Contacts of the strand formed by residues 222 - 230 (chain A) in PDB entry 4QY2
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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88A TYR* 3.9 1.9 + - - -
89A PRO* 3.5 21.7 - - - +
90A GLY* 4.2 6.7 - - - +
176A HIS* 3.4 5.9 - - - -
177A HIS* 2.7 41.3 + - + +
213A ARG* 3.6 27.4 - - - +
214A PRO 2.7 22.4 + - - -
216A VAL* 3.5 18.6 - - - +
219A GLN 3.1 20.2 + - - -
220A SER* 3.3 11.1 - - - +
221A GLY* 1.3 96.5 + - - -
223A ILE* 1.3 61.4 + - - +
224A ASP* 4.2 9.6 - - - +
199C SER 3.2 25.1 + - - -
200C SER* 3.9 7.7 + - - +
201C THR 6.3 0.2 - - - -
202C TYR 6.2 0.2 - - - -
203C ARG* 4.1 24.7 - - + +
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Residues in contact with ILE 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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88A TYR* 3.6 26.7 - - + +
89A PRO 3.0 10.9 + - - +
90A GLY* 3.1 20.1 - - - -
91A ALA 3.3 2.6 + - - -
138A PHE* 3.7 36.1 - - + -
139A TYR* 4.8 2.2 - - + -
144A TRP* 4.5 5.6 - - + -
174A GLY* 4.0 6.1 - - - -
175A ILE 3.4 6.1 - - - +
176A HIS* 4.0 10.8 - - + -
222A ARG* 1.3 77.3 - - - +
224A ASP* 1.3 64.6 + - - +
225A PHE* 3.7 34.6 - - + -
245A ILE* 3.7 26.9 - - + -
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Residues in contact with ASP 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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90A GLY* 4.4 2.6 - - - -
91A ALA* 3.3 21.1 + - - +
93A VAL* 5.3 5.1 - - + +
174A GLY* 3.1 2.8 - - - -
175A ILE 2.8 38.6 + - - +
177A HIS* 3.5 7.7 + - + +
222A ARG* 4.2 4.0 - - - +
223A ILE* 1.3 76.7 - - - +
225A PHE* 1.3 63.5 + - - +
226A HIS* 3.7 20.8 + - + -
203C ARG* 2.5 47.6 + - - +
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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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61A ILE* 3.9 14.8 - - + -
86A TYR* 3.7 37.7 - + - -
88A TYR 5.1 1.6 - - - -
91A ALA 2.8 15.5 + - - -
92A THR* 3.6 16.1 - - - +
93A VAL* 3.0 27.4 + - - +
139A TYR* 3.7 31.4 - + - -
142A LEU* 3.4 32.8 - - + -
172A MET* 3.9 13.9 - - + -
173A TRP 3.3 11.2 - - - +
174A GLY* 4.0 4.7 - - - -
223A ILE* 3.7 30.5 - - + -
224A ASP* 1.3 72.9 - - - +
226A HIS* 1.3 65.9 + - - +
245A ILE* 5.1 0.7 - - + -
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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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93A VAL* 3.3 36.0 - - + +
172A MET* 3.2 6.5 - - - +
173A TRP* 2.7 59.1 + - + +
175A ILE* 4.1 12.1 - - + +
177A HIS* 5.9 0.9 - - - -
202A TYR* 4.8 3.1 - - - +
204A ASN* 5.7 0.9 - - - -
206A PHE* 3.3 40.1 - + + -
224A ASP* 3.7 29.9 + - + -
225A PHE* 1.3 73.5 - - - +
227A TRP* 1.3 66.6 + - - +
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Residues in contact with TRP 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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92A THR* 4.1 5.6 - - + -
93A VAL 3.0 27.6 + - - -
94A ASN* 3.6 31.1 + - + +
97A ALA* 4.3 8.7 - - + -
98A LEU* 3.8 40.8 - - + +
101A LYS* 4.0 28.9 - - - -
170A LEU* 3.8 22.9 - - + -
171A ILE 3.2 13.7 - - - +
172A MET* 3.6 14.1 - - + -
173A TRP* 3.8 7.1 - - - -
202A TYR* 4.8 2.9 + - - -
226A HIS* 1.3 81.1 - - - +
228A THR* 1.3 81.8 + - + +
229A LEU* 4.7 6.1 - - + -
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Residues in contact with THR 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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170A LEU* 3.5 4.9 - - - +
171A ILE* 3.0 31.4 + - - +
173A TRP* 3.9 12.3 - - - -
202A TYR* 3.3 46.7 - - + +
227A TRP* 1.3 89.9 - - + +
229A LEU* 1.3 72.1 + - - +
236A ILE* 4.3 8.5 - - - +
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Residues in contact with LEU 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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101A LYS* 4.2 26.5 - - + +
168A GLU* 3.2 42.6 - - + +
169A HIS 3.1 4.0 - - - +
170A LEU* 3.7 40.6 - - + +
199A SER* 5.5 2.6 + - - -
201A THR* 4.7 9.0 + - - -
202A TYR* 5.9 1.2 - - - +
227A TRP* 4.7 5.2 - - + -
228A THR* 1.3 82.6 - - - +
230A VAL* 1.3 60.9 + - - +
231A GLN* 3.8 13.9 + - - +
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Residues in contact with VAL 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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161A TYR* 4.4 11.7 - - + -
163A ASN* 2.9 20.4 + - + -
168A GLU* 4.4 1.3 - - - -
169A HIS* 2.6 44.2 + - + +
171A ILE* 3.5 31.0 - - + -
199A SER* 5.6 2.7 - - - -
229A LEU* 1.3 72.8 - - - +
231A GLN* 1.3 63.6 + - - +
234A ASP* 3.5 33.2 - - + +
235A ASN 4.9 0.4 - - - -
236A ILE* 3.8 28.5 - - + -
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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