Contacts of the strand formed by residues 222 - 228 (chain A) in PDB entry 6N8Q
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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177A ARG* 4.2 13.7 - - + +
216A TRP* 3.8 6.9 - - - -
217A ASP* 2.8 49.6 + - + +
220A GLY* 3.8 20.3 - - - +
221A SER* 1.3 78.3 - - - +
223A VAL* 1.3 66.6 + - - +
224A LEU* 3.3 25.1 - - + +
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Residues in contact with VAL 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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174A VAL* 4.0 19.7 - - + +
177A ARG* 3.9 28.7 - - + +
178A LEU* 3.8 21.3 - - + -
214A VAL* 4.1 8.1 - - + -
215A ILE 3.7 6.3 - - - +
216A TRP* 3.8 22.9 - - + -
222A ARG* 1.3 77.5 + - - +
224A LEU* 1.3 62.2 + - - +
225A TYR 3.3 29.4 - - - +
226A HIS* 4.3 1.8 - - + -
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Residues in contact with LEU 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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203A GLN* 3.8 37.0 - - + +
215A ILE* 2.9 15.6 + - + +
217A ASP* 3.7 41.5 - - + +
222A ARG* 3.3 31.9 - - - +
223A VAL* 1.3 75.2 - - - +
225A TYR* 1.3 63.2 + - + +
264A GLN* 5.0 8.5 + - - -
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Residues in contact with TYR 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 VAL* 5.4 1.3 - - + -
214A VAL 5.0 0.7 - - - -
215A ILE* 2.9 56.4 + - + -
223A VAL* 3.3 9.5 - - - +
224A LEU* 1.3 80.6 - - + +
226A HIS* 1.3 68.8 + - - +
227A PHE* 3.6 30.3 - + - -
245A LEU* 4.0 12.5 - - + +
257A TRP* 3.8 8.7 - - - +
258A PRO 2.7 30.6 + - - -
259A VAL* 3.9 20.6 - - + +
260A SER 4.5 11.0 - - - -
264A GLN* 3.6 17.7 - - - +
266A PRO* 3.2 27.7 - - + +
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Residues in contact with HIS 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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178A LEU* 3.8 19.9 - - + +
179A PRO* 4.2 18.8 - - + +
182A ALA* 4.3 18.6 - - + -
212A LEU* 4.1 11.9 - - + +
213A VAL 3.1 15.7 - - - +
214A VAL* 3.9 12.8 - - + -
223A VAL* 5.1 2.0 - - + -
225A TYR* 1.3 85.0 - - - +
227A PHE* 1.3 76.1 + - - +
228A LEU* 5.3 1.6 - - + -
264A GLN 3.9 3.6 + - - -
265A GLN* 3.3 46.1 - - + +
266A PRO* 3.5 3.6 - - - +
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Residues in contact with PHE 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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212A LEU* 3.5 4.7 - - - +
213A VAL* 3.0 69.9 + - + +
225A TYR* 3.6 33.7 - + - -
226A HIS* 1.3 84.0 - - - +
228A LEU* 1.3 60.9 + - - +
229A SER* 3.9 9.6 - - - -
236A ILE* 4.7 7.2 - - + -
245A LEU* 4.2 6.3 - - + -
247A SER* 5.0 2.5 - - - -
257A TRP* 3.4 75.8 - + + -
265A GLN* 5.0 2.5 - - - -
266A PRO* 4.1 11.0 - - + +
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Residues in contact with LEU 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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181A GLU 5.3 3.8 - - - +
182A ALA* 5.0 10.8 - - + -
210A ARG* 3.9 31.0 - - - +
211A GLY* 3.7 5.8 - - - -
212A LEU* 3.5 32.3 - - + +
226A HIS* 4.8 2.1 + - + +
227A PHE* 1.3 75.8 - - - +
229A SER* 1.3 76.7 + - - +
230A SER* 3.8 2.3 + - - -
257A TRP* 4.7 3.9 - - - -
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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
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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