Contacts of the strand formed by residues 292 - 299 (chain A) in PDB entry 2Z9I
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 THR 292 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270A ASP* 3.9 8.5 - - - +
287A LYS* 5.6 0.5 + - - +
290A GLY 3.7 2.1 + - - -
291A ALA* 1.3 72.3 - - - +
293A VAL* 1.3 69.5 + - - +
308A GLN* 4.1 25.1 - - + +
309A VAL 3.3 6.5 - - - +
310A THR* 2.9 32.1 + - - +
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Residues in contact with VAL 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A LEU* 6.3 0.2 - - + -
269A VAL* 3.7 32.1 - - + -
270A ASP* 3.7 11.9 - - - +
284A VAL* 6.3 1.8 - - + -
287A LYS* 4.1 23.6 - - + +
291A ALA 5.2 0.2 - - - -
292A THR* 1.3 80.9 - - - +
294A ALA* 1.3 64.6 + - - +
295A LEU* 3.6 13.9 + - + +
307A VAL 3.5 0.3 - - - +
308A GLN* 3.3 5.3 - - - -
309A VAL* 2.6 48.3 + - + +
311A LEU* 4.2 24.0 - - + -
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Residues in contact with ALA 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A LYS 3.5 1.2 - - - +
269A VAL* 3.3 7.4 - - - +
270A ASP* 2.7 51.4 + - - +
271A ASP* 5.4 1.6 - - - +
293A VAL* 1.3 71.1 - - - +
295A LEU* 1.3 60.3 + - - +
296A THR* 3.9 2.2 + - - +
306A THR* 4.0 9.0 - - + -
307A VAL 3.4 4.9 - - - -
308A GLN* 3.5 28.4 + - - +
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Residues in contact with LEU 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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231A LEU* 4.3 21.1 - - + -
246A ILE* 5.6 0.2 - - + -
260A VAL* 3.8 33.9 - - + -
266A VAL* 3.7 40.4 - - + -
268A LYS 3.7 0.9 - - - -
269A VAL* 3.9 16.8 - - + -
280A LEU* 4.3 9.2 - - + -
284A VAL* 6.1 0.4 - - + -
293A VAL* 3.6 11.2 + - + -
294A ALA* 1.3 71.6 - - - +
296A THR* 1.3 62.8 + - - +
297A PHE* 3.8 7.8 - - + -
305A ARG 3.7 1.0 - - - +
306A THR* 3.3 2.1 - - - -
307A VAL* 2.6 45.9 + - + +
309A VAL* 4.2 11.0 - - + -
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Residues in contact with THR 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A VAL* 3.4 5.9 - - - +
267A THR* 2.8 39.3 + - - +
268A LYS* 3.0 41.5 + - + +
271A ASP* 4.1 4.2 + - - -
294A ALA* 4.9 2.3 + - - +
295A LEU* 1.3 72.0 - - - +
297A PHE* 1.3 58.5 + - - +
304A SER* 3.6 19.3 - - - +
305A ARG 3.2 12.1 - - - +
306A THR* 2.7 22.6 + - - +
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Residues in contact with PHE 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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259A GLY 5.2 1.1 - - - -
260A VAL* 4.6 3.8 - - + -
261A PRO* 3.7 21.1 - - + -
264A VAL* 3.4 42.0 - - + -
265A VAL 3.0 19.5 - - - +
266A VAL* 3.9 4.7 - - + -
267A THR* 4.1 3.1 - - - -
295A LEU* 3.8 20.2 - - + -
296A THR* 1.3 75.1 - - - +
298A GLN* 1.3 63.4 + - - +
299A ASP* 4.3 1.1 + - - -
304A SER* 3.3 7.6 + - - -
305A ARG* 2.9 74.5 + - + +
307A VAL* 3.7 33.2 - - + -
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Residues in contact with GLN 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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241A THR* 4.1 18.4 + - - -
242A LEU 5.1 1.0 - - - +
264A VAL* 3.2 9.6 - - - -
265A VAL* 2.8 42.0 + - + +
267A THR* 3.7 27.4 - - + +
297A PHE* 1.3 73.2 - - - +
299A ASP* 1.3 67.8 + - - +
300A PRO* 3.7 1.6 - - - +
302A GLY* 4.9 10.1 - - - -
303A GLY 3.1 14.1 + - - +
304A SER* 4.5 3.1 - - - +
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Residues in contact with ASP 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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264A VAL* 4.3 13.0 - - + +
297A PHE* 4.2 2.8 + - + -
298A GLN* 1.3 78.8 + - - +
300A PRO* 1.4 60.5 - - + +
301A SER* 2.4 43.9 + - - +
302A GLY* 2.8 31.9 + - - -
303A GLY* 2.9 21.6 + - - +
304A SER* 5.1 0.4 - - - +
305A ARG* 3.0 32.8 + - - +
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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