Contacts of the strand formed by residues 245 - 255 (chain A) in PDB entry 2WIN
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 GLY 245 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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243A VAL* 4.5 0.6 - - - +
244A GLU* 1.3 73.3 - - - +
246A THR* 1.3 60.1 + - - -
270A PRO* 4.0 0.9 - - - +
271A ILE* 2.8 41.4 + - - +
308A VAL* 5.0 4.7 - - - -
309A ILE 3.4 12.8 - - - -
310A LEU* 4.1 1.6 - - - -
311A HIS* 3.3 24.3 + - - -
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Residues in contact with THR 246 (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 GLY* 1.3 74.7 + - - -
247A ALA* 1.3 64.0 + - - +
248A PHE* 4.2 10.6 - - + -
268A ARG* 3.7 33.4 - - + +
269A ILE 3.8 13.7 - - - +
270A PRO* 4.6 5.7 - - + +
271A ILE* 4.2 1.8 - - - +
307A THR 3.8 1.7 - - - +
308A VAL* 3.6 0.8 - - - +
309A ILE* 2.8 40.4 + - - +
311A HIS* 3.9 13.7 + - - -
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Residues in contact with ALA 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A ILE* 4.4 10.3 - - + -
246A THR* 1.3 74.6 - - - +
248A PHE* 1.3 65.1 + - - +
249A VAL* 4.0 2.2 + - + +
267A LYS 3.9 0.2 - - - +
268A ARG* 3.5 7.3 - - - +
269A ILE* 3.1 37.0 + - + +
271A ILE* 3.7 20.3 - - + +
306A ALA* 5.4 1.1 - - + -
307A THR 3.3 7.2 - - - +
308A VAL* 3.7 24.7 - - + -
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Residues in contact with PHE 248 (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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246A THR* 4.2 16.6 - - + -
247A ALA* 1.3 74.0 - - - +
249A VAL* 1.3 60.4 + - - +
250A ILE* 5.6 0.2 - - - +
266A LEU* 4.7 13.9 - - + +
267A LYS 3.5 5.8 - - - +
268A ARG* 3.6 38.1 - - + -
305A SER 3.4 6.9 - - - +
306A ALA 3.4 0.3 - - - -
307A THR* 2.8 52.8 + - + +
309A ILE* 4.2 24.5 - - + -
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Residues in contact with VAL 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A ILE* 4.7 4.9 - - + -
247A ALA* 5.1 1.8 - - + +
248A PHE* 1.3 72.9 - - - +
250A ILE* 1.3 65.2 + - - +
251A PHE* 4.1 13.7 - - + -
265A SER 3.8 1.7 - - - +
266A LEU* 3.5 3.4 - - - +
267A LYS* 2.9 45.5 + - + +
269A ILE* 4.6 12.1 - - + -
278A VAL* 3.5 39.0 - - + -
304A VAL* 3.5 28.9 - - + -
305A SER 3.5 4.3 - - - +
306A ALA* 4.1 8.5 - - + +
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Residues in contact with ILE 250 (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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249A VAL* 1.3 73.9 - - - +
251A PHE* 1.3 83.9 + - - +
261A SER* 3.5 23.8 - - - +
262A LEU 3.8 17.7 - - - +
263A PRO* 4.7 4.0 - - + -
265A SER* 3.9 2.7 - - - +
266A LEU* 4.1 26.2 - - + -
303A TYR* 5.7 2.9 - - + -
304A VAL* 3.5 6.4 - - - +
305A SER* 2.9 55.1 + - - +
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Residues in contact with PHE 251 (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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229A LEU* 4.2 7.2 - - + -
231A VAL* 3.8 18.2 - - + -
249A VAL* 4.1 21.3 - - + -
250A ILE* 1.3 88.2 - - - +
252A GLY* 1.3 60.4 + - - +
261A SER* 4.0 4.7 + - - -
262A LEU* 3.3 21.3 + - + -
265A SER* 3.2 36.2 + - - +
267A LYS* 5.2 0.4 - - + -
278A VAL* 4.1 18.2 - - + -
279A VAL 4.8 0.9 - - - -
280A LEU* 3.5 52.7 - - + -
302A LEU* 5.8 2.5 - - + -
303A TYR* 3.4 15.4 + - - -
304A VAL* 3.5 31.4 - - + -
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Residues in contact with GLY 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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251A PHE* 1.3 80.9 - - - +
253A ILE* 1.3 62.5 + - - -
260A ILE 3.3 14.1 - - - -
262A LEU* 3.7 9.2 - - - +
302A LEU* 3.3 10.6 - - - +
303A TYR* 3.1 41.9 + - - -
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Residues in contact with ILE 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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252A GLY* 1.3 74.1 - - - -
254A GLN* 1.3 65.3 + - - +
255A ASP* 5.9 0.2 - - + -
258A GLN 4.0 0.3 - - - +
259A ARG* 3.4 2.3 - - - -
260A ILE* 2.8 46.8 + - + +
262A LEU* 4.5 12.6 - - + -
285A LEU* 3.9 25.8 - - + +
289A VAL* 4.7 13.2 - - + +
297A LEU* 4.0 23.1 - - + -
300A LYS* 3.8 31.6 - - + -
301A SER 3.3 9.6 - - - +
302A LEU* 3.5 17.9 - - + -
303A TYR* 3.9 2.4 - - - -
326A ILE* 5.2 2.0 - - + -
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Residues in contact with GLN 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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253A ILE* 1.3 75.6 - - - +
255A ASP* 1.3 66.8 + - - +
256A GLY 3.9 22.0 + - - +
257A GLU* 4.5 6.3 + - - +
258A GLN 3.4 10.8 - - - +
259A ARG* 3.9 36.4 + - + +
300A LYS* 3.6 11.6 - - - +
301A SER* 2.8 46.9 + - - +
303A TYR* 4.4 6.7 - - + +
322A SER* 4.7 7.8 - - - -
323A GLY* 4.7 5.2 + - - -
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Residues in contact with ASP 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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253A ILE* 5.9 0.2 - - + -
254A GLN* 1.3 75.7 - - - +
256A GLY* 1.3 61.3 + - - +
257A GLU* 2.8 11.1 + - - +
258A GLN* 2.7 34.0 + - + +
260A ILE* 6.3 2.5 - - + -
300A LYS* 4.2 26.1 - - + +
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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