Contacts of the strand formed by residues 1180 - 1183 (chain B) in PDB entry 5NPK
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 ALA1180 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1035B LEU* 4.7 2.5 - - - -
1174B GLY 3.3 13.7 - - - +
1175B ILE* 4.1 17.0 - - + -
1176B ALA* 4.1 2.5 - - - +
1179B MET* 1.3 76.2 - - - +
1181B THR* 1.3 62.8 + - - +
1334B ASN* 3.0 25.2 + - - +
1336B ILE* 3.2 16.2 - - - +
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Residues in contact with THR1181 (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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1035B LEU* 3.8 18.2 - - + -
1036B PRO* 3.9 17.0 - - + -
1172B ALA* 4.6 4.5 - - + -
1173B SER* 3.4 7.7 - - - -
1174B GLY* 2.8 48.6 + - - +
1180B ALA* 1.3 78.9 - - - +
1182B ASN* 1.4 63.2 + - - +
1183B ILE* 3.8 8.1 - - - +
1334B ASN* 3.4 4.4 + - - +
1336B ILE* 2.5 37.3 + - - -
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Residues in contact with ASN1182 (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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1172B ALA 3.4 2.6 - - - +
1173B SER* 3.8 19.1 - - - -
1181B THR* 1.4 75.0 + - - +
1183B ILE* 1.3 59.8 + - - +
1267B GLN* 4.9 2.6 + - - +
1331B PHE* 3.4 31.9 - - - +
1332B GLY 2.8 32.0 + - - +
1333B VAL* 3.5 8.0 - - - +
1334B ASN* 2.9 41.8 + - + +
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Residues in contact with ILE1183 (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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1036B PRO* 4.8 0.2 - - + -
1167B LEU* 3.9 42.2 - - + +
1168B LEU* 4.2 15.9 - - + -
1171B GLY* 3.2 1.3 - - - -
1172B ALA* 2.7 43.7 + - + +
1181B THR* 3.8 16.2 - - - +
1182B ASN* 1.3 77.4 + - - +
1184B PRO* 1.3 77.6 - - + +
1185B PRO* 3.9 1.2 - - - +
1266B PHE* 5.8 0.5 - - - -
1331B PHE* 3.7 4.8 - - - -
1335B MET* 3.6 39.9 - - + -
1336B ILE 4.0 11.0 - - - +
1337B ALA* 4.8 0.9 - - + -
1346B ILE* 5.8 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