* 3.3 38.1 - - + +
1118B MET* 1.3 89.9 - - + +
1120B GLU* 1.3 57.1 + - - +
1122B ASN* 3.9 5.6 - - + +
1123B LYS* 3.0 28.5 + - - +
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Residues in contact with GLU1120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1116B ASP 5.1 2.0 + - - +
1117B VAL* 2.8 36.0 + - + +
1119B PRO* 1.3 75.8 - - - +
1121B VAL* 1.3 65.9 + - + +
1123B LYS* 3.4 10.1 + - + +
1124B VAL* 3.2 29.1 + - - +
1266B TRP* 3.2 37.5 + - + +
1268B TRP* 3.5 24.4 + - - -
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Residues in contact with VAL1121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1101B ALA 3.8 23.8 - - - +
1102B LEU* 3.9 25.4 - - + +
1117B VAL* 3.0 18.9 + - + +
1118B MET* 3.0 19.4 + - + +
1120B GLU* 1.3 79.4 - - - +
1122B ASN* 1.3 61.3 + - - +
1124B VAL* 3.4 4.3 + - - +
1125B LEU* 3.2 30.0 + - + +
1266B TRP* 3.7 13.0 - - + -
1268B TRP* 3.8 27.6 - - + -
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Residues in contact with ASN1122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1105B ARG* 5.2 2.8 + - - -
1107B ASN* 3.1 36.0 + - - +
1118B MET* 2.8 31.4 + - - +
1119B PRO* 4.1 4.6 - - + +
1121B VAL* 1.3 74.8 - - - +
1123B LYS* 1.3 59.7 + - - +
1125B LEU* 3.2 20.8 + - - +
1126B ASP* 2.9 41.6 + - - +
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Residues in contact with LYS1123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1119B PRO 3.0 19.0 + - - +
1120B GLU* 3.6 9.9 - - + +
1122B ASN* 1.3 76.5 - - - +
1124B VAL* 1.3 60.1 + - + +
1126B ASP* 3.5 8.9 + - - +
1127B LYS* 3.0 27.3 + - + +
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Residues in contact with VAL1124 (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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1120B GLU 3.2 15.4 + - - +
1121B VAL 3.7 6.5 - - - +
1122B ASN 3.2 0.4 - - - -
1123B LYS* 1.3 77.9 - - + +
1125B LEU* 1.3 60.0 + - + +
1127B LYS* 3.2 8.7 + - + +
1128B MET* 2.8 50.0 + - + +
1263B PHE* 4.6 5.6 - - + -
1264B GLU* 3.5 43.1 - - + +
1266B TRP* 3.6 14.6 - - + -
1278B ALA* 4.1 11.7 - - + +
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Residues in contact with LEU1125 (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 LEU 4.3 9.2 - - - +
1105B ARG* 3.9 20.9 - - - +
1121B VAL* 3.2 27.0 + - + +
1122B ASN* 3.2 27.8 + - - +
1124B VAL* 1.3 75.8 - - + +
1126B ASP* 1.3 62.3 + - - +
1128B MET* 3.2 12.6 + - - -
1129B LYS* 2.9 25.8 + - - +
1276B TRP 4.9 6.1 - - - +
1277B SER* 6.0 1.1 - - - -
1289B PHE* 3.2 25.5 - - + -
1292B PHE* 3.9 28.5 - - + -
1296B LEU* 3.9 8.5 - - + -
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Residues in contact with ASP1126 (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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1122B ASN* 2.9 28.3 + - - +
1123B LYS* 3.7 8.5 - - - +
1125B LEU* 1.3 78.7 - - - +
1127B LYS* 1.3 61.2 + - - +
1129B LYS* 3.3 9.0 + - - +
1130B ALA* 2.9 25.3 + - - +
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Residues in contact with LYS1127 (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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1123B LYS* 3.0 16.9 + - + +
1124B VAL* 3.5 13.2 - - + +
1126B ASP* 1.3 76.4 - - - +
1128B MET* 1.3 62.1 + - - +
1130B ALA* 3.4 6.2 + - - +
1131B PHE* 3.0 23.8 + - + +
1260B GLN* 2.6 46.4 + - - +
1262B MET 3.6 23.8 - - - +
1263B PHE* 3.8 24.2 - - + -
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Residues in contact with MET1128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1124B VAL* 2.8 29.3 + - + +
1125B LEU* 3.3 24.2 - - - +
1127B LYS* 1.3 73.7 - - - +
1129B LYS* 1.3 61.1 + - - +
1131B PHE* 3.4 2.9 + - - +
1132B CYS* 2.9 33.7 + - - -
1263B PHE* 3.8 24.5 - - + -
1277B SER 3.6 18.8 - - - +
1278B ALA* 3.7 21.1 - - - +
1280B GLY 4.1 0.7 - - - +
1281B LEU* 3.7 35.0 - - + +
1284B ALA* 5.0 1.1 - - + -
1289B PHE* 3.6 9.6 - - + -
1292B PHE* 4.1 19.1 - - + -
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Residues in contact with LYS1129 (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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1125B LEU 2.9 16.6 + - - +
1126B ASP* 3.7 8.7 - - - +
1128B MET* 1.3 77.2 - - - +
1130B ALA* 1.3 59.5 + - - +
1132B CYS* 3.1 2.9 + - - +
1133B GLN* 2.8 53.8 + - + +
1289B PHE* 3.4 45.0 - - + -
1290B ASP* 4.5 13.3 + - - -
1293B GLU* 5.0 9.7 + - - +
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Residues in contact with ALA1130 (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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1126B ASP 2.9 16.6 + - - +
1127B LYS* 3.7 7.4 - - - +
1128B MET 3.3 0.2 - - - -
1129B LYS* 1.3 77.7 - - - +
1131B PHE* 1.3 61.8 + - - +
1133B GLN* 3.3 19.3 + - - +
1134B ARG* 3.3 27.8 + - - +
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Residues in contact with PHE1131 (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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1127B LYS* 3.0 17.2 + - + +
1128B MET 3.7 2.2 - - - +
1130B ALA* 1.3 76.2 - - - +
1132B CYS* 1.3 66.2 + - - +
1134B ARG* 3.2 11.9 + - - +
1135B VAL* 3.1 41.9 + - + +
1140B TRP* 3.5 44.4 - + - -
1204B LEU* 4.5 13.7 - - + -
1243B VAL* 3.8 25.1 - - + -
1263B PHE* 3.5 26.7 - + + -
1281B LEU* 4.0 27.4 - - + -
1285B LEU* 4.5 11.2 - - + -
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Residues in contact with CYS1132 (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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1128B MET 2.9 25.9 + - - +
1129B LYS* 3.4 6.7 - - - +
1131B PHE* 1.3 76.9 - - - +
1133B GLN* 1.3 54.1 + - + +
1135B VAL* 3.2 1.2 + - - +
1136B ARG* 2.8 48.9 + - + +
1281B LEU* 3.8 16.4 - - - -
1284B ALA* 3.5 32.5 - - - +
1285B LEU* 3.9 22.9 - - + -
1289B PHE* 4.3 10.1 - - + +
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Residues in contact with GLN1133 (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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1129B LYS* 2.8 42.0 + - + +
1130B ALA* 3.3 27.6 + - - +
1131B PHE 3.3 0.2 - - - -
1132B CYS* 1.3 75.5 - - + +
1134B ARG* 1.3 58.2 + - + +
1136B ARG* 4.6 4.7 - - - +
1137B SER* 2.8 37.6 + - - -
1289B PHE* 6.3 0.2 - - + -
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Residues in contact with ARG1134 (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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1130B ALA* 3.3 16.1 + - - +
1131B PHE* 3.2 14.2 + - - +
1133B GLN* 1.3 80.4 - - + +
1135B VAL* 1.3 60.4 + - - +
1137B SER* 3.3 0.4 + - - -
1138B GLY 3.2 1.6 + - - -
1139B ASP* 2.7 61.2 + - + +
1140B TRP* 2.9 50.0 + - + +
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Residues in contact with VAL1135 (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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1131B PHE* 3.1 51.2 + - + +
1132B CYS 3.8 2.5 - - - +
1134B ARG* 1.3 74.4 - - - +
1136B ARG* 1.3 64.4 + - - +
1138B GLY* 3.3 12.6 + - - -
1140B TRP* 3.8 20.3 - - + +
1148B ILE* 3.8 41.9 + - + +
1151B VAL* 4.9 3.8 - - + -
1178B PRO* 4.6 10.4 - - + +
1204B LEU* 5.3 3.4 - - + -
1285B LEU* 3.8 16.6 - - + -
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Residues in contact with ARG1136 (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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1132B CYS* 2.8 36.3 + - - +
1133B GLN* 4.0 3.8 - - - +
1135B VAL* 1.3 75.2 - - - +
1137B SER* 1.3 60.6 + - - +
1138B GLY* 3.1 1.4 + - - -
1173B TYR 5.6 0.2 + - - -
1175B SER 3.9 9.9 + - - -
1176B GLY 3.6 5.1 - - - +
1177B GLY* 2.6 40.3 - - - +
1178B PRO* 4.8 9.8 - - + +
1284B ALA 4.3 3.1 - - - -
1285B LEU* 2.9 32.3 + - + +
1286B HIS 3.5 11.9 + - - -
1287B VAL* 4.1 2.6 + - - +
1288B GLY* 3.2 32.0 - - - +
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Residues in contact with SER1137 (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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1133B GLN* 2.8 27.0 + - - -
1134B ARG* 3.3 1.7 + - - -
1136B ARG* 1.3 72.7 - - - +
1138B GLY* 1.3 60.0 + - - +
1139B ASP* 3.2 21.1 + - - +
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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
------------------------------------------------------------
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