Contacts of the strand formed by residues 1120 - 1127 (chain A) in PDB entry 6BM0
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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1028A HIS* 4.3 2.0 - - - -
1105A THR* 3.4 9.9 - - - +
1106A VAL* 2.7 34.8 + - + +
1108A LEU* 3.7 24.0 - - + -
1110A SER* 4.8 4.6 + - - -
1112A GLU* 5.5 0.5 + - - -
1118A LYS* 3.3 38.5 - - + +
1119A GLY* 1.3 80.4 - - - +
1121A VAL* 1.3 64.3 + - - +
1122A ALA* 5.1 0.7 - - + +
1141A ILE* 3.7 24.2 - - + -
1142A MET 3.6 6.5 - - - +
1143A ASP* 3.2 37.7 - - + -
1163A LEU* 3.6 21.7 - - + +
1195A LEU* 3.6 28.5 - - + +
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Residues in contact with VAL1121 (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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1026A ALA* 4.8 5.6 - - + -
1028A HIS* 3.6 31.9 - - + -
1035A ALA* 4.2 16.4 - - + -
1103A MET* 3.7 30.1 - - + -
1104A LYS 3.8 7.9 - - - +
1105A THR* 4.7 9.2 - - - +
1120A TYR* 1.3 75.6 - - - +
1122A ALA* 1.3 60.3 + - - +
1140A LEU 3.8 1.0 - - - +
1141A ILE 3.6 0.3 - - - -
1142A MET* 2.6 62.9 + - + +
1144A VAL* 5.3 5.6 - - + -
1160A PHE* 5.5 2.7 - - + -
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Residues in contact with ALA1122 (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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1103A MET* 3.6 2.4 - - - +
1104A LYS* 3.2 30.8 + - - +
1106A VAL* 3.9 24.9 - - + -
1108A LEU* 6.3 0.7 - - + -
1120A TYR* 4.1 1.5 - - + -
1121A VAL* 1.3 77.1 - - - +
1123A ALA* 1.3 60.5 + - - +
1139A ILE* 5.6 0.2 - - + -
1140A LEU 3.3 6.1 - - - +
1141A ILE* 4.2 18.2 - - + +
1175A LEU* 3.7 20.4 - - + +
1182A LEU* 4.2 6.7 - - + -
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Residues in contact with ALA1123 (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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1076A ILE* 4.4 9.9 - - + -
1100A VAL* 4.6 5.8 - - + -
1102A CYS 3.4 5.4 - - - +
1103A MET* 3.7 21.5 - - + -
1121A VAL 4.3 0.2 - - - -
1122A ALA* 1.3 73.9 - - - +
1124A GLY* 1.3 60.5 + - - +
1125A THR* 4.0 2.8 + - + +
1138A ARG 3.9 1.0 - - - +
1139A ILE* 3.8 0.3 - - - -
1140A LEU* 2.7 53.2 + - + +
1142A MET* 4.4 13.5 - - + -
1175A LEU* 3.6 3.6 - - - -
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Residues in contact with GLY1124 (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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1100A VAL* 3.8 1.0 - - - +
1101A THR* 2.9 31.9 + - - -
1102A CYS* 3.1 19.6 + - - +
1123A ALA* 1.3 72.1 - - - +
1125A THR* 1.3 62.6 + - - -
1138A ARG 4.0 2.2 - - - -
1139A ILE* 4.8 1.1 - - - -
1172A VAL* 3.7 23.3 - - - -
1175A LEU* 3.4 8.9 - - - +
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Residues in contact with THR1125 (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 LEU* 3.3 15.3 - - + +
1098A GLU* 3.2 28.0 - - - +
1099A HIS 2.6 28.1 + - - -
1100A VAL* 3.8 9.6 - - + -
1101A THR* 4.2 2.9 - - - +
1123A ALA* 4.3 7.6 - - + +
1124A GLY* 1.3 76.4 - - - -
1126A CYS* 1.3 56.7 + - - +
1137A GLY* 3.3 0.5 - - - -
1138A ARG* 2.7 55.7 + - + +
1140A LEU* 4.9 9.2 - - + -
1172A VAL* 4.1 5.3 + - - +
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Residues in contact with CYS1126 (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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1098A GLU* 4.1 0.7 - - - -
1099A HIS* 2.8 38.3 + - - +
1101A THR* 3.7 15.9 - - - -
1125A THR* 1.3 75.2 + - - +
1127A LEU* 1.3 64.6 + - - +
1128A MET* 4.0 0.8 + - - -
1135A CYS* 3.8 13.5 - - - -
1136A ARG 3.4 16.6 - - - +
1137A GLY* 3.6 7.6 - - - -
1171A PRO* 4.1 12.8 - - + -
1172A VAL 4.1 3.8 - - - +
1173A THR* 6.0 0.2 - - - -
64B ILE* 3.6 32.1 - - - -
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Residues in contact with LEU1127 (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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1055A LYS* 4.9 7.6 - - - +
1095A GLN* 5.4 9.2 - - + -
1097A TRP* 3.6 19.1 - - + +
1098A GLU* 4.0 24.9 - - + +
1126A CYS* 1.3 81.2 - - - +
1128A MET* 1.3 62.3 + - - +
1129A GLN* 3.5 34.2 + - + +
1135A CYS* 3.3 26.0 - - - +
1136A ARG* 3.3 19.6 + - + +
1137A GLY* 5.5 2.7 - - - -
1138A ARG* 6.0 1.1 - - + -
1167A GLU* 6.3 3.8 - - + -
61B PRO* 4.7 0.3 - - - +
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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