Contacts of the helix formed by residues 1212 - 1226 (chain A) in PDB entry 2E1F
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 LEU1212 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1178A LEU* 4.1 14.6 - - + +
1179A ALA* 3.9 24.0 - - + -
1183A ILE* 4.5 2.7 - - + -
1187A MET* 4.1 15.0 - - + -
1198A VAL* 4.0 24.9 - - + -
1204A VAL* 4.0 15.3 - - + -
1208A LYS* 2.8 35.4 + - + +
1209A ALA* 3.1 9.1 + - - +
1211A MET* 1.3 76.2 - - - +
1213A ALA* 1.3 63.2 + - - +
1214A PRO* 3.4 2.9 - - - -
1215A LEU* 3.0 37.6 + - + +
1216A LEU* 3.1 14.8 + - + +
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Residues in contact with ALA1213 (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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1195A VAL* 5.6 5.2 - - + -
1209A ALA 3.3 6.7 + - - +
1210A ALA* 3.5 15.0 - - - +
1211A MET 3.3 0.2 - - - -
1212A LEU* 1.3 76.2 - - - +
1214A PRO* 1.4 70.7 - - + +
1216A LEU* 3.1 22.9 + - + +
1217A GLU* 3.1 14.7 + - - +
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Residues in contact with PRO1214 (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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1163A ALA* 5.6 2.9 - - + +
1167A HIS* 3.4 39.5 - - + +
1210A ALA 4.6 0.7 - - - +
1211A MET 3.5 9.4 - - - +
1212A LEU 3.5 3.6 - - - -
1213A ALA* 1.4 96.8 - - + +
1215A LEU* 1.3 64.4 + - + +
1217A GLU* 3.3 10.9 - - + +
1218A VAL* 3.2 27.5 + - - +
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Residues in contact with LEU1215 (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 LEU* 3.8 26.4 - - + +
1163A ALA* 4.0 26.7 - - + +
1164A ARG* 4.1 15.3 - - + +
1167A HIS* 5.0 0.7 - - + -
1178A LEU* 4.7 7.9 - - + -
1184A LEU* 3.7 30.1 - - + -
1187A MET* 4.0 11.0 - - + -
1211A MET 5.1 0.2 - - - +
1212A LEU* 3.0 32.5 + - + +
1214A PRO* 1.3 85.4 - - + +
1216A LEU* 1.3 62.5 + - - +
1218A VAL* 3.2 9.4 + - - +
1219A ILE* 3.0 32.3 + - - +
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Residues in contact with LEU1216 (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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1187A MET* 3.9 12.8 - - + -
1192A PRO* 3.8 23.2 - - + +
1193A THR* 4.1 9.4 - - - +
1194A THR* 3.4 31.0 - - - +
1195A VAL* 3.8 20.2 - - + +
1198A VAL* 3.8 33.2 - - + -
1209A ALA 4.8 1.6 - - - +
1212A LEU 3.1 12.6 + - - +
1213A ALA* 3.4 14.8 - - - +
1215A LEU* 1.3 77.4 - - - +
1217A GLU* 1.3 56.1 + - - +
1219A ILE* 3.4 3.4 + - + +
1220A LYS* 3.0 35.2 + - - +
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Residues in contact with GLU1217 (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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1213A ALA 3.1 10.6 + - - +
1214A PRO* 3.3 15.0 - - + +
1216A LEU* 1.3 75.3 - - - +
1218A VAL* 1.3 58.8 + - + +
1220A LYS* 3.2 34.6 + - - +
1221A HIS* 3.0 31.6 + - + +
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Residues in contact with VAL1218 (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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1156A LEU* 4.3 4.9 - - + -
1159A LYS* 3.9 34.3 - - + +
1160A LEU* 4.2 12.6 - - + -
1163A ALA* 3.9 22.7 - - + -
1214A PRO 3.2 14.6 + - - +
1215A LEU* 3.2 10.2 + - - +
1217A GLU* 1.3 77.4 - - + +
1219A ILE* 1.3 57.4 + - - +
1221A HIS* 3.5 4.6 + - - +
1222A PHE* 2.9 33.7 + - + +
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Residues in contact with ILE1219 (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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1156A LEU* 4.1 15.0 - - + -
1160A LEU* 3.8 13.9 - - + -
1187A MET* 3.7 43.5 - - + +
1191A ARG* 3.7 29.8 - - + -
1192A PRO* 3.5 31.6 - - + +
1193A THR* 4.0 7.2 - - + -
1215A LEU 3.0 17.9 + - - +
1216A LEU* 3.7 7.4 - - - +
1218A VAL* 1.3 76.6 - - - +
1220A LYS* 1.3 57.5 + - - +
1222A PHE* 3.8 0.2 - - - +
1223A CYS* 3.0 31.2 + - - -
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Residues in contact with LYS1220 (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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1193A THR* 3.7 42.8 + - + -
1216A LEU* 3.0 19.1 + - - +
1217A GLU* 3.2 49.1 + - - +
1219A ILE* 1.3 75.1 - - - +
1221A HIS* 1.3 64.2 + - - +
1223A CYS* 4.0 2.2 - - - +
1224A GLN* 3.2 26.6 + - - +
1230A THR* 5.8 0.2 - - - -
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Residues in contact with HIS1221 (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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1217A GLU* 3.0 20.3 + - + +
1218A VAL* 3.8 5.8 - - - +
1220A LYS* 1.3 77.3 - - + +
1222A PHE* 1.3 63.7 + - - +
1224A GLN* 3.2 13.6 + - - +
1225A THR* 3.0 46.1 + - + -
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Residues in contact with PHE1222 (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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1152A THR* 3.8 37.0 - - + -
1155A VAL* 3.7 32.1 - - + -
1156A LEU* 3.6 30.1 - - + -
1159A LYS* 3.6 28.3 - - + -
1218A VAL 2.9 18.7 + - - +
1219A ILE 3.8 2.7 - - - +
1221A HIS* 1.3 80.3 + - - +
1223A CYS* 1.3 66.3 + - - +
1225A THR* 3.3 2.3 + - - -
1226A ASN* 2.8 69.4 + - + +
1228A VAL* 4.4 6.1 - - + -
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Residues in contact with CYS1223 (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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1191A ARG* 3.6 29.8 - - - -
1219A ILE* 3.0 22.4 + - - +
1220A LYS* 4.3 2.5 - - - +
1222A PHE* 1.3 79.8 - - - +
1224A GLN* 1.3 53.9 + - - +
1226A ASN 2.3 23.9 - - - +
1227A SER* 3.9 1.7 - - - -
1228A VAL* 3.4 39.3 + - + +
1230A THR* 3.4 28.9 - - + -
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Residues in contact with GLN1224 (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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1220A LYS 3.2 19.9 + - - +
1221A HIS* 3.4 12.0 - - - +
1222A PHE 3.1 0.4 - - - -
1223A CYS* 1.3 75.9 - - - +
1225A THR* 1.3 67.7 + - - +
1226A ASN 3.2 7.0 - - - +
1227A SER* 4.5 5.2 + - - -
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Residues in contact with THR1225 (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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1221A HIS* 3.0 37.7 + - + -
1222A PHE* 3.9 2.7 - - - -
1224A GLN* 1.3 77.6 - - - +
1226A ASN* 1.3 68.0 + - - +
1227A SER* 4.2 3.3 + - - -
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Residues in contact with ASN1226 (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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1222A PHE* 2.8 64.8 + - + +
1223A CYS 2.3 34.3 - - - +
1224A GLN 3.2 2.5 - - - +
1225A THR* 1.3 85.7 - - - +
1227A SER* 1.3 55.0 + - - +
1228A VAL* 3.5 10.5 - - + -
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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