Contacts of the strand formed by residues 221 - 225 (chain A) in PDB entry 2ZH1
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 221 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120A PRO* 5.6 2.6 - - + +
129A ARG* 4.4 23.3 + - - +
218A ASP* 2.3 42.0 + - + +
219A PRO 3.3 0.6 - - - -
220A VAL* 1.3 79.9 - - + +
222A GLU* 1.3 60.9 + - - +
223A LYS* 3.0 30.4 + - - +
224A ARG* 3.8 21.2 + - + +
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Residues in contact with GLU 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A ASP* 3.6 27.4 - - - +
204A ALA* 4.2 9.7 - - - +
205A LYS* 4.7 9.3 - - - +
215A PHE* 4.5 4.9 - - - -
217A VAL* 3.5 21.3 - - + +
218A ASP 2.9 26.2 - - - +
219A PRO* 3.7 12.9 - - - +
221A ASP* 1.3 72.8 + - - +
223A LYS* 1.3 78.3 + - + +
224A ARG 3.5 0.2 - - - -
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Residues in contact with LYS 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215A PHE* 3.7 13.3 - - - -
221A ASP* 3.0 12.2 + - - +
222A GLU* 1.3 97.4 + - + +
224A ARG* 1.3 62.1 + - - +
225A ASN 4.0 0.3 + - - -
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Residues in contact with ARG 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A ALA* 5.1 6.9 - - - +
129A ARG* 3.0 50.9 - - - +
133A HIS* 4.3 9.4 - - - -
173A TYR* 5.0 2.0 - - - -
215A PHE* 3.4 9.5 - - - -
217A VAL* 3.6 0.7 - - - +
218A ASP* 3.2 52.4 + - + -
221A ASP* 3.8 13.4 + - + +
222A GLU 3.5 0.6 - - - -
223A LYS* 1.3 79.3 - - - +
225A ASN* 1.3 68.7 + - - +
226A VAL* 3.9 13.9 - - - +
31B C 3.9 20.2 + - - +
32B A 4.1 22.1 + - - -
33B A 5.8 1.0 + - - -
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Residues in contact with ASN 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213A GLU* 4.0 7.7 + - - -
214A PHE 2.9 26.5 + - - -
215A PHE* 3.4 30.7 - - + +
216A VAL 3.2 19.7 + - - -
223A LYS 4.0 0.6 + - - -
224A ARG* 1.3 79.7 + - - +
226A VAL* 1.3 63.3 + - - +
227A ALA* 2.7 29.6 + - - +
228A ALA* 3.1 40.9 + - + +
31B C 5.0 3.2 + - - -
32B A 5.0 2.4 + - - -
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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