Contacts of the helix formed by residues 1186 - 1195 (chain O) in PDB entry 5Z3U
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 ASN1186 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97I A 3.9 23.7 + - - +
900O LYS* 4.6 5.9 - - - +
928O GLN* 2.9 38.4 + - - +
1184O ASP* 2.6 17.8 + - - +
1185O TRP* 1.3 77.0 - - - +
1187O PRO* 1.3 70.9 - - - +
1188O HIS* 3.0 41.0 + - - +
1189O GLN* 3.7 20.8 + - - +
1190O ASP 3.6 10.6 + - - -
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Residues in contact with PRO1187 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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929O ASN* 4.3 6.7 - - - +
1184O ASP* 4.6 2.5 - - - +
1185O TRP 4.1 4.7 - - - +
1186O ASN* 1.3 91.0 - - - +
1188O HIS* 1.3 56.1 + - + +
1189O GLN 3.0 3.4 - - - -
1190O ASP* 2.7 19.8 + - + +
1191O LEU* 2.6 44.7 + - + +
1225O ALA* 4.2 28.5 - - + +
1228O LYS* 4.2 17.5 - - + -
1229O LEU* 4.6 16.2 - - + -
1232O ASP* 5.3 3.8 - - - +
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Residues in contact with HIS1188 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
897O HIS* 6.1 3.1 - - + -
925O THR* 2.8 43.7 + - + +
926O PRO 3.7 3.1 - - - -
927O LEU 3.1 28.7 + - - -
928O GLN* 3.7 11.3 - - - -
929O ASN* 4.1 8.9 + - - -
1186O ASN* 3.0 40.8 + - - +
1187O PRO* 1.3 78.0 - - + +
1189O GLN* 1.3 59.5 + - + +
1191O LEU* 3.1 16.8 - - + +
1192O GLN* 2.9 27.5 + - - +
1232O ASP* 4.7 6.3 - - + -
1236O ILE* 4.0 21.6 - - + +
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Residues in contact with GLN1189 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97I A 5.3 2.8 + - - -
897O HIS* 5.0 20.1 + - + +
898O ARG* 5.7 2.8 - - - +
900O LYS* 5.7 3.6 - - - +
1111O GLN* 4.8 9.1 + - - +
1163O THR* 4.9 25.0 + - - +
1164O ARG* 3.0 53.3 + - - +
1184O ASP* 5.6 3.3 - - + +
1186O ASN* 3.7 22.6 + - - +
1187O PRO 3.0 0.4 - - - -
1188O HIS* 1.3 80.0 - - + +
1190O ASP* 1.3 65.2 + - - +
1191O LEU 3.3 0.2 - - - -
1192O GLN* 3.2 10.8 - - + +
1193O ALA* 2.9 26.2 + - - +
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Residues in contact with ASP1190 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1180O ILE* 4.1 12.5 - - - +
1184O ASP* 2.8 37.2 + - - +
1186O ASN 3.6 2.6 + - - -
1187O PRO* 2.7 23.6 + - + +
1189O GLN* 1.3 73.8 - - - +
1191O LEU* 1.3 59.7 + - - +
1193O ALA* 3.9 2.4 - - - +
1194O GLN* 2.9 26.9 + - - +
1210O ARG* 2.4 51.4 + - - -
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Residues in contact with LEU1191 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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794O MET* 3.6 19.5 - - + -
924O GLY 4.2 9.0 - - - +
925O THR* 4.5 6.7 - - - +
1187O PRO* 2.6 32.8 + - + +
1188O HIS* 3.1 34.3 - - - +
1190O ASP* 1.3 75.0 - - - +
1192O GLN* 1.3 69.9 + - - +
1194O GLN* 3.1 11.8 - - + +
1195O ASP* 3.0 34.5 + - - +
1229O LEU* 5.6 7.9 - - + -
1232O ASP* 5.8 0.9 - - - +
1236O ILE* 5.2 9.0 - - + -
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Residues in contact with GLN1192 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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794O MET* 3.2 32.8 - - - +
895O GLU* 3.9 10.2 + - - +
897O HIS* 3.9 20.2 + - + +
924O GLY* 4.2 9.2 - - - -
925O THR* 5.3 0.9 - - - +
1163O THR 6.0 0.9 - - - +
1166O GLY* 5.2 0.4 - - - -
1167O GLY* 4.4 10.8 - - - +
1168O LEU* 3.8 14.9 - - - +
1188O HIS 2.9 22.4 + - - +
1189O GLN* 3.0 16.5 + - + +
1191O LEU* 1.3 78.2 - - - +
1193O ALA* 1.3 62.9 + - - +
1195O ASP 3.4 4.3 + - - -
1196O ARG* 2.7 61.8 + - - +
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Residues in contact with ALA1193 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1109O PHE* 3.7 46.3 - - + -
1163O THR* 5.3 10.5 - - + +
1166O GLY* 5.6 5.2 - - - -
1178O VAL* 4.5 3.7 - - - +
1180O ILE* 5.5 4.3 - - + -
1189O GLN 2.9 15.9 + - - +
1190O ASP 4.4 1.6 - - - +
1192O GLN* 1.3 73.1 - - - +
1194O GLN* 1.3 66.1 + - - +
1195O ASP 3.0 1.2 + - - -
1196O ARG* 3.2 28.3 + - - +
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Residues in contact with GLN1194 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1008O GLU* 5.0 16.6 + - + +
1178O VAL* 4.7 3.5 - - - +
1180O ILE* 3.8 22.6 - - - +
1190O ASP 2.9 21.9 + - - +
1191O LEU* 3.0 18.3 + - + +
1193O ALA* 1.3 76.8 - - - +
1195O ASP* 1.3 66.5 + - - +
1196O ARG 3.5 0.5 + - - -
1197O ALA* 4.2 5.2 + - - +
1198O HIS* 5.2 1.6 + - - -
1208O ILE* 3.0 56.8 - - + +
1210O ARG* 3.5 28.7 - - - +
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Residues in contact with ASP1195 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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793O GLU* 4.4 13.8 - - - +
794O MET* 3.2 46.6 - - + +
1191O LEU* 3.0 17.2 + - - +
1192O GLN 3.4 0.9 + - - -
1193O ALA 3.0 1.2 + - - -
1194O GLN* 1.3 86.9 - - - +
1196O ARG* 1.3 66.7 + - - +
1197O ALA 3.1 4.9 + - - -
1198O HIS* 3.4 41.7 + - + +
1199O ARG* 4.2 4.9 + - - -
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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