Contacts of the helix formed by residues 1174 - 1185 (chain A) in PDB entry 3F2B
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 THR1174 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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938A ASP* 2.8 35.7 + - - +
1130A MET* 3.7 5.8 - - - -
1173A LYS* 1.3 81.2 + - - +
1175A PHE* 1.3 63.8 + - - +
1176A SER* 3.1 14.1 - - - +
1177A GLU* 3.2 30.0 + - + +
1178A LEU* 3.0 23.2 + - - +
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Residues in contact with PHE1175 (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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935A SER* 3.9 14.8 - - - -
937A PHE* 3.5 39.0 - + + -
938A ASP* 3.1 10.9 + - - +
956A HIS* 3.7 21.3 - + - -
1124A THR* 4.2 20.8 + - + +
1130A MET* 3.6 10.9 - - + +
1174A THR* 1.3 73.4 - - - +
1176A SER* 1.3 60.0 + - - +
1178A LEU* 2.9 8.4 + - - +
1179A VAL* 2.8 47.0 + - + +
1277A ALA* 3.6 24.2 - - + -
1280A VAL* 3.7 20.4 - - + -
1281A LEU* 3.8 17.0 - - + -
1284A VAL* 4.8 8.5 - - + -
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Residues in contact with SER1176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
934A GLY* 4.0 13.1 - - - -
935A SER* 4.0 17.9 - - - -
938A ASP* 3.0 22.1 + - - -
1174A THR* 3.1 6.7 - - - +
1175A PHE* 1.3 80.5 - - - +
1177A GLU* 1.3 57.7 + - - +
1179A VAL* 3.3 13.2 + - - +
1180A GLN* 2.8 28.5 + - - +
1273A LYS* 6.1 3.1 - - - -
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Residues in contact with GLU1177 (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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1171A ARG 4.4 2.0 - - - +
1172A PRO* 3.6 17.9 - - + +
1173A LYS* 2.9 32.4 + - - +
1174A THR* 3.2 25.8 + - + +
1175A PHE 3.2 0.6 - - - -
1176A SER* 1.3 80.9 + - - +
1178A LEU* 1.3 57.4 + - - +
1180A GLN* 3.2 8.6 + - + +
1181A ILE* 3.0 31.9 + - - +
1206A LEU* 5.9 7.6 - - + -
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Residues in contact with LEU1178 (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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1130A MET* 3.6 31.4 - - + +
1133A PHE* 3.7 47.3 - - + -
1158A PHE* 3.9 13.9 - - + -
1172A PRO* 3.4 33.9 - - + +
1173A LYS 5.4 1.1 - - - -
1174A THR 3.0 7.4 + - - +
1175A PHE* 2.9 8.0 + - - +
1177A GLU* 1.3 71.7 - - - +
1179A VAL* 1.3 63.1 + - - +
1181A ILE* 3.1 3.9 + - - +
1182A SER* 2.8 30.5 + - - -
1280A VAL* 3.8 17.7 - - + +
1284A VAL* 4.3 10.1 - - + -
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Residues in contact with VAL1179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
956A HIS* 5.9 0.2 - - - +
1175A PHE* 2.8 45.4 + - + +
1176A SER* 3.5 12.1 - - - +
1178A LEU* 1.3 76.7 - - - +
1180A GLN* 1.3 63.1 + - - +
1182A SER* 3.4 2.1 + - - -
1183A GLY* 3.2 18.7 + - - -
1211A GLY 4.6 1.6 - - - +
1212A CYS* 6.3 1.1 - - + -
1273A LYS* 4.2 29.4 - - + +
1276A ALA* 3.8 18.3 - - + +
1277A ALA* 4.0 18.4 - - + +
1280A VAL* 3.9 13.0 - - + +
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Residues in contact with GLN1180 (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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1176A SER 2.8 17.0 + - - +
1177A GLU* 3.2 12.1 + - - +
1179A VAL* 1.3 75.9 - - - +
1181A ILE* 1.3 63.9 + - + +
1183A GLY* 3.4 1.9 + - - -
1184A LEU* 3.1 33.2 + - + +
1206A LEU* 2.9 37.3 - - + +
1207A SER* 3.7 11.8 + - - +
1209A VAL* 3.4 20.5 + - - +
1211A GLY* 3.7 26.8 - - - +
1212A CYS* 5.8 0.8 - - - -
1215A ASP* 4.5 10.3 + - - -
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Residues in contact with ILE1181 (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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1158A PHE* 3.6 23.6 - - + -
1163A VAL* 4.1 11.7 - - + -
1166A MET* 4.1 14.4 - - + -
1167A LEU* 3.5 28.9 - - + -
1170A THR* 3.9 29.6 - - + +
1172A PRO* 4.5 9.2 - - + -
1177A GLU 3.0 15.4 + - - +
1178A LEU 3.1 3.5 + - - +
1180A GLN* 1.3 84.2 - - + +
1182A SER* 1.3 67.2 + - - +
1184A LEU* 3.3 15.3 - - + +
1185A SER* 2.9 26.7 + - - +
1206A LEU* 5.0 7.2 - - + -
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Residues in contact with SER1182 (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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1157A GLU* 6.1 0.2 - - - +
1158A PHE* 4.3 12.0 - - - -
1178A LEU 2.8 20.2 + - - -
1179A VAL 3.5 5.6 - - - -
1181A ILE* 1.3 72.3 - - - +
1183A GLY* 1.3 63.3 + - - +
1185A SER* 3.1 9.7 + - - -
1186A HIS* 2.8 31.7 + - - -
1271A PHE* 3.5 18.9 - - - -
1276A ALA* 3.6 14.4 + - - +
1279A TYR* 5.0 4.7 - - - +
1280A VAL* 3.7 18.0 - - - +
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Residues in contact with GLY1183 (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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1179A VAL 3.2 9.6 + - - -
1180A GLN 3.7 1.1 - - - -
1182A SER* 1.3 80.8 + - - +
1184A LEU* 1.3 60.1 + - - +
1185A SER 3.3 0.7 + - - -
1186A HIS* 3.6 14.9 + - - +
1190A VAL* 4.0 5.9 - - - +
1211A GLY 3.2 26.0 - - - -
1270A MET* 5.2 4.4 - - - +
1271A PHE* 4.0 21.1 + - - -
1276A ALA* 4.3 2.0 - - - +
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Residues in contact with LEU1184 (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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1162A PHE* 5.0 0.9 - - - -
1166A MET* 3.2 32.3 - - + -
1180A GLN* 3.1 23.9 + - + +
1181A ILE* 3.2 22.6 + - + -
1183A GLY* 1.3 77.1 - - - +
1185A SER* 1.3 56.9 + - - +
1186A HIS 3.4 2.4 + - - -
1187A GLY 4.9 1.0 - - - +
1190A VAL* 3.5 27.4 - - + +
1191A TRP* 3.5 43.4 + - + +
1195A ALA* 4.7 1.1 - - + -
1206A LEU* 4.4 5.2 - - + -
1209A VAL* 3.4 32.1 - - + -
1210A ILE 4.8 0.7 - - - +
1211A GLY* 4.1 6.3 + - - -
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Residues in contact with SER1185 (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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1158A PHE* 5.5 0.7 - - - -
1162A PHE* 4.2 4.0 - - - -
1163A VAL* 3.9 20.1 - - - +
1166A MET* 3.7 24.7 - - - -
1181A ILE* 2.9 24.4 + - - +
1182A SER* 3.1 11.6 + - - -
1183A GLY 3.2 0.2 - - - -
1184A LEU* 1.3 75.9 - - - +
1186A HIS* 1.3 74.0 + - - +
1187A GLY 4.1 1.3 - - - -
5T C 3.4 27.3 + - - +
6T G 4.2 2.6 - - - +
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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