Contacts of the strand formed by residues 261 - 273 (chain A) in PDB entry 1ORH
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 ASP 261 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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186A GLU* 3.4 19.8 - - - +
228A VAL* 3.8 28.0 - - + -
259A ARG* 2.7 39.4 + - - +
260A ASN* 1.3 75.5 - - - +
262A TYR* 1.3 84.8 + - - +
306A THR* 3.7 4.9 - - - +
307A VAL* 2.9 35.9 + - - +
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Residues in contact with TYR 262 (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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186A GLU* 3.4 26.4 - - + +
188A ARG* 6.3 3.1 - - - -
261A ASP* 1.3 92.5 + - - +
263A VAL* 1.3 61.7 + - - +
264A HIS* 3.4 22.7 + - + +
304A TYR* 4.0 19.7 - + + -
305A LEU 3.1 6.5 - - - +
306A THR* 3.4 37.4 - - + +
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Residues in contact with VAL 263 (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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184A ALA* 3.9 23.1 - - + -
185A ILE 3.6 12.3 - - - +
228A VAL* 4.1 21.1 - - + -
262A TYR* 1.3 74.6 - - - +
264A HIS* 1.3 63.8 + - - +
265A ALA 3.9 9.9 - - - +
266A LEU* 5.4 2.2 - - + -
301A MET* 3.5 15.1 - - + +
304A TYR* 3.2 7.7 - - - -
305A LEU* 2.8 49.7 + - + -
307A VAL* 4.1 23.1 - - + -
313A ILE* 4.4 9.4 - - + -
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Residues in contact with HIS 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A ILE 3.3 4.0 + - - -
186A GLU* 4.2 4.0 - - + -
187A ASP* 3.0 37.1 + - + +
188A ARG* 3.5 46.1 + - + +
191A LYS* 4.2 24.0 - - + +
262A TYR* 3.4 32.8 + - + +
263A VAL* 1.3 73.0 - - - +
265A ALA* 1.3 62.9 + - + +
300A TYR* 3.8 4.7 - - - -
301A MET* 3.0 31.7 + - - +
304A TYR* 3.9 25.0 - + + +
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Residues in contact with ALA 265 (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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184A ALA* 3.7 4.2 - - - -
185A ILE* 3.2 38.6 + - + +
187A ASP* 5.3 0.2 - - + -
263A VAL* 3.8 5.2 - - - +
264A HIS* 1.3 82.8 - - + +
266A LEU* 1.3 64.7 + - - +
298A VAL* 3.7 18.2 - - + -
299A PHE 3.3 14.1 - - - +
300A TYR* 3.6 20.0 - - + -
301A MET* 4.2 5.8 - - - -
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Residues in contact with LEU 266 (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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182A VAL* 5.2 9.6 - - + -
183A THR 3.4 11.7 - - - +
184A ALA* 4.3 12.1 - - + -
253A PHE* 3.9 22.2 - - + -
255A LEU* 4.4 12.8 - - + -
263A VAL* 5.4 2.0 - - + -
265A ALA* 1.3 78.7 - - - +
267A VAL* 1.3 66.0 + - - +
298A VAL* 3.6 0.7 - - - +
299A PHE* 2.8 46.8 + - + +
301A MET* 4.8 11.9 - - + -
313A ILE* 5.7 4.0 - - + -
317A ILE* 6.1 1.3 - - + -
333A ILE* 3.9 35.2 - - + -
335A LEU* 4.2 10.5 - - + -
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Residues in contact with VAL 267 (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 TYR 3.8 0.3 - - - +
182A VAL* 3.2 6.9 - - - -
183A THR* 2.8 51.6 + - + +
185A ILE* 3.8 33.4 - - + -
222A VAL* 4.1 8.5 - - + -
266A LEU* 1.3 80.1 - - - +
268A ALA* 1.3 65.5 + - - +
269A TYR* 4.3 3.1 + - + -
287A PRO* 4.7 8.3 - - + -
296A GLN* 3.9 26.5 - - + -
297A THR 3.3 7.2 - - - +
298A VAL* 4.0 19.7 - - + -
299A PHE* 5.2 0.4 - - - -
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Residues in contact with ALA 268 (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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149A CYS* 4.1 17.5 - - - -
180A LEU* 4.7 9.4 - - + -
181A TYR 3.1 12.3 - - - +
182A VAL* 4.8 7.9 - - + -
234A ILE* 5.6 0.9 - - + -
267A VAL* 1.3 75.5 - - - +
269A TYR* 1.3 61.1 + - - +
296A GLN* 3.9 1.2 - - - +
297A THR* 2.9 35.1 + - - +
299A PHE* 4.0 21.7 - - + -
317A ILE* 6.1 2.5 - - + -
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Residues in contact with TYR 269 (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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149A CYS* 6.1 1.1 - - - +
180A LEU* 3.6 4.6 - - - +
181A TYR* 2.9 62.9 + + + +
183A THR* 4.5 17.0 - - + -
231A ALA* 3.4 26.9 - - + +
267A VAL* 4.8 2.5 - - + -
268A ALA* 1.3 75.9 - - - +
270A PHE* 1.3 64.2 + - - +
271A ASN* 4.0 14.8 - - - -
284A SER* 4.3 0.4 - - - -
285A THR* 3.4 21.3 - - - +
286A SER* 3.4 33.6 - - - -
287A PRO* 3.8 17.7 - - + -
288A GLU* 5.2 2.7 + - - -
295A LYS 5.3 0.4 - - - -
296A GLN* 4.0 8.3 - - + +
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Residues in contact with PHE 270 (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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146A MET* 4.0 15.7 - - + -
147A GLY 3.4 22.7 - - - -
149A CYS* 4.2 7.4 - - - -
150A LEU* 3.5 35.7 - - + -
179A THR 3.1 13.9 - - - +
180A LEU* 3.9 11.4 - - + -
181A TYR* 4.9 0.2 - - - -
269A TYR* 1.3 75.5 - - - +
271A ASN* 1.3 76.2 + - - +
272A ILE* 3.8 24.5 - - + -
283A PHE* 4.5 5.6 - + - -
285A THR* 2.7 48.0 + - + +
294A TRP* 3.8 36.6 - + + -
295A LYS 6.0 0.2 - - - -
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Residues in contact with ASN 271 (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 ALA* 3.4 4.7 - - - +
179A THR* 2.8 41.5 + - - +
181A TYR* 3.5 23.1 + - - -
269A TYR* 4.0 9.6 - - - -
270A PHE* 1.3 85.4 + - - +
272A ILE* 1.3 69.4 + - - +
273A GLU* 5.2 7.2 - - - +
283A PHE 3.6 6.3 - - - +
284A SER* 2.6 36.0 + - - -
285A THR 3.7 0.2 - - - +
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Residues in contact with ILE 272 (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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145A TRP* 4.5 4.9 - - + -
146A MET* 3.4 32.3 - - + -
150A LEU* 4.5 0.2 - - + -
175A PRO* 3.5 28.5 - - + -
177A ARG 3.6 3.1 - - - +
178A ALA* 3.8 19.3 - - + -
270A PHE* 3.8 20.9 - - + -
271A ASN* 1.3 83.1 - - - +
273A GLU* 1.3 73.1 + - - +
274A PHE* 4.2 13.0 - - + -
282A GLY* 3.3 1.4 - - - -
283A PHE* 3.1 51.6 + - + +
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Residues in contact with GLU 273 (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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175A PRO* 3.3 2.8 - - - +
176A ASP* 3.2 19.8 + - - +
177A ARG* 3.0 54.4 + - + +
179A THR* 5.2 2.1 + - - -
271A ASN* 5.2 6.4 - - + +
272A ILE* 1.3 83.8 - - - +
274A PHE* 1.3 64.3 + - - +
275A THR* 3.5 20.0 - - + +
280A ARG* 3.2 40.0 + - + -
281A THR 3.6 10.8 - - - +
282A GLY* 4.8 2.0 - - - -
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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