Contacts of the strand formed by residues 203 - 207 (chain H) 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 ASP 203 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179H GLU* 2.9 17.7 + - + +
180H LYS* 3.4 27.9 + - + +
181H MET 2.7 34.1 + - - +
201H GLY 4.0 0.8 + - - -
202H ALA* 1.3 69.8 - - - +
204H VAL* 1.3 56.6 + - - +
205H THR* 4.1 2.3 + - - -
236H LYS* 2.6 40.7 + - - +
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Residues in contact with VAL 204 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181H MET* 3.4 17.3 - - + +
183H VAL* 4.2 13.5 - - + -
194H GLY* 3.9 21.3 - - - +
197H TRP* 4.3 3.1 - - + -
198H GLN* 3.8 30.4 - - + +
202H ALA* 3.4 23.3 + - + +
203H ASP* 1.3 81.7 + - - +
205H THR* 1.3 68.5 + - - +
234H GLY 4.1 1.1 + - - +
235H PHE* 4.1 19.2 - - + -
236H LYS* 3.1 31.9 + - - +
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Residues in contact with THR 205 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180H LYS* 4.4 9.7 + - - -
181H MET 3.1 9.1 + - - -
182H VAL* 3.3 14.1 - - + +
183H VAL* 2.9 23.6 + - - +
203H ASP* 4.1 1.9 + - - -
204H VAL* 1.3 75.8 - - - +
206H ALA* 1.3 71.4 + - - +
207H VAL* 4.4 11.2 - - + -
236H LYS* 3.3 39.5 - - + +
238H LYS* 4.6 15.9 - - + -
269H ILE* 4.6 10.5 - - + -
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Residues in contact with ALA 206 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183H VAL* 3.2 20.2 - - + +
185H GLY 4.9 1.6 - - - +
186H ALA* 4.5 11.2 - - + -
190H GLY 5.7 0.7 - - - +
205H THR* 1.3 73.8 - - - +
207H VAL* 1.3 62.1 + - - +
208H GLU 3.8 0.8 + - - -
235H PHE* 3.7 23.7 - - + -
236H LYS 2.9 7.3 + - - -
237H PHE* 3.5 20.6 - - + -
238H LYS* 2.8 26.7 + - - +
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Residues in contact with VAL 207 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182H VAL* 4.0 22.4 - - + -
183H VAL 2.8 11.2 + - - +
184H ILE* 3.7 1.0 - - - -
185H GLY* 2.9 26.0 + - - -
186H ALA 5.0 0.2 - - - -
205H THR* 4.4 2.9 - - + -
206H ALA* 1.3 73.9 - - - +
208H GLU* 1.3 59.4 + - - +
238H LYS* 3.5 13.5 - - + +
241H THR* 3.5 40.6 - - + +
243H VAL* 3.5 28.9 - - + -
258H ILE* 4.1 5.4 - - + -
269H ILE* 4.4 17.7 - - + -
481H NAD 3.4 7.3 - - - -
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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