Contacts of the helix formed by residues 1217 - 1227 (chain B) in PDB entry 2ZM3
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 SER1217 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1177B ARG* 3.4 4.0 - - - +
1215B GLY 4.2 0.4 + - - -
1216B LEU* 1.3 76.1 - - - +
1218B ASN* 1.3 66.9 + - - +
1219B GLU* 4.0 7.5 + - - +
1220B GLN* 3.0 33.5 + - - +
1221B VAL* 2.9 19.9 + - - +
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Residues in contact with ASN1218 (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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1176B VAL* 3.9 29.8 - - + +
1177B ARG* 2.9 31.1 + - - +
1211B GLN* 5.1 0.5 + - - -
1217B SER* 1.3 73.0 - - - +
1219B GLU* 1.3 67.3 + - + +
1221B VAL* 3.0 17.2 + - - +
1222B LEU* 3.0 12.9 + - - +
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Residues in contact with GLU1219 (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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1217B SER* 3.3 7.4 + - - +
1218B ASN* 1.3 81.0 - - + +
1220B GLN* 1.3 60.4 + - + +
1222B LEU* 3.5 24.7 - - + +
1223B ARG* 3.5 36.2 + - - +
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Residues in contact with GLN1220 (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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1215B GLY 4.2 3.5 - - - +
1216B LEU* 3.6 26.0 - - + +
1217B SER* 3.0 38.0 + - - +
1219B GLU* 1.3 76.1 - - + +
1221B VAL* 1.3 58.1 + - - +
1222B LEU 3.2 0.2 - - - -
1223B ARG* 3.3 25.9 + - - +
1224B PHE* 2.9 31.2 + - - +
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Residues in contact with VAL1221 (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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1176B VAL* 4.4 9.6 - - + +
1177B ARG* 3.5 47.1 - - + +
1184B LEU* 5.9 0.2 - - + -
1213B TYR* 3.5 36.1 - - + -
1216B LEU* 3.8 6.7 - - + -
1217B SER 2.9 18.9 + - - +
1218B ASN* 3.3 8.5 - - - +
1220B GLN* 1.3 76.0 - - - +
1222B LEU* 1.3 56.7 + - - +
1224B PHE* 4.2 5.8 - - - -
1225B VAL* 2.8 41.7 + - + +
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Residues in contact with LEU1222 (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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1176B VAL* 4.2 12.1 - - + +
1184B LEU* 3.4 49.7 - - + +
1218B ASN 3.0 10.6 + - - +
1219B GLU* 3.5 19.1 - - + +
1221B VAL* 1.3 77.0 - - - +
1223B ARG* 1.3 62.7 + - + +
1226B MET* 3.0 44.5 + - + +
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Residues in contact with ARG1223 (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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1219B GLU* 3.5 31.2 + - - +
1220B GLN* 3.3 41.6 + - - +
1221B VAL 3.3 0.4 - - - -
1222B LEU* 1.3 80.6 - - + +
1224B PHE* 1.3 67.8 + - - +
1226B MET* 4.5 8.7 - - + -
1227B GLU* 3.2 44.6 + - - +
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Residues in contact with PHE1224 (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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1213B TYR* 3.7 31.4 - + - -
1216B LEU* 3.8 20.4 - - + -
1220B GLN 2.9 18.9 + - - +
1221B VAL 3.6 2.5 - - - +
1223B ARG* 1.3 79.5 - - - +
1225B VAL* 1.3 58.9 + - + +
1227B GLU* 3.5 5.3 + - - +
1228B GLY 3.5 0.3 + - - -
1229B GLY* 2.7 35.8 + - - -
1230B LEU 3.3 42.4 - - - -
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Residues in contact with VAL1225 (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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1176B VAL 5.7 1.3 - - - +
1177B ARG 6.4 0.2 - - - -
1179B MET 3.9 7.9 - - - +
1181B PRO* 3.5 20.1 - - + +
1184B LEU* 3.8 20.9 - - + -
1196B TRP* 3.7 26.9 - - + -
1213B TYR* 3.3 40.8 - - + +
1221B VAL* 2.8 29.7 + - + +
1224B PHE* 1.3 72.3 - - + +
1226B MET* 1.3 64.5 + - - +
1227B GLU 3.3 0.5 + - - -
1228B GLY* 3.3 10.2 + - - -
1229B GLY 3.9 8.6 + - - +
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Residues in contact with MET1226 (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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1181B PRO* 4.2 21.0 - - - +
1184B LEU* 4.0 15.0 - - + +
1185B LYS* 3.8 38.4 - - + -
1222B LEU* 3.0 38.5 + - + +
1223B ARG* 4.1 8.7 - - + +
1225B VAL* 1.3 77.7 - - - +
1227B GLU* 1.3 64.6 + - + +
1228B GLY 3.3 0.4 - - - -
1251B TYR* 2.8 27.9 + - - +
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Residues in contact with GLU1227 (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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1223B ARG* 3.2 31.9 + - - +
1224B PHE* 3.5 2.2 + - - +
1225B VAL 3.2 0.2 - - - -
1226B MET* 1.3 86.2 - - + +
1228B GLY* 1.3 56.6 + - - +
1229B GLY 3.7 2.2 - - - -
1251B TYR* 4.6 3.4 - - - -
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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