Contacts of the strand formed by residues 1191 - 1197 (chain M) in PDB entry 3HOU
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 TRP1191 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1152M ILE* 4.2 9.4 - - + -
1153M TYR 3.1 23.1 - - - -
1154M TYR* 3.4 35.6 - + + -
1189M SER* 3.3 11.0 + - - +
1190M PRO* 1.3 84.0 - - + +
1192M LEU* 1.3 61.7 + - - +
1193M LEU 4.0 0.5 + - - -
1241M ARG* 3.6 25.6 - - - +
1256M GLU* 3.3 35.9 - - + +
1257M ASP* 4.0 23.2 + - + +
1260M LEU* 4.1 17.1 - - + +
16U PRO* 4.9 7.9 - - + -
17U ARG* 5.2 2.9 - - - -
18U GLU* 4.9 13.2 + - + +
25U LEU* 3.3 29.6 - - + -
43U VAL* 3.5 22.2 - - + -
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Residues in contact with LEU1192 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1151M GLU 3.5 1.2 - - - +
1152M ILE* 3.1 6.4 - - - +
1153M TYR* 2.6 66.9 + - + +
1155M ASP* 4.3 14.6 - - + +
1163M ILE* 4.0 16.4 - - + -
1190M PRO 3.3 1.6 + - - -
1191M TRP* 1.3 72.4 - - - +
1193M LEU* 1.3 64.1 + - - +
1194M ARG* 4.3 7.6 - - + -
1239M ARG* 3.3 59.0 - - + +
1240M CYS 3.7 15.3 - - - +
1241M ARG* 3.9 12.3 - - - +
1260M LEU* 4.1 2.2 - - - -
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Residues in contact with LEU1193 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1150M SER* 4.3 4.3 - - - -
1151M GLU 3.5 14.6 - - - +
1152M ILE* 4.8 4.7 - - + -
1191M TRP 4.0 0.6 + - - -
1192M LEU* 1.3 73.2 - - - +
1194M ARG* 1.3 65.7 + - - +
1195M LEU* 3.8 22.1 - - + +
1238M ILE 3.7 1.0 - - - +
1239M ARG* 3.6 2.3 - - - -
1240M CYS* 2.9 46.1 + - + +
1260M LEU* 3.4 48.2 - - + +
1263M ILE* 4.6 6.5 - - + -
1264M GLU* 4.0 22.4 - - + +
1267M MET* 4.0 16.6 - - + -
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Residues in contact with ARG1194 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1149M ALA 4.2 0.2 - - - +
1150M SER* 3.3 3.3 - - - -
1151M GLU* 2.8 61.5 + - + +
1153M TYR* 3.9 25.9 + - + -
1163M ILE* 4.2 11.6 - - - +
1165M GLU* 2.9 36.8 + - - +
1166M ASP* 2.5 41.4 + - - +
1192M LEU* 4.3 12.3 - - + -
1193M LEU* 1.3 75.7 - - - +
1195M LEU* 1.3 65.2 + - - +
1196M GLU* 6.1 4.5 - - - +
1235M LYS* 5.1 4.2 - - - +
1237M ILE* 3.7 34.2 - - + +
1238M ILE 3.4 3.8 - - - +
1239M ARG* 4.5 3.6 - - + -
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Residues in contact with LEU1195 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1143M LEU* 4.2 21.1 - - + -
1147M THR* 4.4 9.0 - - + -
1149M ALA 3.6 3.6 - - - +
1150M SER* 3.3 30.7 - - - -
1193M LEU* 3.8 6.3 - - + +
1194M ARG* 1.3 77.6 - - - +
1196M GLU* 1.3 60.5 + - - +
1197M LEU* 3.8 13.3 + - + -
1216M ILE* 4.8 0.2 - - + -
1237M ILE* 3.3 8.8 - - - +
1238M ILE* 3.0 54.3 + - + +
1240M CYS* 5.5 1.1 - - - -
1264M GLU* 5.2 1.1 - - - +
1267M MET* 3.2 41.1 - - + -
1268M LEU* 5.7 4.5 - - + -
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Residues in contact with GLU1196 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1148M ILE* 2.7 59.6 + - + +
1149M ALA* 3.0 20.7 + - + +
1151M GLU* 6.1 1.1 - - - +
1194M ARG* 4.3 4.5 - - - +
1195M LEU* 1.3 72.1 - - - +
1197M LEU* 1.3 57.8 + - - +
1235M LYS* 3.7 36.3 + - + +
1236M LEU 3.4 14.8 - - - +
1237M ILE* 4.6 5.2 - - + +
45U ARG* 5.3 7.6 + - - -
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Residues in contact with LEU1197 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1143M LEU* 4.2 10.3 - - + -
1146M VAL* 3.5 7.9 - - + +
1147M THR* 3.9 26.0 - - - +
1148M ILE* 3.4 7.7 - - - +
1195M LEU* 3.8 9.8 + - + +
1196M GLU* 1.3 82.4 - - - +
1198M ASP* 1.3 62.9 + - - +
1199M ARG 4.0 1.0 + - - -
1202M MET* 3.9 35.4 - - + -
1209M MET* 4.0 15.9 - - + -
1212M VAL* 4.0 11.2 - - + -
1236M LEU* 3.3 29.6 + - + +
1238M ILE* 3.8 29.2 - - + -
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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