Contacts of the strand formed by residues 225 - 230 (chain A) in PDB entry 3ZXR
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 GLN 225 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135A GLU* 4.5 2.8 - - - +
136A PHE 3.3 17.0 - - - +
137A TYR* 3.4 34.7 + - + -
218A HIS* 3.0 15.1 + - - -
219A GLU* 2.8 32.6 + - + +
220A VAL 3.4 7.8 + - - -
221A GLY* 2.8 42.0 + - - +
224A GLY* 1.3 77.5 - - - +
226A ALA* 1.3 61.3 + - - +
271A ASN* 3.8 7.4 - - - +
272A GLY 2.7 28.7 + - - -
273A SER* 3.1 18.8 + - - +
505A P3S 4.3 3.0 + - - -
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Residues in contact with ALA 226 (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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135A GLU* 3.4 7.6 - - - +
136A PHE* 2.7 62.4 + - + -
138A ILE* 4.2 4.9 - - + -
199A ARG* 3.7 26.9 - - - +
217A HIS 3.4 5.4 - - - -
219A GLU* 3.8 5.6 - - - +
224A GLY 4.2 4.9 - - - +
225A GLN* 1.3 76.9 - - - +
227A GLU* 1.3 62.6 + - - +
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Residues in contact with GLU 227 (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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133A GLU* 2.8 17.1 - - + +
134A ALA 4.7 5.6 - - - +
135A GLU* 3.2 9.1 - - + +
136A PHE* 4.5 2.9 - - - -
199A ARG* 4.9 0.3 - - - -
216A GLY* 3.2 2.4 - - - -
217A HIS* 2.8 56.2 + - + +
219A GLU* 2.9 6.7 - - + +
226A ALA* 1.3 77.4 - - - +
228A ILE* 1.3 64.2 + - - +
229A ASN* 3.1 28.6 + - - +
502A MG 1.9 33.0 - - - -
504A MG 2.1 27.0 - - - -
505A P3S 2.9 0.6 + - - -
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Residues in contact with ILE 228 (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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132A ALA 5.0 1.4 - - - +
134A ALA 4.8 5.0 + - - +
136A PHE* 4.4 6.2 - - + -
199A ARG* 4.2 17.9 - - + +
202A MET* 3.8 36.6 - - + -
203A LEU* 3.7 9.4 - - + +
206A LEU* 3.7 13.0 - - + -
213A LEU* 3.7 25.8 - - + -
215A LYS 3.3 8.1 - - - +
216A GLY* 3.8 11.9 - - - -
217A HIS 4.9 0.2 - - - +
227A GLU* 1.3 79.6 - - - +
229A ASN* 1.3 71.9 + - - +
230A TYR* 4.3 2.8 + - + -
245A TYR* 3.3 35.1 + - + +
249A ILE* 4.1 10.5 - - + -
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Residues in contact with ASN 229 (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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132A ALA 4.6 3.1 + - - -
133A GLU* 3.9 16.6 - - - +
213A LEU* 3.5 9.9 - - - +
214A GLU* 2.9 30.6 + - + -
215A LYS* 2.7 51.9 + - - +
227A GLU* 3.1 33.7 + - - +
228A ILE* 1.3 80.2 + - - +
230A TYR* 1.3 60.5 + - - +
501A IQ1 4.0 22.9 - - + +
504A MG 4.1 1.7 - - - -
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Residues in contact with TYR 230 (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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132A ALA* 4.6 20.4 + - + +
134A ALA 6.2 0.7 - - - -
206A LEU* 5.6 0.2 - - + -
211A PHE* 3.8 24.2 - + + -
212A ILE 3.2 15.7 - - - +
213A LEU* 4.4 7.0 - - + -
214A GLU* 4.3 5.2 - - - +
228A ILE* 4.6 4.5 - - + -
229A ASN* 1.3 76.2 - - - +
231A GLN* 1.3 80.2 + - - +
232A PHE* 3.5 2.1 + - - -
238A ALA* 4.4 4.1 + - + -
241A ASP* 3.7 26.7 - - + -
242A MET* 3.3 42.7 + - + +
245A TYR* 3.5 43.1 - + + -
501A IQ1 3.5 14.7 - - - +
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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