Contacts of the helix formed by residues 1120 - 1132 (chain B) in PDB entry 1M8X
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 TYR1120 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1073B SER 3.4 12.0 - - - +
1074B GLN 3.4 21.3 - - - -
1075B HIS 4.1 0.7 - - - +
1076B LYS* 3.8 45.2 + - + +
1079B SER* 3.8 13.7 - - - +
1118B ASP* 2.7 12.2 + - - +
1119B GLN* 1.3 126.3 + - + +
1121B ALA* 1.3 64.4 + - - +
1122B ASN 3.2 2.0 - - - -
1123B TYR* 3.1 24.4 + - - +
1124B VAL 3.8 1.9 + - - -
14D G 3.1 51.6 + - - +
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Residues in contact with ALA1121 (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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1073B SER* 3.0 25.8 + - - +
1074B GLN* 4.4 2.9 - - + +
1115B MET* 3.3 41.5 - - + +
1118B ASP* 2.6 21.4 + - + +
1120B TYR* 1.3 70.6 - - - +
1122B ASN* 1.3 55.9 + - - +
1124B VAL* 2.6 27.2 + - - +
1125B VAL* 2.9 11.8 + - - +
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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
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1115B MET 3.0 14.5 + - - +
1116B MET 3.9 6.3 - - - +
1118B ASP 2.8 24.4 + - - +
1119B GLN 3.2 12.7 + - - -
1121B ALA* 1.3 73.8 - - - +
1123B TYR* 1.3 77.4 + - - +
1125B VAL* 3.3 4.4 + - - +
1126B GLN* 2.8 49.5 + - - +
1156B TYR* 3.5 11.2 - - - +
1160B ILE* 3.6 22.9 - - + +
13D U 3.0 32.1 + - - -
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Residues in contact with TYR1123 (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 GLU* 3.1 22.7 - - - +
1119B GLN 3.4 12.3 - - - -
1120B TYR 3.1 14.7 + - - +
1121B ALA 3.0 0.8 - - - -
1122B ASN* 1.3 107.5 + - - +
1124B VAL* 1.3 65.4 + - - +
1126B GLN* 3.2 14.0 + - - +
1127B LYS* 3.1 26.0 + - - +
1159B HIS* 5.8 0.7 - - - -
13D U 2.9 52.6 + + - +
14D G 3.3 56.2 + + - +
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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
----------------------------------------------------------
1073B SER* 3.6 26.5 - - - +
1079B SER* 3.7 24.0 - - - +
1082B VAL* 3.7 21.3 - - + -
1083B GLU* 4.1 10.8 - - + -
1086B VAL* 4.6 3.8 - - + -
1115B MET* 3.5 20.4 - - + -
1120B TYR 4.5 3.8 - - - +
1121B ALA* 2.6 18.7 + - - +
1123B TYR* 1.3 69.9 - - - +
1125B VAL* 1.3 65.5 + - - +
1127B LYS* 3.1 5.9 + - - +
1128B MET* 3.0 39.6 + - + +
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Residues in contact with VAL1125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1112B LEU* 3.9 25.8 - - + -
1115B MET* 3.5 43.1 - - + -
1116B MET* 4.0 4.3 - - + +
1121B ALA 2.9 11.4 + - - +
1122B ASN* 3.5 7.6 - - - +
1124B VAL* 1.3 77.2 - - - +
1126B GLN* 1.3 62.1 + - - +
1128B MET* 3.1 19.0 + - + +
1129B ILE* 3.1 28.9 + - + +
1140B VAL* 5.2 2.2 - - + -
1144B ILE* 4.6 10.5 - - + -
1160B ILE* 4.0 15.0 - - + -
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Residues in contact with GLN1126 (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* 2.8 43.0 + - - +
1123B TYR* 3.4 19.9 - - - +
1124B VAL 3.2 0.2 - - - -
1125B VAL* 1.3 76.8 - - - +
1127B LYS* 1.3 62.5 + - + +
1129B ILE* 3.3 11.7 + - + +
1130B ASP* 3.2 27.1 + - - +
1156B TYR 5.0 0.2 + - - -
1159B HIS* 3.6 27.4 + - + +
1160B ILE* 4.0 16.8 - - + +
1163B LYS* 4.3 17.2 - - + +
13D U 3.2 16.1 + - - +
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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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1083B GLU* 2.7 46.0 + - + +
1084B LYS* 5.1 9.5 - - - +
1086B VAL* 3.9 15.9 - - + -
1087B THR* 3.8 19.3 + - - +
1123B TYR 3.1 14.5 + - - +
1124B VAL* 3.1 9.9 + - - +
1126B GLN* 1.3 78.1 - - + +
1128B MET* 1.3 61.9 + - - +
1130B ASP* 3.3 18.4 + - + +
1131B VAL* 3.1 28.1 + - - +
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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
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1069B VAL* 4.4 10.3 - - + -
1086B VAL* 3.8 32.8 - - + -
1097B LEU* 3.3 31.2 - - + +
1098B ILE* 3.6 35.5 - - + +
1101B VAL* 5.1 7.6 - - + -
1112B LEU* 5.3 7.2 - - + -
1115B MET* 4.8 6.7 - - - -
1124B VAL* 3.0 29.5 + - + +
1125B VAL* 3.1 12.8 + - + +
1127B LYS* 1.3 73.6 - - - +
1129B ILE* 1.3 63.9 + - + +
1132B ALA* 2.9 32.4 + - - +
1140B VAL* 5.6 5.2 - - + -
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Residues in contact with ILE1129 (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 VAL* 3.1 25.9 + - + +
1126B GLN* 3.6 9.4 - - + +
1127B LYS 3.2 0.2 - - - -
1128B MET* 1.3 77.8 - - - +
1130B ASP* 1.3 65.6 + - - +
1132B ALA* 3.7 7.1 + - - +
1137B ARG* 3.8 45.2 + - + +
1140B VAL* 4.1 20.0 - - + -
1141B MET* 4.6 17.3 - - + -
1144B ILE* 4.4 15.5 - - + -
1160B ILE* 5.2 6.5 - - + +
1163B LYS* 4.3 37.0 - - + +
1164B LEU* 5.6 1.8 - - + +
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Residues in contact with ASP1130 (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 GLN* 3.2 11.3 + - - +
1127B LYS* 3.4 24.2 - - + +
1129B ILE* 1.3 80.1 - - - +
1131B VAL* 1.3 66.4 + - + +
1132B ALA 3.5 4.0 + - - +
1137B ARG* 5.0 7.4 + - - +
1163B LYS* 2.7 41.5 + - - -
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Residues in contact with VAL1131 (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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1086B VAL* 3.4 28.5 - - + +
1087B THR* 4.0 32.8 - - + +
1094B ARG* 3.1 38.1 + - + +
1098B ILE* 4.3 0.9 - - + -
1127B LYS* 3.1 15.2 + - + +
1128B MET 4.1 3.1 - - - +
1130B ASP* 1.3 77.8 - - + +
1132B ALA* 1.3 66.5 + - - +
1133B GLU* 3.4 4.5 + - - +
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Residues in contact with ALA1132 (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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1094B ARG* 4.4 2.2 - - - +
1098B ILE* 3.8 20.2 - - + -
1128B MET 2.9 22.7 + - - +
1129B ILE* 4.0 4.9 - - - +
1130B ASP 3.3 7.4 - - - +
1131B VAL* 1.3 78.3 - - - +
1133B GLU* 1.3 63.4 + - - +
1134B PRO* 4.6 0.3 - - - +
1136B GLN* 4.4 7.0 - - + -
1137B ARG* 3.8 37.7 + - + +
1140B VAL* 5.0 1.1 - - + -
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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