Contacts of the strand formed by residues 251 - 264 (chain A) in PDB entry 1OZ2
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 HIS 251 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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248A ASP* 2.9 26.9 + - + +
250A GLN* 1.3 80.2 - - - +
252A PRO* 1.3 63.1 - - - +
253A SER* 3.2 14.2 + - - -
254A MET* 2.9 58.1 + - + +
256A PHE* 5.8 0.2 - - + -
383A ASP* 5.1 3.6 - - - -
384A ASP* 3.7 22.9 + - + +
385A THR* 3.6 20.7 - - + +
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Residues in contact with PRO 252 (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 ILE* 4.0 17.2 - - + +
248A ASP 3.3 9.9 - - - +
249A PRO 3.9 15.7 - - - +
250A GLN 3.7 3.8 - - - +
251A HIS* 1.3 86.2 - - - +
253A SER* 1.3 58.1 + - - +
254A MET 3.2 2.1 + - - -
376A LEU* 4.3 6.3 - - + -
384A ASP 3.9 16.2 - - - +
385A THR* 4.6 3.8 - - - +
387A ASP* 3.5 22.4 - - + +
388A TYR* 4.8 2.0 - - + -
389A TRP* 2.9 46.2 + - + +
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Residues in contact with SER 253 (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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251A HIS* 3.0 10.9 + - - -
252A PRO* 1.3 77.8 - - - +
254A MET* 1.3 77.9 + - - +
255A TYR* 3.8 17.2 - - - -
368A THR* 5.8 0.2 - - - -
369A ASP* 4.9 2.2 - - - +
376A LEU* 3.7 17.8 - - - +
384A ASP* 2.8 28.7 + - - +
387A ASP* 3.7 15.1 + - - -
389A TRP* 5.5 0.4 - - - -
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Residues in contact with MET 254 (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 ILE* 3.3 7.3 - - - +
248A ASP 3.0 25.7 + - - -
251A HIS* 2.9 39.1 + - + +
253A SER* 1.3 112.2 - - - +
255A TYR* 1.3 62.3 + - - +
256A PHE* 3.9 12.8 - - + -
304A GLN* 3.4 39.7 - - + +
384A ASP* 4.0 7.9 - - - +
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Residues in contact with TYR 255 (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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245A GLU* 5.8 3.6 - - + -
246A GLY* 3.3 15.3 - - - +
247A ILE* 3.4 28.9 - - + -
253A SER 3.8 14.8 - - - -
254A MET* 1.3 74.3 - - - +
256A PHE* 1.3 61.9 + - - +
291A HIS* 4.4 8.1 - + - -
295A TRP* 3.5 39.2 - + + -
296A PHE* 5.3 5.4 - - + -
301A HIS* 3.6 25.0 - + + -
302A LYS 3.7 22.8 + - - +
303A LEU* 3.7 7.1 - - + +
304A GLN* 2.9 32.4 + - - +
369A ASP* 2.9 21.3 + - - -
371A VAL* 3.8 1.7 - - - +
389A TRP* 3.4 19.4 - + - -
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Residues in contact with PHE 256 (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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245A GLU* 3.4 5.4 - - - +
246A GLY 2.9 30.6 + - - +
248A ASP* 3.9 32.3 - - + -
251A HIS* 5.8 0.2 - - + -
254A MET* 3.9 8.1 - - + -
255A TYR* 1.3 78.8 - - - +
257A ILE* 1.3 65.2 + - - +
258A LEU* 3.7 3.9 + - + +
272A PHE* 3.6 38.6 - + + -
275A TYR* 4.2 29.2 - + - -
303A LEU* 4.0 6.5 - - - -
304A GLN* 3.5 44.0 - - + -
305A PRO 4.7 0.7 - - - -
306A PRO* 6.1 0.2 - - + -
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Residues in contact with ILE 257 (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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243A LYS* 4.8 1.6 - - + -
244A LEU 3.5 1.6 - - - +
245A GLU* 4.3 6.1 - - + -
256A PHE* 1.3 75.1 - - - +
258A LEU* 1.3 68.9 + - - +
272A PHE* 3.8 1.4 - - - -
273A ASP* 3.2 41.4 + - - +
296A PHE* 4.4 0.4 - - + -
303A LEU* 3.5 26.0 - - + +
304A GLN 4.4 2.0 + - - -
306A PRO* 4.0 19.0 - - + +
314A PHE* 3.6 25.6 - - + -
316A TRP* 3.4 43.7 - - + +
319A TYR* 3.9 11.2 - - + -
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Residues in contact with LEU 258 (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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243A LYS* 3.3 5.2 - - - +
244A LEU* 2.9 44.9 + - + +
245A GLU 4.2 2.7 - - - +
246A GLY* 3.7 29.8 - - - +
256A PHE* 3.8 8.7 - - + +
257A ILE* 1.3 83.4 - - - +
259A THR* 1.3 59.2 + - - +
270A LEU* 4.0 30.5 - - + -
271A HIS 3.2 13.0 - - - +
272A PHE* 3.6 33.7 - - + -
273A ASP* 3.4 6.1 - - - -
281A PHE* 4.0 18.4 - - + -
290A ILE* 4.6 1.3 - - + -
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Residues in contact with THR 259 (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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241A GLY* 3.8 19.3 - - - +
242A MET 3.4 10.8 - - - +
243A LYS* 2.8 21.6 + - - +
258A LEU* 1.3 73.2 - - - +
260A VAL* 1.3 77.3 + - - +
261A ALA* 3.2 1.6 + - - -
270A LEU* 3.4 6.5 - - - -
271A HIS* 2.8 43.4 + - + +
273A ASP* 2.5 23.2 + - - -
600A SO4 5.3 0.6 + - - -
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Residues in contact with VAL 260 (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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238A PHE* 4.2 12.3 - - + -
239A LYS 3.4 26.2 - - - +
240A LEU* 3.7 4.8 - - - +
241A GLY 2.9 25.5 + - - +
242A MET* 3.0 17.3 + - + +
244A LEU* 3.8 17.3 - - + -
259A THR* 1.3 74.4 - - - +
261A ALA* 1.3 60.8 + - - +
262A GLU 3.8 9.9 - - - +
263A VAL* 3.7 28.0 - - + -
268A LEU* 4.1 21.8 - - + -
269A ARG 3.7 4.7 - - - +
270A LEU* 4.1 1.3 - - + -
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Residues in contact with ALA 261 (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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240A LEU* 4.0 19.6 - - - +
259A THR* 3.2 1.9 + - - -
260A VAL* 1.3 73.4 - - - +
262A GLU* 1.3 59.0 + - - +
269A ARG* 2.7 46.6 + - - +
271A HIS* 4.2 15.7 - - + -
280A ASP* 4.2 7.9 - - - +
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Residues in contact with GLU 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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240A LEU* 5.0 6.3 - - - -
260A VAL* 3.6 2.1 - - - +
261A ALA* 1.3 81.5 - - - +
263A VAL* 1.3 78.0 + - - +
264A CYS* 4.8 4.7 - - - +
268A LEU* 3.3 5.4 - - - +
269A ARG* 2.9 66.0 + - + +
282A TRP* 3.5 25.8 - - + -
464A ALA* 5.7 1.3 - - - +
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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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236A ASN* 3.5 27.6 - - - +
238A PHE* 3.5 28.5 - - + +
239A LYS* 4.2 0.7 - - + -
240A LEU* 4.2 11.8 - - + +
260A VAL* 3.7 18.8 - - + -
262A GLU* 1.3 88.0 - - - +
264A CYS* 1.3 64.6 + - - +
265A GLY 4.2 4.9 - - - +
267A ARG 3.6 3.1 - - - -
268A LEU* 4.8 1.8 - - + -
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Residues in contact with CYS 264 (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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262A GLU* 4.8 5.4 - - - +
263A VAL* 1.3 76.0 - - - +
265A GLY* 1.3 60.9 + - - +
266A TYR 3.1 0.3 + - - -
267A ARG* 2.8 36.0 + - - +
282A TRP* 3.9 24.6 - - + -
464A ALA 5.4 1.1 - - - -
511A GLY 4.9 0.7 - - - -
512A HIS* 3.4 29.1 - - + -
513A PRO* 3.5 26.5 - - - -
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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