Contacts of the helix formed by residues 1120 - 1132 (chain A) in PDB entry 1M8W
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1073A SER 3.5 13.2 - - - +
1074A GLN 3.5 16.2 - - - -
1076A LYS* 3.5 54.3 - - + +
1079A SER* 3.7 13.2 - - - +
1118A ASP* 3.0 3.5 + - - +
1119A GLN* 1.3 122.1 + - + +
1121A ALA* 1.3 65.9 + - - +
1122A ASN 3.2 2.2 - - - -
1123A TYR* 3.1 25.4 + - - +
1124A VAL* 3.8 3.1 + - - +
14C G 3.5 50.2 + - - +
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Residues in contact with ALA1121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1073A SER* 3.1 32.7 + - - +
1074A GLN* 4.2 3.1 - - + -
1115A MET* 3.3 35.9 - - + +
1118A ASP* 2.9 15.3 + - + +
1120A TYR* 1.3 72.1 - - - +
1122A ASN* 1.3 58.6 + - - +
1123A TYR 3.0 2.5 - - - -
1124A VAL* 2.8 21.4 + - - +
1125A VAL* 3.0 14.4 + - - +
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Residues in contact with ASN1122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1115A MET 3.1 9.7 + - - -
1116A MET* 3.7 18.2 - - - +
1118A ASP 3.0 23.7 + - - +
1119A GLN 3.3 13.3 + - - -
1121A ALA* 1.3 76.0 - - - +
1123A TYR* 1.3 67.0 + - - +
1125A VAL* 3.5 0.6 + - - -
1126A GLN* 2.9 45.6 + - - +
1156A TYR* 3.6 13.6 - - - +
1159A HIS* 4.3 0.2 - - - +
1160A ILE* 3.5 17.8 - - + +
13C U 2.9 44.2 + - - -
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Residues in contact with TYR1123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1083A GLU* 3.5 22.6 - - - +
1119A GLN 3.5 20.4 - - - -
1120A TYR 3.1 17.0 + - - +
1121A ALA 3.0 0.8 - - - -
1122A ASN* 1.3 85.9 + - - +
1124A VAL* 1.3 60.5 + - - +
1126A GLN* 3.5 9.4 + - - +
1127A LYS* 3.1 22.5 + - - +
13C U 3.1 67.9 - + + +
14C G 3.3 62.0 + + + +
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Residues in contact with VAL1124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1073A SER* 3.5 35.2 - - - +
1079A SER* 3.8 27.1 - - - +
1082A VAL* 3.7 17.7 - - + -
1083A GLU* 3.9 14.6 - - + +
1086A VAL* 4.9 2.7 - - + -
1115A MET* 3.5 13.7 - - + -
1120A TYR 4.4 0.7 - - - +
1121A ALA* 2.8 14.3 + - - +
1123A TYR* 1.3 76.2 - - - +
1125A VAL* 1.3 64.3 + - - +
1127A LYS* 3.2 3.5 + - - +
1128A MET* 2.9 35.2 + - + +
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Residues in contact with VAL1125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1112A LEU* 4.0 20.4 - - + -
1115A MET* 3.7 26.9 - - + -
1116A MET* 4.0 22.7 - - + +
1121A ALA 3.0 12.4 + - - +
1122A ASN 3.8 6.3 - - - +
1124A VAL* 1.3 75.7 - - - +
1126A GLN* 1.3 57.6 + - - +
1128A MET* 3.0 14.3 + - + +
1129A ILE* 2.9 32.2 + - + +
1140A VAL* 5.2 2.0 - - + -
1144A ILE* 4.2 19.1 - - + -
1160A ILE* 4.0 14.8 - - + -
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Residues in contact with GLN1126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1122A ASN* 2.9 38.5 + - - +
1123A TYR* 3.7 11.9 - - - +
1124A VAL 3.2 0.2 - - - -
1125A VAL* 1.3 74.0 - - - +
1127A LYS* 1.3 64.6 + - - +
1129A ILE* 3.1 10.2 + - + +
1130A ASP* 3.0 29.0 + - - +
1159A HIS* 4.2 9.1 + - - +
1160A ILE* 3.7 16.6 - - + +
1163A LYS* 3.7 40.9 + - + +
13C U 3.0 20.6 + - - +
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Residues in contact with LYS1127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1083A GLU* 3.6 43.6 + - + +
1084A LYS* 6.0 2.6 - - - +
1086A VAL* 4.5 8.3 - - + -
1087A THR* 3.4 26.7 + - - +
1123A TYR 3.1 14.3 + - - +
1124A VAL* 3.6 8.1 - - - +
1126A GLN* 1.3 75.8 - - - +
1128A MET* 1.3 63.0 + - - +
1130A ASP* 3.2 15.2 + - + -
1131A VAL* 3.1 32.7 + - + +
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Residues in contact with MET1128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1069A VAL* 4.1 17.7 - - + -
1086A VAL* 4.1 28.9 - - + -
1097A LEU* 3.6 28.0 - - + +
1098A ILE* 3.6 31.8 - - + +
1101A VAL* 3.7 22.7 - - + -
1112A LEU* 4.8 4.7 - - - -
1115A MET* 4.6 3.1 - - + -
1124A VAL* 2.9 25.8 + - + +
1125A VAL* 3.0 15.0 + - + +
1127A LYS* 1.3 74.3 - - - +
1129A ILE* 1.3 61.3 + - + +
1131A VAL* 4.4 0.2 - - - -
1132A ALA* 2.9 35.0 + - - +
1140A VAL* 5.5 5.4 - - + -
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Residues in contact with ILE1129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1125A VAL* 2.9 22.5 + - + +
1126A GLN* 3.1 8.7 + - + +
1128A MET* 1.3 76.8 - - - +
1130A ASP* 1.3 60.9 + - - +
1132A ALA* 3.8 4.9 + - - +
1137A ARG* 2.9 36.0 + - + +
1140A VAL* 4.0 18.2 - - + -
1141A MET* 3.4 35.9 - - + -
1144A ILE* 4.0 21.1 - - + -
1160A ILE* 5.5 1.1 - - + -
1163A LYS* 4.5 13.9 - - + -
1164A LEU* 4.4 10.8 - - + -
1167A TYR* 3.4 26.7 - - + -
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Residues in contact with ASP1130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1126A GLN* 3.0 16.0 + - - +
1127A LYS* 3.2 21.5 + - + +
1129A ILE* 1.3 77.7 - - - +
1131A VAL* 1.3 64.4 + - + +
1132A ALA 4.4 0.2 - - - +
1137A ARG* 3.3 13.5 + - - -
1163A LYS* 2.8 39.0 + - - -
1167A TYR* 3.1 17.0 + - - -
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Residues in contact with VAL1131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1086A VAL* 3.2 35.4 - - + +
1087A THR* 4.2 26.9 - - + +
1094A ARG* 3.4 33.9 + - + +
1098A ILE* 4.8 0.7 - - + -
1127A LYS* 3.1 17.6 + - + +
1128A MET* 4.2 2.0 - - - +
1130A ASP* 1.3 77.6 - - + +
1132A ALA* 1.3 71.0 + - - +
1133A GLU* 3.4 3.6 + - - +
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Residues in contact with ALA1132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1094A ARG* 4.6 1.8 - - - +
1098A ILE* 3.8 20.4 - - + -
1128A MET 2.9 22.4 + - - +
1129A ILE* 3.8 2.9 + - - +
1130A ASP 3.5 0.8 - - - -
1131A VAL* 1.3 80.2 - - - +
1133A GLU* 1.3 64.0 + - - +
1134A PRO* 3.8 1.4 - - - +
1136A GLN* 4.3 6.3 - - + -
1137A ARG* 3.3 46.9 + - + +
1140A VAL* 5.1 3.6 - - + -
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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