Contacts of the strand formed by residues 227 - 234 (chain B) in PDB entry 3ORH
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 GLN 227 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A PRO* 3.6 29.3 - - + +
185B ILE* 3.4 21.1 + - + +
211B VAL* 3.7 21.4 - - + +
212B MET 3.3 13.0 - - - +
213B ALA* 4.7 5.4 - - + -
214B LEU 4.2 0.9 - - - -
223B TYR* 2.7 28.9 + - - -
225B PHE* 3.2 27.1 + - + -
226B PRO* 1.3 83.8 - - - +
228B MET* 1.3 62.5 + - - +
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Residues in contact with MET 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B TRP* 4.4 8.5 - - + -
46B GLU* 5.8 0.2 - - + -
49B TYR* 3.4 39.9 - - + -
171B LEU* 3.6 33.9 - - + -
174B TRP* 6.4 0.7 - - + -
185B ILE* 3.9 4.5 - - - -
210B GLU 3.8 0.2 - - - +
211B VAL* 3.4 6.2 - - - +
212B MET* 2.9 39.1 + - + +
214B LEU* 3.8 40.2 - - + +
223B TYR* 3.5 25.8 - - + +
227B GLN* 1.3 84.7 - - - +
229B ILE* 1.3 61.0 + - - +
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Residues in contact with ILE 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B TYR* 2.7 28.1 + - - -
174B TRP* 3.6 27.5 - - + -
185B ILE* 3.8 44.5 - - + +
186B THR* 3.9 17.7 - - - +
188B MET* 6.0 1.3 - - - -
189B PHE* 3.9 27.8 - - + -
209B THR* 2.6 37.0 - - + +
210B GLU 3.4 5.4 - - - +
211B VAL* 4.1 7.2 - - + -
228B MET* 1.3 76.2 - - - +
230B THR* 1.3 58.0 + - - +
231B PRO* 3.7 1.0 - - - +
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Residues in contact with THR 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B TYR* 3.3 20.1 - - - -
52B ALA* 3.5 32.8 - - - +
53B LEU* 3.9 9.4 - - + +
56B ALA* 4.4 2.9 - - + -
167B THR* 3.8 16.2 - - - +
209B THR* 3.3 6.5 - - - -
210B GLU* 2.8 56.8 + - - +
212B MET* 5.2 2.9 - - - +
229B ILE* 1.3 70.5 - - - +
231B PRO* 1.4 67.4 - - - +
232B LEU* 3.7 6.6 - - + +
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Residues in contact with PRO 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B LEU* 4.2 2.5 - - + -
166B LEU 4.3 0.4 - - - -
167B THR* 2.7 36.4 + - - +
168B TYR* 3.2 52.3 - - + +
174B TRP* 4.3 2.7 - - + -
189B PHE* 3.6 32.1 - - + -
208B ARG 3.6 6.5 - - - +
209B THR* 4.5 3.4 - - - +
229B ILE 3.7 7.0 - - - +
230B THR* 1.4 85.0 - - + +
232B LEU* 1.3 62.9 + - - +
233B VAL* 4.1 8.1 - - + -
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Residues in contact with LEU 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B ALA* 3.8 27.6 - - + -
59B SER* 5.4 4.0 - - - +
165B VAL* 4.4 13.2 - - + -
166B LEU 3.7 2.9 - - - -
206B ASN 3.6 3.6 - - - +
207B ILE* 3.7 0.3 - - - -
208B ARG* 2.9 47.9 + - + +
210B GLU* 3.5 40.6 - - + +
230B THR* 3.7 15.5 - - + +
231B PRO* 1.3 74.4 - - - +
233B VAL* 1.3 60.2 + - - +
234B THR* 4.0 4.1 + - - +
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Residues in contact with VAL 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160B LEU* 4.5 0.2 - - - +
164B GLY 3.8 0.7 - - - +
165B VAL* 3.6 2.2 - - - +
166B LEU* 2.7 57.6 + - + +
168B TYR* 4.8 2.2 - - + -
197B LEU* 3.7 30.7 - - + -
202B PHE* 3.4 47.4 - - + -
206B ASN 3.4 3.1 - - - -
207B ILE* 4.1 15.7 - - + -
231B PRO* 4.3 9.4 - - + -
232B LEU* 1.3 79.7 - - - +
234B THR* 1.3 60.6 + - - +
235B LYS 4.1 0.5 + - - -
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Residues in contact with THR 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163B GLY* 3.7 22.9 - - - +
164B GLY 3.3 4.3 + - - +
165B VAL* 4.5 10.2 - - - +
202B PHE* 3.5 13.7 - - - -
206B ASN* 2.9 44.2 + - - +
232B LEU* 4.9 3.1 + - - +
233B VAL* 1.3 75.2 + - - +
235B LYS* 1.3 74.7 + - - +
236B GLY 3.7 0.9 + - - -
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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