Contacts of the strand formed by residues 222 - 227 (chain A) in PDB entry 4GV1
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 ARG 222 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147A MET* 3.5 21.8 - - - +
180A ILE* 3.6 27.6 - - + -
181A LEU 3.1 12.8 - - - +
182A LYS* 4.6 10.3 - - + +
183A LYS* 3.7 3.9 - - - +
218A GLN* 3.3 7.4 - - - +
219A THR* 2.9 39.4 + - - +
220A HIS* 5.8 3.2 - - - -
221A ASP* 1.3 108.5 + - - +
223A LEU* 1.3 65.6 + - - +
224A CYS* 4.6 6.5 - - - -
449A ILE* 3.7 17.4 - - - +
450A THR* 3.1 44.1 + - - +
451A PRO 4.1 11.7 + - - -
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Residues in contact with LEU 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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179A LYS 3.5 1.4 - - - +
180A ILE* 3.4 5.0 - - - +
181A LEU* 2.8 42.8 + - + +
183A LYS* 3.9 19.3 - - + -
186A ILE* 5.2 7.6 - - + -
195A THR* 3.6 30.1 - - + -
196A LEU* 5.5 0.9 - - + -
217A PHE 3.8 1.8 - - - -
218A GLN* 3.6 25.4 - - + +
222A ARG* 1.3 73.2 - - - +
224A CYS* 1.3 62.0 + - - +
225A PHE* 4.3 8.1 - - + -
469A PHE* 3.9 27.8 - - + -
472A PHE* 4.0 29.4 - - + -
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Residues in contact with CYS 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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147A MET* 3.9 26.5 - - - -
178A MET* 4.1 18.6 - - + -
179A LYS 3.3 4.3 - - - -
180A ILE* 4.4 4.9 - - - -
215A TYR 4.0 0.3 - - - +
216A SER* 3.3 7.1 - - - -
217A PHE* 2.9 74.2 + - + +
219A THR* 5.2 1.3 - - - -
222A ARG* 4.6 9.2 - - - -
223A LEU* 1.3 77.5 - - - +
225A PHE* 1.3 61.5 + - - +
226A VAL 4.0 0.4 - - - -
472A PHE* 4.6 0.9 - - - -
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Residues in contact with PHE 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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177A ALA 3.4 2.8 - - - +
178A MET* 3.2 3.4 - - - -
179A LYS* 2.8 58.0 + - + +
181A LEU* 3.9 24.0 - - + -
195A THR* 3.9 18.6 - - + -
198A GLU* 4.3 9.9 - - + -
199A ASN* 3.8 38.6 - - + -
202A LEU* 4.3 15.9 - - + -
213A LEU* 4.0 12.1 - - + -
215A TYR 3.6 4.0 - - - -
216A SER* 4.4 2.9 - - - -
223A LEU* 4.4 5.4 - - + -
224A CYS* 1.3 76.1 - - - +
226A VAL* 1.3 61.4 + - - +
227A MET* 3.7 17.9 + - + +
472A PHE* 3.6 25.6 - + - -
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Residues in contact with VAL 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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150A PHE* 4.0 12.3 - - + -
167A VAL* 4.8 2.7 - - + -
176A TYR* 3.4 41.3 - - + -
177A ALA 3.7 3.1 - - - +
178A MET* 3.7 30.5 - - + +
213A LEU* 3.5 2.9 - - - +
214A LYS* 2.8 26.4 + - + +
215A TYR* 2.8 35.7 + - + +
217A PHE* 4.0 20.4 - - + -
225A PHE* 1.3 72.6 - - - +
227A MET* 1.3 58.8 + - - +
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Residues in contact with MET 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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164A VAL* 5.2 0.4 - - + -
176A TYR* 3.3 12.2 - - - +
177A ALA* 2.8 37.6 + - + +
179A LYS* 3.7 37.0 - - + +
198A GLU* 5.0 5.8 - - - +
202A LEU* 4.1 21.5 - - + -
211A THR* 3.8 15.5 - - + -
212A ALA 3.4 11.4 - - - +
213A LEU* 3.8 17.9 - - + -
214A LYS 4.4 0.4 - - - +
225A PHE* 3.8 13.2 - - + +
226A VAL* 1.3 77.6 - - - +
228A GLU* 1.3 60.1 + - - +
229A TYR 3.3 0.2 + - - -
291A THR* 6.4 0.9 - - - -
292A ASP 6.2 1.1 - - - -
501A 0XZ 3.7 30.3 - - + -
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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