Contacts of the strand formed by residues 1182 - 1187 (chain A) in PDB entry 1NDX
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 LYS1182 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1147A LEU* 4.2 0.8 - - - +
1176A LEU* 3.2 7.0 - - - -
1177A ASP* 2.8 38.6 + - + +
1180A ILE* 3.3 38.3 - - + +
1181A SER* 1.3 82.0 + - - +
1183A GLU* 1.3 65.8 + - - +
1184A THR* 3.4 4.2 + - + +
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Residues in contact with GLU1183 (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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1147A LEU* 5.6 0.7 - - + -
1148A GLU* 3.1 37.1 - - + +
1150A LEU* 4.5 11.0 - - - +
1174A VAL* 3.7 18.0 - - + +
1175A ALA 4.1 0.9 - - - -
1176A LEU* 3.4 13.2 - - + -
1182A LYS* 1.3 74.5 - - - +
1184A THR* 1.3 63.5 + - - +
1185A ASP 5.1 2.0 - - - +
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Residues in contact with THR1184 (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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960A GLU* 3.1 23.9 + - - +
1162A ASN* 3.9 2.5 + - - +
1175A ALA 2.9 22.6 + - - -
1177A ASP* 3.6 31.4 - - + +
1182A LYS* 3.8 6.5 - - + +
1183A GLU* 1.3 76.8 - - - +
1185A ASP* 1.3 72.4 + - - +
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Residues in contact with ASP1185 (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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959A LEU* 3.8 23.0 - - + +
960A GLU* 2.8 35.2 - - - +
967A THR* 4.6 6.7 + - + +
1174A VAL* 3.6 7.3 - - - +
1175A ALA* 2.8 30.8 + - + +
1183A GLU* 3.7 2.3 - - - +
1184A THR* 1.3 96.8 + - - +
1186A ALA* 1.3 62.0 + - - +
1187A PHE 4.0 0.2 - - - -
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Residues in contact with ALA1186 (chain A).
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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967A THR* 6.3 0.2 - - - -
1172A SER* 5.4 4.5 - - - -
1173A VAL 3.6 6.1 - - - -
1174A VAL* 4.4 11.4 - - + +
1183A GLU* 6.2 0.4 - - - +
1185A ASP* 1.3 77.3 + - - +
1187A PHE* 1.3 61.7 + - - +
1188A GLN* 3.0 33.8 + - - +
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Residues in contact with PHE1187 (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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946A LEU* 4.2 5.6 - - + -
948A PHE* 3.3 33.9 - + + -
957A LEU* 3.3 58.8 - - + -
959A LEU* 3.4 39.6 - - + +
967A THR* 3.4 43.5 - - + -
1164A TYR* 4.9 0.7 - + - -
1172A SER* 3.0 10.0 - - - -
1173A VAL* 2.9 40.0 + - + +
1185A ASP 4.0 0.6 - - - -
1186A ALA* 1.3 67.0 - - - +
1188A GLN* 1.3 69.7 + - - +
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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