Contacts of the helix formed by residues 1187 - 1200 (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 ASN1187 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1101B TYR* 3.5 2.5 - - - -
1186B HIS* 1.3 74.0 - - - +
1188B LEU* 1.3 58.5 + - - +
1189B THR* 3.1 29.1 + - - -
1190B GLU* 3.1 36.6 + - + +
1191B LEU* 2.9 29.0 + - - +
1215B GLY 5.0 2.0 + - - -
1217B ASP* 3.0 35.7 + - + +
1482B ASP* 2.8 29.2 + - - +
1483B ASP 3.2 13.5 + - - -
1484B ARG* 3.4 4.0 - - - +
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Residues in contact with LEU1188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1101B TYR* 2.6 31.2 + - + +
1131B ILE* 4.2 15.7 - - + -
1164B PHE* 3.8 25.6 - - + -
1165B PRO* 4.2 10.8 - - + -
1169B ALA* 4.5 7.2 - - + -
1186B HIS 3.6 0.6 + - - -
1187B ASN* 1.3 70.3 - - - +
1189B THR* 1.3 65.5 + - - +
1191B LEU* 4.2 4.5 - - + -
1192B ILE* 3.0 50.6 + - + +
1476B ILE* 4.6 6.5 - - + +
1480B PHE* 3.9 36.1 - - + +
1481B GLY* 4.4 4.5 - - - +
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Residues in contact with THR1189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1187B ASN* 3.1 11.2 + - - -
1188B LEU* 1.3 77.6 - - - +
1190B GLU* 1.3 63.3 + - + +
1193B ASN* 3.1 39.5 + - - +
1477B ARG* 3.9 28.4 - - + +
1481B GLY* 3.1 25.4 - - - -
1482B ASP 3.2 12.2 + - - -
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Residues in contact with GLU1190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1186B HIS* 6.4 0.2 - - + -
1187B ASN* 3.1 23.2 + - - +
1189B THR* 1.3 75.8 - - + +
1191B LEU* 1.3 65.3 + - + +
1193B ASN* 3.3 8.6 + - - +
1194B GLY 2.9 18.2 + - - -
1212B ASP* 3.2 22.2 - - - +
1213B ILE* 3.5 15.0 - - + +
1214B GLU* 3.1 27.6 + - - +
1215B GLY 4.1 2.3 - - - +
1484B ARG* 2.8 52.9 + - - +
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Residues in contact with LEU1191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1165B PRO* 3.7 22.9 - - + +
1168B LEU* 3.7 30.1 - - + -
1169B ALA* 3.3 42.8 - - + +
1186B HIS* 3.7 18.4 - - + -
1187B ASN 2.9 19.4 + - - +
1188B LEU* 3.3 6.7 + - - +
1190B GLU* 1.3 76.4 - - + +
1192B ILE* 1.3 57.7 + - - +
1194B GLY* 3.0 4.0 + - - -
1195B VAL* 2.9 31.9 + - - +
1213B ILE* 3.9 24.9 - - + +
1348B LEU* 5.3 0.2 - - + -
1352B LEU* 4.6 2.7 - - + -
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Residues in contact with ILE1192 (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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1165B PRO* 4.0 21.8 - - + -
1188B LEU* 3.0 36.0 + - + +
1189B THR 4.3 0.7 - - - +
1191B LEU* 1.3 72.3 - - - +
1193B ASN* 1.3 61.3 + - - +
1195B VAL* 3.2 7.4 + - - +
1196B LEU* 2.8 38.4 + - + +
1473B LEU* 3.5 45.1 - - + +
1476B ILE* 4.0 11.2 - - + -
1477B ARG* 3.7 34.5 - - + +
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Residues in contact with ASN1193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1189B THR* 3.1 31.9 + - - +
1190B GLU* 3.5 8.4 - - - +
1191B LEU 3.2 0.2 - - - -
1192B ILE* 1.3 76.6 - - - +
1194B GLY* 1.3 56.3 + - - +
1196B LEU* 3.3 8.4 + - - +
1197B SER* 2.9 32.1 + - - -
1212B ASP* 3.7 22.3 + - + +
1477B ARG* 3.0 31.5 + - - +
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Residues in contact with GLY1194 (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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1190B GLU 2.9 14.8 + - - -
1191B LEU 3.0 5.1 + - - -
1193B ASN* 1.3 75.9 - - - +
1195B VAL* 1.3 57.5 + - - +
1197B SER* 3.4 0.7 + - - -
1198B LEU* 2.9 28.4 + - - +
1209B LEU* 3.6 18.1 - - - +
1212B ASP* 3.8 16.1 - - - +
1213B ILE* 4.4 9.0 - - - -
1352B LEU* 4.6 4.0 - - - -
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Residues in contact with VAL1195 (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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1165B PRO* 4.7 4.3 - - + -
1191B LEU 2.9 19.5 + - - +
1192B ILE* 3.6 10.8 - - - +
1194B GLY* 1.3 73.7 - - - +
1196B LEU* 1.3 60.8 + - - +
1198B LEU* 3.3 7.2 + - + +
1199B SER* 2.9 28.2 + - - -
1352B LEU* 3.7 28.3 - - + +
1355B TYR* 4.3 22.4 - - + -
1356B LEU* 4.1 27.1 - - + +
1473B LEU* 3.7 26.0 - - + -
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Residues in contact with LEU1196 (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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1192B ILE* 2.8 30.0 + - + +
1193B ASN* 3.6 9.2 - - - +
1195B VAL* 1.3 73.7 - - - +
1197B SER* 1.3 64.5 + - - +
1199B SER* 2.7 20.1 + - - -
1200B LYS* 3.3 28.1 + - - +
1470B ARG* 3.8 46.0 - - + +
1473B LEU* 4.7 11.7 - - + -
1474B THR* 3.7 16.2 - - + +
1477B ARG* 4.0 21.1 - - - +
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Residues in contact with SER1197 (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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1193B ASN 2.9 10.6 + - - -
1194B GLY* 3.7 4.3 - - - -
1196B LEU* 1.3 75.6 - - - +
1198B LEU* 1.3 62.0 + - - +
1200B LYS* 3.3 10.5 + - - +
1201B ASN* 3.2 23.2 + - - +
1204B ILE* 3.8 21.7 - - - +
1208B GLU* 5.5 2.6 + - - -
1209B LEU* 4.9 0.2 - - - -
1212B ASP* 2.7 28.6 + - - -
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Residues in contact with LEU1198 (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 2.9 17.4 + - - +
1195B VAL* 3.6 6.3 - - - +
1196B LEU 3.2 0.2 - - - -
1197B SER* 1.3 77.8 - - - +
1199B SER* 1.3 62.4 + - - +
1201B ASN 3.0 27.5 + - - +
1202B PRO* 3.5 10.2 - - + +
1204B ILE* 3.6 26.2 - - + +
1209B LEU* 4.5 4.3 - - + -
1349B LYS* 4.0 11.9 - - + -
1352B LEU* 3.6 40.6 - - + +
1353B VAL* 3.8 24.2 - - + +
1356B LEU* 3.8 20.5 - - + +
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Residues in contact with SER1199 (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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1195B VAL* 2.9 14.2 + - - -
1196B LEU* 2.7 24.2 + - - -
1198B LEU* 1.3 76.2 - - - +
1200B LYS* 1.3 56.6 + - - +
1201B ASN 3.8 0.5 + - - -
1202B PRO* 5.0 4.7 - - - +
1356B LEU* 3.9 22.4 - - - +
1466B LEU* 3.7 23.6 - - - +
1470B ARG* 2.9 42.8 + - - +
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Residues in contact with LYS1200 (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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1196B LEU* 3.3 32.8 + - - +
1197B SER* 3.9 6.5 - - - +
1198B LEU 3.1 1.0 - - - -
1199B SER* 1.3 77.9 - - - +
1201B ASN* 1.3 60.0 + - + +
1202B PRO* 4.2 3.3 - - - +
1470B ARG* 3.6 37.9 - - - +
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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