Contacts of the helix formed by residues 1175 - 1179 (chain D) 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 PRO1175 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1135D ASP* 3.8 8.7 - - - +
1139D ARG* 3.0 40.8 - - - +
1173D LEU 3.8 4.2 - - - +
1174D LEU* 1.3 87.5 - - + +
1176D VAL* 1.3 65.4 + - - +
1177D ARG 3.2 0.9 + - - +
1178D TRP* 3.4 37.1 + - + +
1179D MET* 3.5 11.0 + - - +
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Residues in contact with VAL1176 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1174D LEU 3.4 5.4 + - - +
1175D PRO* 1.3 72.4 - - - +
1177D ARG* 1.3 65.2 + - + +
1178D TRP 3.2 1.8 + - - -
1179D MET* 3.2 26.5 + - - +
1184D LEU* 4.2 22.3 - - + +
1218D ASN* 4.0 32.3 - - + +
1221D VAL* 3.5 27.1 - - + +
1222D LEU* 4.3 15.5 - - + +
1225D VAL* 5.6 0.7 - - - +
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Residues in contact with ARG1177 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1175D PRO* 3.2 2.4 + - + +
1176D VAL* 1.3 77.2 - - + +
1178D TRP* 1.3 80.3 + - + +
1179D MET 3.6 1.1 - - - -
1196D TRP* 5.3 1.0 + - - -
1200D VAL* 4.0 13.3 - - - +
1211D GLN* 3.5 36.9 + - - +
1212D PRO* 2.8 45.8 + - + +
1213D TYR* 3.1 37.6 + - + -
1216D LEU 2.7 21.8 + - - -
1217D SER* 3.7 5.7 - - - +
1218D ASN* 2.8 29.3 + - - +
1221D VAL* 3.6 28.7 - - + +
1225D VAL* 6.3 0.4 - - - -
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Residues in contact with TRP1178 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1088D LYS* 5.3 10.1 - - + -
1135D ASP* 6.2 1.1 - - - -
1136D LEU 3.3 26.7 - - - +
1137D ALA* 3.3 16.9 - - + +
1139D ARG* 4.3 10.8 - - + -
1175D PRO* 3.4 31.9 + - + +
1176D VAL 3.2 0.8 - - - -
1177D ARG* 1.3 98.8 - - + +
1179D MET* 1.3 62.7 + - + +
1180D SER 3.8 0.2 + - - -
1196D TRP* 3.6 10.8 - - - -
1197D SER* 2.8 32.1 + - - +
1200D VAL* 3.6 27.6 - - + +
1201D VAL* 4.8 0.2 - - + -
1204D GLU* 2.9 45.8 + - - -
1211D GLN* 6.0 1.1 - - + -
1212D PRO* 3.9 20.9 - - + -
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Residues in contact with MET1179 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1134D ARG 5.9 1.1 - - - +
1168D LYS* 5.5 4.3 - - + -
1174D LEU* 4.1 33.9 - - + +
1175D PRO 3.5 13.5 - - - +
1176D VAL* 3.2 10.9 + - - +
1177D ARG 3.6 0.7 - - - -
1178D TRP* 1.3 81.3 - - + +
1180D SER* 1.3 64.5 + - - +
1183D SER* 3.5 39.7 - - - +
1184D LEU* 3.6 37.9 - - + +
1189D PHE* 4.0 16.6 - - + -
1196D TRP* 3.4 9.8 + - - -
1197D SER* 5.0 0.2 - - - -
1225D VAL* 3.8 6.4 - - - +
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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