Contacts of the strand formed by residues 1140 - 1145 (chain B) 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 ARG1140 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A LEU* 3.3 5.5 - - - -
17A GLU* 2.7 61.7 + - + +
19A SER* 4.6 16.2 + - - -
20A ALA 5.4 3.8 + - - -
21A LEU* 4.3 18.3 - - - +
25A ASP* 3.7 21.4 + - - -
249A PRO* 5.5 11.9 + - - +
1098B CYS* 3.7 36.0 + - - +
1099B GLY 3.2 19.8 + - - +
1100B LEU* 4.4 11.7 - - + +
1109B THR* 5.9 0.4 - - - +
1138B ALA* 2.5 24.5 + - + +
1139B PRO* 1.3 70.5 - - - +
1141B LEU* 1.3 60.4 + - - +
1142B ARG 3.8 0.2 - - - -
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Residues in contact with LEU1141 (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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13A ILE* 4.1 20.6 - - + -
15A GLY 4.2 1.8 - - - -
16A LEU* 3.7 31.4 - - + -
17A GLU* 5.6 0.7 - - - -
1417A LEU* 5.3 1.1 - - + -
1094B VAL* 4.2 27.1 - - + -
1095B CYS 4.9 0.2 - - - +
1096B ASP 4.4 5.7 - - - +
1099B GLY* 3.5 27.5 + - - +
1100B LEU* 5.5 1.6 - - - +
1101B MET* 5.4 2.2 - - + -
1119B MET* 5.9 2.2 - - - -
1121B ILE* 5.4 5.4 - - + -
1129B PHE* 3.8 32.8 - - + -
1139B PRO 3.4 8.9 + - - +
1140B ARG* 1.3 70.7 - - - +
1142B ARG* 1.3 66.3 + - - +
1143B LEU* 3.6 19.1 + - + +
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Residues in contact with ARG1142 (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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13A ILE* 4.0 0.9 - - - +
14A LYS* 2.7 80.6 + - - +
15A GLY* 3.7 10.7 + - - +
17A GLU* 3.9 28.9 + - + +
1405A LYS* 2.9 39.5 - - - +
1407A ALA* 5.6 5.7 - - - +
1096B ASP 5.7 1.6 - - - -
1140B ARG 3.7 4.0 + - - -
1141B LEU* 1.3 73.9 - - - +
1143B LEU* 1.3 72.4 + - - +
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Residues in contact with LEU1143 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A LYS* 4.6 19.5 + - + -
12A ARG 3.7 18.4 - - - +
13A ILE* 3.8 17.9 - - + +
14A LYS* 4.8 3.0 - - - -
1094B VAL* 3.7 29.4 - - + -
1095B CYS 5.2 0.2 - - - -
1096B ASP* 3.8 36.4 + - - +
1117B ILE* 4.7 10.3 - - + -
1119B MET* 4.3 12.1 - - - -
1141B LEU* 3.6 15.4 + - + +
1142B ARG* 1.3 91.8 - - - +
1144B GLU* 1.3 62.5 + - - +
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Residues in contact with GLU1144 (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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11A LYS* 3.4 9.4 - - - +
12A ARG* 3.0 52.8 + - + +
14A LYS* 3.2 52.8 + - + +
1143B LEU* 1.3 75.3 - - - +
1145B ASP* 1.3 73.5 + - - +
1149B GLN 5.2 9.5 - - - -
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Residues in contact with ASP1145 (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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9A THR* 3.7 23.4 - - + +
10A PRO 3.2 14.1 - - - +
11A LYS* 3.3 15.5 - - - +
12A ARG* 5.5 0.6 + - - -
1144B GLU* 1.3 88.1 - - - +
1146B ILE* 1.3 66.6 + - - +
1147B PHE 3.6 15.2 - - - +
1148B GLN* 4.5 6.7 - - - +
1149B GLN 3.4 13.9 - - - +
10G LEU* 6.0 0.2 - - - +
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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