Contacts of the strand formed by residues 291 - 301 (chain A) in PDB entry 2Q5H
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 GLU 291 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92A GLY 4.7 0.9 - - - +
93A LEU* 3.7 23.7 - - + +
274A ASN* 4.4 17.0 + - + -
275A SER 3.7 6.1 - - - +
276A PHE* 3.4 37.1 - - + -
289A VAL* 3.4 13.3 - - - +
290A ARG* 1.3 77.9 - - - +
292A PHE* 1.3 68.4 + - - +
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Residues in contact with PHE 292 (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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244A PRO 4.5 7.2 - - - -
274A ASN* 3.1 8.3 - - - -
275A SER* 3.0 58.1 + - - -
276A PHE 4.3 0.4 - - - -
277A ARG* 3.6 41.3 - - + -
289A VAL* 3.7 31.2 - - + -
291A GLU* 1.3 83.7 - - - +
293A THR* 1.3 59.0 + - - +
294A MET* 3.7 32.3 - - + -
528A GLY* 6.0 4.9 - - - +
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Residues in contact with THR 293 (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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104A LYS* 3.5 28.0 + - - +
108A ILE* 4.8 5.6 - - + -
272A ILE* 4.2 7.4 - - + -
273A GLY* 3.3 17.0 - - - +
274A ASN* 2.4 20.9 + - - +
292A PHE* 1.3 74.2 - - - +
294A MET* 1.3 72.4 + - - +
526A GLY* 4.4 0.2 - - - -
527A LEU* 3.3 50.5 + - + +
528A GLY 4.4 1.4 + - - -
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Residues in contact with MET 294 (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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244A PRO 6.0 1.1 - - - +
245A GLU* 5.9 2.2 - - + -
246A THR* 4.7 3.8 - - + +
271A GLN 3.7 0.6 - - - +
272A ILE* 3.2 4.0 - - - +
273A GLY 2.7 35.5 + - - +
275A SER* 3.9 17.9 - - - +
292A PHE* 3.7 33.0 - - + +
293A THR* 1.3 81.7 - - - +
295A ALA* 1.3 60.2 + - - +
296A GLU* 3.9 24.9 - - + +
524A SER* 3.4 26.5 - - - +
525A PHE 3.3 17.9 - - - +
526A GLY* 3.9 13.5 - - - -
527A LEU* 4.2 1.8 - - - -
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Residues in contact with ALA 295 (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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111A TRP* 3.5 40.8 - - + +
271A GLN 3.3 5.6 - - - -
272A ILE* 4.0 11.9 - - + -
294A MET* 1.3 72.4 - - - +
296A GLU* 1.3 60.8 + - - +
525A PHE* 2.8 41.9 + - + -
527A LEU* 4.2 12.2 - - + +
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Residues in contact with GLU 296 (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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111A TRP* 4.5 0.4 - - - -
245A GLU* 3.8 13.2 - - - +
246A THR* 2.8 49.8 + - - +
247A ALA* 4.2 13.9 - - - +
250A ILE* 4.4 5.2 - - + +
270A ALA* 3.3 5.7 - - - +
271A GLN 3.0 30.8 + - - -
294A MET* 3.9 20.9 - - + +
295A ALA* 1.3 77.1 - - - +
297A ILE* 1.3 64.6 + - - +
298A GLU* 5.3 5.5 - - + +
523A PRO 3.5 4.7 - - - +
524A SER* 3.0 29.6 + - - +
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Residues in contact with ILE 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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111A TRP* 3.6 24.0 - - + -
115A PHE* 3.8 29.4 - - + -
121A ILE* 3.4 27.6 - - + -
268A ALA* 4.3 13.5 - - + -
269A ALA 3.4 9.0 - - - +
270A ALA* 4.4 2.0 - - + -
296A GLU* 1.3 74.6 - - - +
298A GLU* 1.3 77.1 + - - +
299A HIS* 4.1 6.7 - - + +
355A PHE* 4.8 8.1 - - + -
522A GLU* 3.5 9.5 - - - -
523A PRO* 2.9 49.0 + - + +
525A PHE* 4.8 0.4 - - + -
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Residues in contact with GLU 298 (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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247A ALA* 3.4 21.3 - - - +
250A ILE* 3.6 41.3 - - + -
251A PHE* 3.6 16.7 - - + -
268A ALA* 3.3 2.4 - - - -
269A ALA 2.8 33.2 + - - -
296A GLU* 5.3 5.3 - - + +
297A ILE* 1.3 80.4 - - - +
299A HIS* 1.3 59.6 + - - +
300A PHE* 3.5 15.5 - - + -
520A VAL* 3.9 7.0 - - - +
521A ILE 3.8 0.7 - - - -
522A GLU* 2.9 43.7 - - - +
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Residues in contact with HIS 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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119A GLU* 6.4 1.1 - - + -
266A PRO* 4.2 20.2 - - + +
267A PHE 4.8 2.4 - - - -
268A ALA* 3.9 22.2 - - + -
297A ILE* 4.0 4.0 - - + -
298A GLU* 1.3 71.6 + - - +
300A PHE* 1.3 59.3 + - - +
301A VAL* 3.6 19.9 + - + +
308A HIS* 4.4 13.3 + + - -
351A VAL* 3.9 26.9 - - + +
355A PHE* 3.4 37.7 - + + -
520A VAL* 3.3 5.2 - - - +
521A ILE* 3.0 39.3 + - + +
523A PRO* 5.3 0.2 - - + -
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Residues in contact with PHE 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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250A ILE* 3.8 26.0 - - + -
251A PHE* 4.1 15.9 - + - -
254A PHE* 3.8 29.4 - + - -
257A LEU* 5.4 0.9 - - + -
265A LEU* 3.7 12.8 - - + +
266A PRO* 3.3 9.0 - - - +
267A PHE* 2.9 64.4 + + + +
269A ALA* 4.6 1.3 - - + -
298A GLU* 3.5 27.1 - - + -
299A HIS* 1.3 71.6 + - - +
301A VAL* 1.3 58.9 + - - +
413A TYR* 3.8 11.7 - - - -
415A LEU* 4.5 1.6 - - + -
518A PRO* 4.1 11.9 - - + -
519A ASN 3.4 3.1 - - - -
520A VAL* 3.2 28.0 - - + -
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Residues in contact with VAL 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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265A LEU* 4.6 1.8 - - - -
266A PRO* 4.3 11.0 - - + -
299A HIS* 4.1 15.3 - - + +
300A PHE* 1.3 74.1 - - - +
302A ASP* 1.3 77.3 + - - +
303A PRO 3.4 0.2 - - - -
305A GLU 3.4 17.7 - - - +
306A LYS* 4.0 19.7 - - + -
351A VAL* 4.6 8.1 - - + -
518A PRO* 3.5 6.8 - - - +
519A ASN* 2.9 50.0 + - + +
521A ILE* 4.1 20.2 - - + -
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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