Contacts of the strand formed by residues 1173 - 1178 (chain A) in PDB entry 6CNB
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 VAL1173 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1170A ALA* 4.9 10.5 - - + +
1172A TYR* 1.3 81.7 - - - +
1174A GLN* 1.3 66.7 + - - +
1175A ASP* 5.1 2.0 - - - +
1184A ILE* 5.4 4.5 - - + -
1186A VAL* 3.6 20.4 - - + -
1264A ARG* 4.9 14.8 - - + +
1267A LEU* 5.7 4.7 - - + -
1268A PRO* 4.5 26.5 - - + -
41I TYR* 3.0 52.6 - - + +
42I ASP 4.6 4.5 + - - +
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Residues in contact with GLN1174 (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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1172A TYR* 3.8 28.0 + - + -
1173A VAL* 1.3 79.7 - - - +
1175A ASP* 1.3 74.7 + - - +
1176A VAL* 4.1 22.4 - - + +
1184A ILE* 4.7 0.2 - - - +
1185A GLN* 2.4 79.9 + - + +
1186A VAL* 4.6 0.2 - - - -
1187A ARG* 5.1 7.4 - - - +
39I GLU 5.2 2.4 + - - +
40I ILE* 6.1 0.7 - - - -
41I TYR* 3.3 11.2 - - + +
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Residues in contact with ASP1175 (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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1173A VAL* 5.1 0.6 - - - +
1174A GLN* 1.3 87.1 - - - +
1176A VAL* 1.3 69.4 + - - +
1177A TYR* 5.7 4.0 - - + +
1183A PHE 2.9 19.0 - - - +
1184A ILE* 3.0 27.3 - - - +
1185A GLN* 5.8 0.2 - - - -
1260A MET* 4.4 10.8 - - + +
1264A ARG* 3.9 21.0 - - - +
39I GLU* 3.0 34.9 - - - +
41I TYR* 2.9 33.1 + - + +
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Residues in contact with VAL1176 (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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1174A GLN* 4.1 24.0 - - + +
1175A ASP* 1.3 81.4 - - - +
1177A TYR* 1.3 82.3 + - - +
1178A LYS* 4.2 15.5 - - + -
1181A LEU 4.0 0.2 - - - +
1183A PHE* 3.5 36.3 + - + +
1185A GLN* 5.7 2.2 - - - +
37I GLY 3.8 19.7 - - - +
38I ILE* 5.4 0.2 - - - -
39I GLU* 3.1 29.2 - - + +
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Residues in contact with TYR1177 (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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1175A ASP* 5.7 3.4 - - + +
1176A VAL* 1.3 88.7 - - - +
1178A LYS* 1.3 71.9 + - - +
1179A ASP 4.0 8.6 + - - +
1181A LEU 3.4 16.2 - - - +
1182A SER* 4.1 7.4 - - - -
1183A PHE 4.6 2.9 - - - -
1256A VAL* 5.2 3.1 - - + +
1257A PHE* 5.3 0.3 - - - -
1260A MET* 3.1 52.9 - - + +
1I MET* 5.5 3.2 + - + -
14I ILE* 3.3 53.8 - - + +
22I TYR* 5.3 7.2 - + + -
23I THR 6.0 0.4 - - - -
35I ILE* 6.6 0.2 - - + -
37I GLY* 3.8 21.0 + - - +
39I GLU* 3.9 20.5 + - - +
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Residues in contact with LYS1178 (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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1176A VAL* 4.2 20.6 - - + -
1177A TYR* 1.3 77.5 - - - +
1179A ASP* 1.3 64.1 + - - +
1180A ASN 3.0 1.2 + - - -
1181A LEU* 2.6 61.2 + - + +
1183A PHE* 4.9 9.3 - - + -
36I GLU* 5.7 8.5 - - - +
37I GLY 4.5 9.9 - - - +
38I ILE* 6.5 0.7 - - - -
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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