Contacts of the strand formed by residues 296 - 307 (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 GLN 296 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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219A VAL* 3.3 6.6 - - - +
220A ASP 3.0 30.6 + - - +
221A VAL* 3.7 4.4 - - - +
222A VAL* 2.7 40.6 + - + +
267A VAL* 3.9 15.9 - - + -
268A ALA 3.9 4.3 - - - +
269A TYR* 4.0 12.1 - - + +
285A THR* 2.8 29.6 + - - +
286A SER 3.6 11.9 + - - -
287A PRO* 3.7 20.7 - - + +
289A SER 5.4 1.4 + - - -
294A TRP 4.1 2.5 - - - -
295A LYS* 1.3 89.4 + - - +
297A THR* 1.3 63.4 + - - +
298A VAL* 4.7 0.6 - - - +
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Residues in contact with THR 297 (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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148A TYR* 4.5 0.7 - - - +
149A CYS* 3.4 37.6 + - - +
217A PRO* 3.9 16.2 - - + -
218A LEU 3.3 8.1 - - - +
219A VAL* 4.5 7.8 - - - +
267A VAL* 3.3 5.6 - - - -
268A ALA 2.9 39.8 + - - -
294A TRP 5.4 0.7 + - - -
296A GLN* 1.3 74.6 + - - +
298A VAL* 1.3 64.5 + - - +
299A PHE* 3.6 28.0 - - + -
352A MET* 4.3 10.9 - - + +
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Residues in contact with VAL 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A ILE* 4.7 6.3 - - + -
187A ASP* 5.1 1.8 - - - +
216A GLU 4.7 0.3 - - - +
217A PRO* 3.4 5.1 - - - +
218A LEU* 2.6 48.7 + - + +
220A ASP* 4.7 14.6 - - + +
222A VAL* 3.8 29.4 - - + -
265A ALA* 3.7 24.9 - - + -
266A LEU 3.6 3.8 - - - +
267A VAL* 4.0 7.9 - - + -
296A GLN 4.7 0.9 - - - +
297A THR* 1.3 78.0 - - - +
299A PHE* 1.3 65.2 + - - +
300A TYR* 4.0 23.7 + - + +
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Residues in contact with PHE 299 (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 12.8 - - - -
217A PRO* 3.8 24.0 - - + -
265A ALA* 3.3 4.2 - - - +
266A LEU* 2.8 49.7 + - + +
268A ALA* 4.0 17.3 - - + -
297A THR* 3.6 32.1 - - + -
298A VAL* 1.3 74.1 - - - +
300A TYR* 1.3 63.2 - - - +
301A MET* 3.8 1.2 + - - +
317A ILE* 5.2 4.9 - - + -
331A PHE* 3.9 32.1 - + + -
333A ILE* 3.9 27.6 - - + -
350A TYR* 4.0 26.9 + + + +
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Residues in contact with TYR 300 (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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187A ASP* 2.9 22.8 + - + -
190A TYR* 2.9 32.9 - - - +
191A LYS* 3.3 40.6 - - + -
194A LYS* 4.4 11.7 - - + -
195A ILE* 6.4 1.3 - - + -
214A ILE* 3.2 32.9 + - + +
216A GLU 5.7 3.5 + - - -
217A PRO* 5.9 0.4 - - - +
218A LEU* 3.5 31.6 - - + -
220A ASP* 5.5 0.2 + - - -
264A HIS 3.8 4.0 - - - -
265A ALA* 3.6 19.5 - - + -
298A VAL* 4.0 14.0 + - + +
299A PHE* 1.3 73.4 - - - +
301A MET* 1.3 58.7 + - - +
350A TYR* 2.6 28.2 + - - -
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Residues in contact with MET 301 (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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191A LYS* 3.3 17.3 - - - -
214A ILE* 4.7 2.9 - - - +
263A VAL* 3.5 29.2 - - + +
264A HIS 3.0 22.1 + - - +
265A ALA* 4.2 11.2 - - - -
266A LEU* 4.8 8.5 - - - -
299A PHE 5.1 0.4 - - - +
300A TYR* 1.3 75.8 - - - +
302A GLU* 1.3 68.8 + - - +
303A ASP 3.3 20.7 - - - +
305A LEU* 3.8 34.1 - - + -
335A LEU* 3.7 27.6 - - + -
348A THR* 5.3 4.5 - - - +
350A TYR* 4.2 4.7 - - - +
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Residues in contact with GLU 302 (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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191A LYS* 3.6 12.8 + - - -
195A ILE* 5.3 3.9 - - + +
211A ASP* 4.1 27.0 - - - +
214A ILE* 3.9 21.8 - - + +
301A MET* 1.3 74.7 - - - +
303A ASP* 1.3 75.8 + - - +
304A TYR* 5.6 0.5 - - - -
348A THR* 5.1 8.7 + - + +
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Residues in contact with ASP 303 (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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191A LYS* 4.6 1.0 + - - -
301A MET* 3.3 31.7 - - - +
302A GLU* 1.3 97.7 - - - +
304A TYR* 1.3 69.7 + - - +
344A LEU* 4.3 27.4 - - + +
346A CYS* 5.3 4.7 - - - +
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Residues in contact with TYR 304 (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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191A LYS* 4.9 6.3 - - - +
262A TYR* 4.0 20.3 - + + -
263A VAL 3.2 15.9 - - - +
264A HIS* 3.9 24.0 - + + -
301A MET* 4.3 0.7 - - - -
302A GLU 5.6 0.2 - - - -
303A ASP* 1.3 81.5 - - + +
305A LEU* 1.3 78.8 + - - +
306A THR* 3.9 16.7 + - - -
342A CYS* 4.5 4.3 - - - -
344A LEU* 3.9 8.5 - - - +
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Residues in contact with LEU 305 (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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261A ASP 3.8 0.2 - - - +
262A TYR* 3.1 9.0 - - - +
263A VAL* 2.8 45.4 + - + -
301A MET* 3.8 24.0 - - + -
304A TYR* 1.3 76.1 - - - +
306A THR* 1.3 62.9 + - - +
307A VAL* 3.8 8.2 + - + -
313A ILE* 4.0 38.1 - - + -
335A LEU* 5.1 9.4 - - + -
337A PHE* 4.0 23.8 - - + -
342A CYS* 4.4 2.9 - - - -
344A LEU* 3.1 36.3 - - + -
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Residues in contact with THR 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A ASP 3.7 4.7 - - - +
262A TYR* 3.4 34.0 - - + +
304A TYR* 3.9 10.6 + - - -
305A LEU* 1.3 73.9 - - - +
307A VAL* 1.3 62.8 + - - +
311A GLU* 4.5 1.4 - - - +
337A PHE* 3.8 5.4 - - - -
339A GLY* 5.7 0.2 - - - -
341A LEU* 3.8 37.9 + - + +
342A CYS* 3.6 34.2 + - - +
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Residues in contact with VAL 307 (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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228A VAL* 3.9 16.8 - - + -
257A VAL* 3.5 36.3 - - + -
260A ASN* 3.3 3.3 - - - +
261A ASP 2.9 44.1 + - - +
263A VAL* 4.1 7.0 - - + -
305A LEU* 4.1 15.5 - - + -
306A THR* 1.3 79.0 - - - +
308A LYS* 1.3 66.3 + - - +
311A GLU* 3.6 3.4 - - - +
313A ILE* 4.3 8.5 - - + -
337A PHE* 3.5 27.8 - - + -
341A LEU* 5.2 0.5 - - - +
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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