Contacts of the strand formed by residues 273 - 276 (chain F) in PDB entry 1ZMC
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 VAL 273 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163F ASP 4.8 2.2 - - - +
164F THR* 3.2 20.0 - - + +
166F VAL* 4.9 5.6 - - + -
174F LEU* 4.5 22.7 - - + -
178F PRO* 3.5 23.8 - - + -
180F LYS 3.4 1.8 + - - -
181F MET* 3.4 35.7 - - + +
182F VAL 3.2 14.6 + - - -
254F ILE* 4.4 0.7 - - - -
271F CYS* 3.1 15.5 - - - -
272F ASP* 1.3 86.6 - - + +
274F LEU* 1.3 63.5 + - - +
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Residues in contact with LEU 274 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158F ILE* 4.0 19.7 - - + -
164F THR 2.7 12.3 + - - +
165F ILE* 3.4 13.9 - - + +
166F VAL* 2.8 31.6 + - - +
182F VAL* 3.5 20.9 - - + +
184F ILE* 3.9 31.0 - - + -
246F ALA* 3.6 31.0 - - + -
254F ILE* 4.1 9.4 - - + +
256F VAL* 4.0 20.6 - - + -
271F CYS* 4.0 3.1 - - - -
273F VAL* 1.3 73.4 - - - +
275F LEU* 1.3 60.3 + - - +
276F VAL* 3.9 4.2 + - + -
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Residues in contact with LEU 275 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166F VAL* 3.6 9.2 - - + +
167F SER 3.7 30.7 - - - +
168F SER* 3.9 3.8 - - - +
171F ALA* 4.0 11.4 - - + -
181F MET* 4.5 14.8 - - + -
182F VAL 2.8 14.8 + - - +
183F VAL* 3.9 29.1 - - + +
184F ILE* 2.8 33.6 + - - +
193F LEU* 3.7 32.8 - - + -
273F VAL 4.1 0.6 - - - -
274F LEU* 1.3 72.7 - - - +
276F VAL* 1.3 58.8 + - - +
277F CYS* 3.5 16.1 + - - -
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Residues in contact with VAL 276 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152F VAL* 4.7 8.3 - - - +
153F THR 4.7 2.7 - - - +
155F PHE* 3.8 27.4 - - + +
158F ILE* 4.4 8.7 - - + -
160F ILE* 4.0 28.7 - - + -
165F ILE* 4.4 14.4 - - + -
166F VAL 3.0 16.5 + - - +
167F SER* 4.0 9.4 - - - -
168F SER 4.6 0.7 + - - -
184F ILE* 4.2 20.2 - - + -
274F LEU* 4.5 3.1 - - + +
275F LEU* 1.3 77.3 - - - +
277F CYS* 1.3 61.1 + - - +
278F ILE* 3.7 19.9 + - + +
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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
------------------------------------------------------------
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