Contacts of the helix formed by residues 1172 - 1176 (chain A) in PDB entry 3ETA
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 PRO1172 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1131A ARG 3.9 17.3 - - - +
1132A ASP* 3.5 16.8 - - - +
1136A ARG* 3.3 28.5 - - - +
1153A MET* 4.1 13.2 - - + -
1161A ASP 3.4 12.6 - - - +
1162A TYR* 3.6 4.2 - - + -
1171A LEU* 1.3 90.0 - - + +
1173A VAL* 1.3 57.6 + - - +
1174A ARG 3.2 2.9 - - - -
1175A TRP* 2.9 26.1 + - + +
1176A MET* 3.3 20.4 + - + +
1186A PHE* 5.6 0.2 - - + -
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Residues in contact with VAL1173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1161A ASP 4.3 2.5 + - - +
1162A TYR 5.6 0.7 - - - -
1163A TYR* 4.0 29.2 - - + +
1165A LYS* 4.7 7.4 - - + -
1171A LEU* 3.0 29.5 + - + +
1172A PRO* 1.3 70.9 - - - +
1174A ARG* 1.3 68.1 + - + +
1175A TRP 3.1 1.4 + - - -
1176A MET* 3.2 24.2 + - - +
1181A LEU* 4.0 13.1 - - + +
1210A TYR* 5.4 0.2 - - - -
1215A ASN* 4.1 20.4 - - - +
1218A VAL* 4.0 12.6 - - + +
1219A LEU* 3.6 32.5 - - + -
1222A VAL* 5.4 1.0 - - - +
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Residues in contact with ARG1174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1160A THR 4.7 8.9 + - - -
1161A ASP* 5.2 2.2 + - - +
1172A PRO 3.2 1.6 + - - -
1173A VAL* 1.3 81.6 - - + +
1175A TRP* 1.3 78.5 + - + +
1176A MET 5.3 0.4 - - - -
1193A TRP* 5.3 0.5 + - - -
1197A VAL* 4.0 9.7 - - - +
1208A GLN* 4.5 20.9 - - - +
1209A PRO* 2.7 50.6 + - + +
1210A TYR* 2.8 39.6 + - + -
1211A GLN* 4.7 3.4 + - - +
1213A LEU 2.8 19.6 + - - -
1214A SER* 3.8 1.4 - - - +
1215A ASN* 3.3 32.7 + - - +
1218A VAL* 3.5 28.1 - - + +
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Residues in contact with TRP1175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1085A LYS* 4.1 3.1 - - - -
1132A ASP* 5.6 0.9 - - - +
1133A LEU 3.5 25.6 - - - +
1134A ALA* 3.4 8.8 - - + +
1136A ARG* 3.3 33.2 - - - -
1161A ASP* 3.4 35.9 - - + -
1172A PRO* 2.9 17.7 + - + +
1174A ARG* 1.3 101.8 - - + +
1176A MET* 1.3 58.9 + - - +
1193A TRP* 3.3 16.0 - - - -
1194A SER* 2.7 30.4 + - - +
1197A VAL* 3.4 28.4 - - + +
1201A GLU* 2.9 42.7 + - - -
1208A GLN* 4.8 0.7 - - - -
1209A PRO* 3.8 22.9 - - + -
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Residues in contact with MET1176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1131A ARG 5.4 0.9 - - - +
1165A LYS* 6.1 1.3 - - + +
1171A LEU* 3.9 32.1 - - + -
1172A PRO* 3.3 21.3 - - + +
1173A VAL* 3.2 29.8 + - + +
1174A ARG 3.6 0.4 - - - -
1175A TRP* 1.3 79.6 - - - +
1177A ALA* 1.3 63.9 + - - +
1178A PRO 3.9 0.3 - - - -
1180A SER* 3.6 30.1 - - - +
1181A LEU* 3.9 21.3 - - + +
1186A PHE* 3.7 31.4 - - + -
1193A TRP* 3.1 14.0 + - - -
1194A SER* 4.7 1.3 - - - -
1222A VAL* 3.9 10.6 - - - +
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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