Contacts of the strand formed by residues 1073 - 1080 (chain A) in PDB entry 3BG5
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 ASN1073 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1067A GLU 4.2 1.0 - - - +
1068A PRO* 3.5 0.2 - - - +
1069A ASP* 2.7 43.0 + - - +
1071A ASN* 4.3 14.8 + - - +
1072A GLY* 1.3 77.7 - - - +
1074A ARG* 1.3 64.4 + - - +
1075A THR* 4.1 1.9 + - - -
1088A TYR* 5.0 14.7 - - + +
1089A ILE 3.4 10.8 - - - +
1090A LYS* 3.4 32.6 - - - +
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Residues in contact with ARG1074 (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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509A ILE* 3.6 30.9 - - + +
1065A ILE* 3.7 16.4 + - + +
1066A SER* 3.1 25.7 + - - +
1067A GLU* 3.2 28.4 + - - -
1068A PRO* 3.4 27.8 - - + +
1073A ASN* 1.3 75.2 - - - +
1075A THR* 1.3 61.9 + - - +
1076A ILE* 3.9 1.5 + - - +
1087A ILE 3.6 0.5 - - - +
1088A TYR* 3.5 5.9 - - - +
1089A ILE* 3.0 29.4 + - - +
1091A ASP* 2.4 45.8 + - + -
1093A ASN* 4.1 3.8 + - - -
1098A ALA* 5.5 2.0 - - - +
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Residues in contact with THR1075 (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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1065A ILE* 3.5 1.4 - - - -
1066A SER* 2.6 46.2 + - - -
1073A ASN 4.1 1.8 + - - -
1074A ARG* 1.3 72.7 - - - +
1076A ILE* 1.3 66.7 + - - +
1077A TYR* 3.8 28.6 - - + +
1086A ARG* 4.4 11.7 - - + -
1087A ILE 3.4 5.8 - - - +
1088A TYR* 3.1 36.6 - - + +
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Residues in contact with ILE1076 (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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505A GLY* 3.5 33.7 - - - +
508A THR* 5.4 0.7 - - - -
509A ILE* 3.9 24.0 - - + -
1062A LEU* 3.8 20.9 - - + -
1064A THR 3.4 10.1 - - - +
1065A ILE* 3.9 16.8 - - + -
1074A ARG 4.7 2.7 - - - +
1075A THR* 1.3 74.6 - - - +
1077A TYR* 1.3 66.2 + - - +
1078A TYR* 3.6 30.9 + - + +
1086A ARG* 3.5 5.7 - - - +
1087A ILE* 2.8 40.7 + - + +
1089A ILE* 4.6 7.9 - - + -
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Residues in contact with TYR1077 (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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1062A LEU* 3.8 1.4 - - - -
1063A GLU* 2.8 46.0 + - + +
1064A THR* 2.8 30.9 + - - +
1066A SER* 4.6 10.2 - - - -
1075A THR* 3.8 32.5 - - + +
1076A ILE* 1.3 73.7 - - - +
1078A TYR* 1.3 61.8 + - - +
1085A ARG 3.7 4.5 - - - +
1086A ARG* 3.4 44.4 + - + -
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Residues in contact with TYR1078 (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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501A LEU* 2.9 51.6 + - + -
504A ILE* 3.5 6.9 - - - +
505A GLY* 3.0 20.6 + - - -
1042A MET* 3.3 24.7 - - + -
1060A ILE* 3.6 11.4 - - + -
1061A LYS 3.3 15.7 - - - -
1062A LEU* 3.8 14.5 - - + +
1063A GLU* 4.5 6.8 - - - +
1076A ILE* 3.6 22.2 + - + +
1077A TYR* 1.3 74.9 - - - +
1079A ALA* 1.3 59.4 + - - +
1080A MET 4.0 0.2 - - - -
1084A ALA* 3.6 3.5 - - - +
1085A ARG* 2.7 48.2 + - + +
1087A ILE* 3.6 29.2 - - + -
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Residues in contact with ALA1079 (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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1059A ILE 3.6 1.0 - - - +
1060A ILE* 3.4 5.9 - - - +
1061A LYS* 2.8 54.6 + - + +
1063A GLU* 4.0 17.3 + - - +
1078A TYR* 1.3 72.8 - - - +
1080A MET* 1.3 62.1 + - - +
1081A ASN 3.8 0.6 + - - -
1082A GLY 5.5 3.1 - - - +
1083A GLN 3.4 12.8 - - - +
1084A ALA* 5.3 1.3 - - - -
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Residues in contact with MET1080 (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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398A ARG* 5.6 3.1 - - - +
495A ASP* 5.1 0.9 - - - +
497A GLY* 3.6 31.4 - - - +
501A LEU* 3.4 39.7 - - + -
1058A LEU* 3.8 26.5 - - + -
1059A ILE 3.7 1.3 - - - -
1060A ILE* 4.3 11.0 - - + -
1078A TYR 4.0 0.8 - - - -
1079A ALA* 1.3 69.9 - - - +
1081A ASN* 1.3 80.5 + - - +
1082A GLY 3.5 0.4 - - - -
1083A GLN* 2.8 28.9 + - + +
1085A ARG* 4.0 30.1 - - + +
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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