Contacts of the helix formed by residues 1214 - 1224 (chain B) 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 SER1214 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1174B ARG* 3.9 2.9 - - - +
1212B GLY 4.3 0.4 + - - -
1213B LEU* 1.3 76.6 - - - +
1215B ASN* 1.3 59.5 + - - +
1216B GLU* 3.6 7.9 + - - +
1217B GLN* 2.9 39.9 + - - +
1218B VAL* 2.9 27.0 + - - +
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Residues in contact with ASN1215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1160B THR 4.8 8.9 + - - +
1162B TYR 4.7 5.2 + - - -
1163B TYR* 3.4 50.5 - - + +
1173B VAL* 3.8 11.3 - - + +
1174B ARG* 3.3 27.9 + - - +
1214B SER* 1.3 72.7 - - - +
1216B GLU* 1.3 62.3 + - - +
1218B VAL* 3.3 8.0 + - - +
1219B LEU* 3.3 27.3 + - - +
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Residues in contact with GLU1216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1163B TYR* 2.6 36.8 + - - +
1165B LYS* 5.5 0.7 - - - -
1214B SER* 3.3 7.2 + - - +
1215B ASN* 1.3 78.0 - - - +
1217B GLN* 1.3 61.5 + - + +
1219B LEU* 3.5 19.1 + - - +
1220B LYS* 3.3 44.2 + - - +
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Residues in contact with GLN1217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1212B GLY 4.2 3.1 - - - +
1213B LEU* 3.4 27.5 - - + +
1214B SER* 2.9 42.3 + - - +
1216B GLU* 1.3 75.9 - - + +
1218B VAL* 1.3 59.7 + - - +
1220B LYS* 3.2 14.4 + - + +
1221B PHE* 2.8 33.4 + - - +
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Residues in contact with VAL1218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1173B VAL* 3.9 26.7 - - + +
1174B ARG* 3.6 44.4 - - + +
1181B LEU* 5.2 0.9 - - + -
1210B TYR* 3.7 20.0 - - + -
1213B LEU* 4.2 4.9 - - + -
1214B SER 2.9 17.3 + - - +
1215B ASN* 3.3 10.5 + - - +
1217B GLN* 1.3 74.6 - - - +
1219B LEU* 1.3 65.7 + - - +
1221B PHE* 4.4 4.3 - - - -
1222B VAL* 2.9 40.4 + - + +
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Residues in contact with LEU1219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1163B TYR* 4.3 9.6 - - + -
1165B LYS* 4.9 10.3 - - + -
1173B VAL* 3.6 24.5 - - + -
1181B LEU* 3.5 37.4 - - + +
1215B ASN 3.4 10.8 - - - +
1216B GLU* 3.5 33.9 - - - +
1217B GLN 3.3 0.4 - - - -
1218B VAL* 1.3 77.5 - - - +
1220B LYS* 1.3 63.7 + - + +
1222B VAL* 4.3 0.2 - - - -
1223B MET* 3.1 45.0 + - + +
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Residues in contact with LYS1220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1216B GLU* 3.3 34.7 + - - +
1217B GLN* 3.2 15.4 + - + +
1219B LEU* 1.3 79.5 - - + +
1221B PHE* 1.3 64.5 + - - +
1223B MET* 4.8 7.2 - - + -
1224B ASP* 3.0 35.4 + - - +
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Residues in contact with PHE1221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1210B TYR* 3.8 29.8 - + - -
1213B LEU* 3.9 20.2 - - + -
1217B GLN 2.8 20.7 + - - +
1218B VAL 3.6 2.2 - - - +
1220B LYS* 1.3 75.2 - - - +
1222B VAL* 1.3 62.6 + - + +
1224B ASP* 3.4 4.3 + - - +
1225B GLY 3.4 4.3 + - - -
1226B GLY* 2.8 37.7 + - - -
1227B TYR 3.5 31.0 - - - -
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Residues in contact with VAL1222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1173B VAL 5.6 0.7 - - - +
1176B MET 3.9 5.4 - - - +
1178B PRO* 3.6 23.6 - - + +
1181B LEU* 3.9 18.8 - - + -
1193B TRP* 3.8 27.0 - - + -
1210B TYR* 3.5 40.8 - - + +
1218B VAL* 2.9 28.0 + - + +
1221B PHE* 1.3 73.9 - - + +
1223B MET* 1.3 62.5 + - - +
1225B GLY* 3.2 13.3 + - - -
1226B GLY 3.6 10.8 + - - +
1248B PHE* 4.1 0.9 - - - -
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Residues in contact with MET1223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1178B PRO* 3.9 14.1 - - - +
1181B LEU* 3.7 24.5 - - + +
1182B LYS* 3.7 36.6 - - + -
1219B LEU* 3.1 42.8 + - + +
1220B LYS* 4.0 6.5 - - + +
1222B VAL* 1.3 76.3 - - - +
1224B ASP* 1.3 65.8 + - - +
1225B GLY 3.3 1.2 + - - -
1248B PHE* 3.6 17.7 - - - -
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Residues in contact with ASP1224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1220B LYS* 3.0 22.0 + - - +
1221B PHE* 3.4 4.2 + - - +
1222B VAL 3.2 0.2 - - - -
1223B MET* 1.3 84.7 - - - +
1225B GLY* 1.3 57.2 + - - +
1226B GLY 3.7 1.6 - - - -
1248B PHE* 4.9 0.9 - - - -
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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