Contacts of the helix formed by residues 1258 - 1265 (chain C) 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 SER1258 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1191C THR* 6.1 1.8 - - - -
1195C VAL* 4.6 3.8 - - - -
1257C PRO* 1.3 76.4 - - - +
1259C PHE* 1.3 65.4 + - - +
1260C LEU* 3.7 10.2 + - - +
1261C GLU* 3.0 34.0 + - - +
1262C ILE* 3.1 23.0 + - - +
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Residues in contact with PHE1259 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1120C ALA* 3.7 28.7 - - + +
1123C MET* 3.5 36.1 - - + -
1124C ALA* 3.8 13.0 - - + -
1127C ASN* 3.3 28.7 - - + -
1191C THR* 5.5 0.2 - - - -
1194C ASP* 3.6 33.4 - - + -
1195C VAL* 3.7 18.8 - - + -
1198C PHE* 3.7 28.0 - + + -
1258C SER* 1.3 72.9 - - - +
1260C LEU* 1.3 61.1 + - + +
1262C ILE* 3.1 12.2 + - + +
1263C ILE* 2.9 34.6 + - - +
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Residues in contact with LEU1260 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1124C ALA* 3.7 24.5 - - + +
1258C SER* 3.3 9.6 + - - +
1259C PHE* 1.3 78.4 - - - +
1261C GLU* 1.3 58.2 + - + +
1263C ILE* 3.5 1.0 + - + -
1264C SER* 2.9 28.4 + - - -
1279C PHE* 4.3 6.3 - - + -
1280C TYR* 3.5 31.6 - - + -
1285C ASN* 3.5 31.4 - - - +
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Residues in contact with GLU1261 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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986B VAL* 3.5 29.9 - - + +
987B TYR* 4.0 25.4 - - - +
1049B ASN* 5.9 0.3 + - - -
1256C ARG 4.6 0.7 - - - +
1257C PRO* 3.3 10.4 - - - +
1258C SER* 3.0 36.1 + - - +
1259C PHE 3.2 0.4 - - - -
1260C LEU* 1.3 76.7 - - + +
1262C ILE* 1.3 65.7 + - - +
1264C SER* 3.3 8.0 + - - -
1265C SER* 3.1 23.7 + - - -
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Residues in contact with ILE1262 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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986B VAL* 4.6 2.2 - - + -
1116C ALA* 6.1 0.2 - - + -
1120C ALA* 4.3 7.4 - - + -
1195C VAL* 4.4 7.9 - - + -
1198C PHE* 3.8 44.9 - - + -
1244C LEU* 4.7 21.3 - - + -
1248C CYS* 4.0 17.0 - - - -
1257C PRO* 3.9 18.2 - - + -
1258C SER 3.1 15.1 + - - +
1259C PHE* 3.1 16.7 + - + +
1261C GLU* 1.3 74.0 - - - +
1263C ILE* 1.3 65.0 + - - +
1265C SER* 2.9 22.9 + - - -
1266C ILE* 3.2 18.1 - - + +
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Residues in contact with ILE1263 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1117C GLY* 4.1 7.9 - - - +
1120C ALA* 3.7 18.6 - - + +
1121C ASP* 3.5 39.9 - - + +
1124C ALA* 4.3 9.4 - - + -
1259C PHE 2.9 20.8 + - - +
1260C LEU 3.8 3.4 - - - +
1262C ILE* 1.3 77.0 - - - +
1264C SER* 1.3 59.2 + - - +
1266C ILE* 2.9 11.1 + - + +
1267C LYS* 2.8 31.0 + - + -
1270C MET* 5.7 0.7 - - + -
1274C PHE* 3.9 19.7 - - + -
1280C TYR* 3.6 36.3 - - + -
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Residues in contact with SER1264 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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985B ASP 5.2 0.4 - - - -
986B VAL 5.7 1.3 - - - -
989B PRO* 5.5 7.1 - - - +
990B ASP* 5.3 10.0 + - - +
1260C LEU 2.9 19.7 + - - -
1261C GLU* 3.4 10.3 - - - -
1263C ILE* 1.3 78.4 - - - +
1265C SER* 1.3 59.8 + - - +
1266C ILE 3.3 0.9 + - - -
1267C LYS* 3.4 31.5 + - - +
1280C TYR* 3.3 22.7 + - - -
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Residues in contact with SER1265 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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981B PHE* 3.6 24.3 - - - -
985B ASP* 3.5 18.9 - - - +
986B VAL* 3.4 34.2 - - - +
1244C LEU* 4.3 3.3 - - - +
1261C GLU 3.1 10.3 + - - -
1262C ILE* 2.9 15.1 + - - -
1263C ILE 3.1 0.2 - - - -
1264C SER* 1.3 76.2 - - - +
1266C ILE* 1.3 63.7 + - - +
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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