Contacts of the strand formed by residues 226 - 230 (chain E) in PDB entry 1OP8
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 GLY 226 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182E CYS* 3.3 4.7 - - - -
183E ALA 3.1 30.9 + - - -
189E ASP* 3.4 24.8 + - - -
190E SER* 4.8 3.8 - - - -
215E PHE 3.7 8.1 - - - -
216E GLY* 4.9 1.6 - - - -
224E GLY 3.7 0.8 + - - -
225E PRO* 1.3 71.6 - - - +
227E VAL* 1.3 59.5 + - - -
228E TYR* 3.3 19.8 - - - -
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Residues in contact with VAL 227 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172E TYR* 3.7 26.5 - - + +
176E ILE* 4.0 10.5 - - + -
180E MET* 4.1 27.1 - - + -
181E VAL 3.5 4.3 - - - +
182E CYS* 4.4 5.4 - - - -
213E THR* 4.3 0.9 - - - +
214E SER* 3.1 23.5 + - - -
215E PHE* 2.8 65.2 + - + +
225E PRO 3.7 3.4 - - - +
226E GLY* 1.3 73.0 - - - +
228E TYR* 1.3 66.6 + - - +
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Residues in contact with TYR 228 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138E VAL* 3.4 23.0 - - + +
160E ILE* 3.7 5.7 - - + +
180E MET* 3.1 8.6 - - - +
181E VAL* 2.7 55.2 + - + -
183E ALA* 4.0 22.0 - - + -
189E ASP* 4.4 2.1 + - - -
190E SER* 2.8 26.8 + - - -
199E LEU* 3.7 31.9 - - + -
211E GLY* 4.6 0.2 - - - -
212E VAL 3.3 8.1 - - - +
213E THR* 3.0 43.7 - - + -
226E GLY* 3.3 29.4 - - - -
227E VAL* 1.3 75.2 - - - +
229E ILE* 1.3 62.1 + - - +
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Residues in contact with ILE 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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99E ARG 4.7 2.9 - - - +
101E GLY* 5.1 2.9 - - - +
102E ASP* 2.9 39.3 - - + +
103E LEU* 3.3 34.3 - - + -
179E ASN 3.8 5.2 - - - +
180E MET* 4.5 6.7 - - + +
211E GLY* 3.0 23.1 - - - -
212E VAL* 2.8 41.4 + - + +
213E THR 4.7 0.2 - - - +
214E SER* 3.2 25.4 - - - -
228E TYR* 1.3 71.0 - - - +
230E LEU* 1.3 64.1 + - - +
231E LEU* 3.5 2.5 + - + +
234E HIS* 3.5 21.3 - - + +
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Residues in contact with LEU 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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127E GLY 5.1 0.4 - - - +
128E ASP 3.3 28.0 - - - +
129E ASP* 3.6 25.8 - - + +
130E VAL* 4.9 4.9 - - + -
165E ARG* 4.6 0.4 - - - +
178E MET 3.7 19.1 - - - +
179E ASN* 2.9 22.2 + - - +
181E VAL* 3.5 23.8 - - + -
210E ARG* 3.5 18.8 - - + +
228E TYR 3.3 4.2 + - - -
229E ILE* 1.3 71.0 - - - +
231E LEU* 1.3 73.7 + - + +
232E SER* 2.8 14.3 + - - +
234E HIS* 2.6 33.6 + - - -
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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
------------------------------------------------------------
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