Contacts of the helix formed by residues 1205 - 1210 (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 SER1205 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1203B ASP 3.5 3.4 + - - -
1204B ILE* 1.3 77.4 - - - +
1206B ILE* 1.3 60.4 + - - +
1207B ALA* 3.7 9.5 + - - +
1208B GLU* 3.2 24.5 + - - +
1209B LEU* 2.9 31.0 + - - +
1349B LYS* 5.3 0.4 - - - -
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Residues in contact with ILE1206 (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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1204B ILE 4.2 0.2 + - - -
1205B SER* 1.3 74.3 - - - +
1207B ALA* 1.3 63.5 + - - +
1209B LEU* 3.2 8.8 + - + +
1210B MET* 3.0 28.5 + - + +
1234B TYR* 3.6 43.5 - - + +
1235B GLU* 3.6 40.6 + - + +
1347B ASN* 4.0 20.4 - - - +
1348B LEU* 5.0 4.5 - - + -
1349B LYS* 3.9 25.3 - - + +
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Residues in contact with ALA1207 (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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1205B SER* 3.2 9.0 + - - +
1206B ILE* 1.3 80.7 - - - +
1208B GLU* 1.3 60.0 + - - +
1210B MET* 3.3 24.2 + - - +
1211B GLU* 3.6 9.2 + - - +
1231B ARG* 6.2 4.3 - - - +
1235B GLU* 4.2 8.6 + - - +
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Residues in contact with GLU1208 (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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1197B SER* 5.5 2.5 - - - -
1201B ASN* 4.3 13.4 + - - +
1204B ILE* 3.8 28.1 - - + +
1205B SER* 3.2 20.2 + - - +
1207B ALA* 1.3 75.6 - - - +
1209B LEU* 1.3 65.9 + - - +
1210B MET 3.1 0.2 - - - -
1211B GLU* 3.0 42.6 + - - +
1212B ASP* 4.0 4.2 + - - +
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Residues in contact with LEU1209 (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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1194B GLY* 3.6 28.9 - - - +
1197B SER* 4.9 0.7 - - - -
1198B LEU* 4.5 3.4 - - + -
1204B ILE* 3.7 28.9 - - + -
1205B SER 2.9 18.1 + - - +
1206B ILE* 3.5 12.8 - - + +
1208B GLU* 1.3 77.1 - - - +
1210B MET* 1.3 58.9 + - - +
1212B ASP* 3.0 11.9 + - - +
1213B ILE* 2.9 27.2 + - + +
1348B LEU* 4.4 12.3 - - + -
1349B LYS* 3.7 42.4 - - + +
1352B LEU* 4.1 17.5 - - + -
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Residues in contact with MET1210 (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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1206B ILE* 3.0 26.7 + - + +
1207B ALA* 3.5 15.5 - - - +
1208B GLU 3.1 0.6 - - - -
1209B LEU* 1.3 73.0 - - - +
1211B GLU* 1.3 61.7 + - - +
1212B ASP 3.2 0.7 - - - -
1213B ILE 3.2 19.5 - - - +
1214B GLU* 4.0 5.7 + - - +
1227B LYS* 3.8 46.7 + - + +
1230B ILE* 3.8 22.0 - - + -
1231B ARG* 4.2 37.2 - - - +
1234B TYR* 3.8 23.1 - - + -
1235B GLU* 5.8 0.2 - - - +
1348B LEU* 4.8 2.2 - - + -
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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