Contacts of the helix formed by residues 1182 - 1196 (chain B) in PDB entry 4Z4Q
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 ASN1182 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1095B ARG* 3.7 14.7 - - - +
1181B HIS* 1.3 71.3 - - - +
1183B LEU* 1.3 68.5 + - - +
1184B ALA* 2.9 32.2 + - - +
1185B GLU* 3.0 48.6 + - - +
1186B VAL* 3.0 13.0 + - - +
1210B GLY 5.2 1.0 + - - -
1212B ASP* 3.2 33.5 + - + +
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Residues in contact with LEU1183 (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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1095B ARG* 5.3 3.0 - - - +
1096B GLU* 4.8 12.6 - - + +
1126B ILE* 4.2 23.1 - - + -
1159B PHE* 4.3 15.9 - - + -
1160B PRO* 4.8 0.2 - - + -
1164B VAL* 4.0 33.5 - - + +
1181B HIS 3.2 6.1 + - - -
1182B ASN* 1.3 71.1 + - - +
1184B ALA* 1.3 62.2 + - - +
1186B VAL* 4.0 0.6 - - - +
1187B ILE* 3.1 47.3 + - + +
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Residues in contact with ALA1184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1182B ASN* 2.9 15.2 + - - +
1183B LEU* 1.3 71.2 - - - +
1185B GLU* 1.3 63.4 + - + +
1187B ILE* 3.4 4.9 + - - +
1188B ASP* 2.8 42.6 + - - +
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Residues in contact with GLU1185 (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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1182B ASN* 3.0 31.8 + - + +
1184B ALA* 1.3 77.4 - - + +
1186B VAL* 1.3 63.5 + - - +
1188B ASP* 2.9 17.1 + - - +
1189B ALA* 2.9 13.3 + - - +
1207B PHE 3.3 20.8 - - - +
1208B LEU* 4.3 10.0 - - + +
1209B PRO* 3.2 32.3 - - + +
1210B GLY 3.9 10.9 - - - +
1212B ASP* 5.4 1.0 - - - +
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Residues in contact with VAL1186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1160B PRO* 3.8 33.9 - - + +
1163B LEU* 4.0 28.9 - - + -
1164B VAL* 4.1 11.4 - - + -
1181B HIS* 3.4 34.5 - - + -
1182B ASN 3.0 12.9 + - - +
1183B LEU 4.0 3.4 - - - +
1185B GLU* 1.3 72.6 - - - +
1187B ILE* 1.3 62.8 + - - +
1189B ALA* 3.3 4.7 + - - +
1190B ALA* 3.0 20.7 + - - +
1208B LEU* 4.4 14.1 - - + +
1346B LEU* 4.4 5.0 - - + +
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Residues in contact with ILE1187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1158B ALA 5.6 2.2 - - - +
1159B PHE* 4.7 8.7 - - + -
1160B PRO* 4.1 15.3 - - + -
1183B LEU* 3.1 43.7 + - + +
1184B ALA* 3.8 5.4 - - - +
1186B VAL* 1.3 72.5 - - - +
1188B ASP* 1.3 72.5 + - - +
1190B ALA* 3.2 7.2 + - + +
1191B VAL* 2.9 35.0 + - + +
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Residues in contact with ASP1188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1184B ALA* 2.8 29.6 + - - +
1185B GLU* 2.9 7.1 + - - +
1187B ILE* 1.3 82.9 - - - +
1189B ALA* 1.3 62.9 + - - +
1191B VAL* 3.2 7.4 + - - +
1192B TYR* 3.0 22.2 + - - +
1207B PHE* 4.1 27.1 - - + +
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Residues in contact with ALA1189 (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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1185B GLU 2.9 10.9 + - - +
1186B VAL* 3.5 8.5 - - - +
1188B ASP* 1.3 75.4 - - - +
1190B ALA* 1.3 62.8 + - - +
1192B TYR* 3.0 6.8 + - - +
1193B MET* 2.9 22.7 + - - +
1204B LEU* 4.4 12.3 - - + +
1207B PHE* 3.7 14.6 - - + +
1208B LEU* 4.1 22.9 - - + -
1346B LEU* 3.6 22.0 - - + -
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Residues in contact with ALA1190 (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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1160B PRO* 4.9 4.5 - - + -
1186B VAL 3.0 14.1 + - - +
1187B ILE* 3.2 11.2 + - + +
1189B ALA* 1.3 76.4 - - - +
1191B VAL* 1.3 65.0 + - + +
1193B MET* 3.1 5.4 + - - +
1194B ILE* 2.9 36.6 + - + +
1346B LEU* 4.2 18.3 - - + +
1349B TYR* 4.9 15.7 - - + -
1350B ILE* 3.7 8.2 - - + +
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Residues in contact with VAL1191 (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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1187B ILE* 2.9 32.2 + - + +
1188B ASP* 3.8 7.0 - - - +
1190B ALA* 1.3 76.5 - - + +
1192B TYR* 1.3 64.1 + - - +
1194B ILE* 3.3 21.0 + - + +
1195B ASP* 3.5 22.5 + - - +
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Residues in contact with TYR1192 (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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1188B ASP 3.0 11.7 + - - +
1189B ALA 3.0 9.2 + - - +
1191B VAL* 1.3 73.2 - - - +
1193B MET* 1.3 65.1 + - - +
1194B ILE 2.9 5.4 + - - -
1195B ASP* 3.0 6.3 + - - +
1196B HIS* 2.9 57.6 + + + +
1199B ALA* 3.6 30.0 - - + +
1203B LYS* 3.6 27.9 - - + +
1204B LEU* 4.4 8.1 - - + -
1207B PHE* 3.2 39.5 - + + -
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Residues in contact with MET1193 (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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1189B ALA 2.9 14.5 + - - +
1190B ALA* 3.1 6.0 + - - +
1192B TYR* 1.3 80.5 - - - +
1194B ILE* 1.3 60.3 + - - +
1195B ASP 3.4 0.2 - - - -
1196B HIS 3.7 13.0 - - - +
1197B PRO* 3.3 36.7 - - + +
1199B ALA* 5.3 3.6 - - + +
1204B LEU* 4.3 15.3 - - + -
1343B VAL* 3.7 32.3 - - + +
1346B LEU* 3.9 20.2 - - + -
1347B SER* 3.2 36.8 - - - -
1350B ILE* 4.0 13.9 - - + +
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Residues in contact with ILE1194 (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 ALA* 2.9 24.8 + - + +
1191B VAL* 3.6 15.9 - - + +
1192B TYR 2.9 0.4 - - - -
1193B MET* 1.3 81.0 - - - +
1195B ASP* 1.3 67.9 + - - +
1197B PRO* 4.1 8.5 - - - +
1349B TYR* 6.4 1.1 - - + -
1350B ILE* 3.2 40.2 - - + -
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Residues in contact with ASP1195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1191B VAL* 3.5 20.3 + - - +
1192B TYR* 3.0 4.6 + - - +
1194B ILE* 1.3 81.7 - - - +
1196B HIS* 1.3 85.0 + - + +
1197B PRO* 3.4 7.5 - - - +
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Residues in contact with HIS1196 (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 TYR* 2.9 58.4 + + + +
1193B MET* 3.3 9.3 - - - +
1195B ASP* 1.3 97.7 + - + +
1197B PRO* 1.3 65.2 - - - +
1198B THR* 3.0 6.5 + - - +
1199B ALA* 3.1 17.9 + - + +
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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