Contacts of the strand formed by residues 222 - 230 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199A SER 3.1 26.7 + - - -
200A SER* 3.8 9.5 + - - +
202A TYR 6.0 0.8 - - - +
203A ARG* 4.4 24.7 - - + +
88E TYR* 3.8 2.3 + - - -
89E PRO* 3.4 24.0 - - - +
90E GLY* 4.2 8.3 - - - +
176E HIS* 3.4 4.9 - - - -
177E HIS* 2.7 40.3 + - + +
213E ARG* 3.6 30.4 - - - +
214E PRO 2.8 20.2 + - - -
216E VAL* 3.8 18.4 - - - +
219E GLN 3.3 16.8 + - - -
220E SER 3.1 13.3 + - - -
221E GLY* 1.3 89.6 + - - -
223E ILE* 1.3 62.6 + - - +
224E ASP* 4.2 1.8 - - - +
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Residues in contact with ILE 223 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88E TYR* 3.6 26.5 - - + +
89E PRO 3.0 11.9 + - - +
90E GLY* 3.1 21.3 - - - -
91E ALA 3.3 3.3 + - - +
138E PHE* 3.9 26.0 - - + -
139E TYR* 4.5 6.5 - - + -
144E TRP* 5.0 2.7 - - + -
174E GLY* 4.0 13.9 - - - -
175E ILE 3.4 7.0 - - - +
176E HIS* 4.0 9.9 - - + -
222E ARG* 1.3 76.8 - - - +
224E ASP* 1.3 64.2 + - - +
225E PHE* 3.5 34.6 + - + -
245E ILE* 3.7 24.5 - - + -
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Residues in contact with ASP 224 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A ARG* 2.5 51.2 + - - +
90E GLY* 4.8 1.2 - - - -
91E ALA* 3.5 20.8 + - - +
93E VAL* 5.9 4.8 - - + +
174E GLY* 3.2 2.4 - - - -
175E ILE* 2.7 37.0 + - + +
177E HIS* 4.0 10.3 - - - +
222E ARG* 4.2 2.0 - - - +
223E ILE* 1.3 77.5 + - - +
225E PHE* 1.3 61.8 + - - +
226E HIS* 3.6 22.0 + - + -
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Residues in contact with PHE 225 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61E ILE* 4.1 13.9 - - + -
86E TYR* 3.8 37.2 - + - -
88E TYR 5.0 1.8 - - - -
90E GLY* 5.1 0.2 - - - -
91E ALA 2.9 10.6 + - - -
92E THR* 3.5 18.2 - - - +
93E VAL* 3.0 28.2 + - - +
139E TYR* 3.7 28.0 - + - -
142E LEU* 3.4 29.4 - - + -
172E MET* 3.9 13.5 - - + -
173E TRP 3.3 13.7 - - - +
174E GLY* 3.9 5.4 - - - -
223E ILE* 3.5 34.8 - - + -
224E ASP* 1.3 71.5 - - - +
226E HIS* 1.3 65.4 + - - +
245E ILE* 4.8 1.1 - - + -
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Residues in contact with HIS 226 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93E VAL* 3.7 33.1 - - + +
172E MET* 3.3 6.7 - - - +
173E TRP* 2.9 59.3 + - + -
175E ILE* 4.0 11.5 - - + +
177E HIS* 6.0 0.2 - - - -
202E TYR* 4.8 2.2 - - - +
204E ASN* 5.1 2.7 - - - -
206E PHE* 3.2 41.6 - + - -
224E ASP* 3.6 33.2 + - + -
225E PHE* 1.3 73.4 - - - +
227E TRP* 1.3 65.7 + - - +
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Residues in contact with TRP 227 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398D HIS* 5.7 1.1 - - + -
92E THR* 4.1 5.2 - - + -
93E VAL* 3.0 27.5 + - + -
94E ASN* 3.6 29.4 + - + +
97E ALA* 4.3 8.1 - - + -
98E LEU* 3.7 37.1 - - + +
101E LYS* 3.5 35.0 - - - -
170E LEU* 3.8 21.3 - - + -
171E ILE 3.1 13.7 - - - +
172E MET* 3.7 15.3 - - + -
173E TRP* 3.8 4.0 - - - -
202E TYR* 4.5 5.5 + - - -
226E HIS* 1.3 79.2 - - - +
228E THR* 1.3 78.2 + - - +
229E LEU* 4.7 6.5 - - + -
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Residues in contact with THR 228 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170E LEU* 3.6 3.1 - - - +
171E ILE* 2.9 36.7 + - - +
173E TRP* 3.3 20.8 - - - -
201E THR* 6.0 0.7 - - - +
202E TYR* 3.3 43.5 - - + -
227E TRP* 1.3 86.1 + - - +
229E LEU* 1.3 80.3 + - - +
230E VAL* 5.5 0.2 - - - -
236E ILE* 4.6 5.6 - - - +
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Residues in contact with LEU 229 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395D GLU* 5.3 8.5 - - - +
101E LYS* 4.0 29.2 - - + +
168E GLU* 3.3 43.5 - - + +
169E HIS 3.3 3.4 - - - +
170E LEU* 3.8 39.0 - - + +
199E SER* 5.4 2.9 + - - -
201E THR* 4.8 8.5 + - - -
202E TYR* 5.9 0.2 - - - +
227E TRP* 4.7 4.3 - - + -
228E THR* 1.3 84.5 - - + +
230E VAL* 1.3 62.8 + - - +
231E GLN* 3.8 10.2 + - - +
253E LEU* 6.5 0.2 - - + -
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Residues in contact with VAL 230 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161E TYR* 4.6 8.1 - - + -
163E ASN* 3.0 19.6 + - + -
168E GLU* 3.4 1.2 - - - -
169E HIS* 2.6 43.2 + - + +
171E ILE* 3.7 24.0 - - + -
199E SER* 5.5 3.8 - - - -
228E THR* 5.5 0.2 - - - -
229E LEU* 1.3 72.6 - - - +
231E GLN* 1.3 62.3 + - - +
234E ASP* 3.6 32.5 - - + +
235E ASN 4.6 2.9 - - - +
236E ILE* 3.6 37.9 - - + -
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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