Contacts of the strand formed by residues 301 - 310 (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 SER 301 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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253A ILE* 3.3 7.4 - - - +
254A GLN* 2.8 60.5 + - - +
299A GLY 5.3 0.7 - - - -
300A LYS* 1.3 77.7 - - - +
302A LEU* 1.3 63.9 - - - +
323A GLY* 4.1 16.1 + - - -
324A ILE 3.1 16.6 - - - -
325A PRO* 4.7 1.3 - - - -
326A ILE* 4.5 0.7 - - - -
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Residues in contact with LEU 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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221A TYR* 4.5 13.5 - - + -
229A LEU* 3.7 28.5 - - + -
251A PHE* 5.8 2.2 - - + -
252A GLY 3.3 7.6 - - - +
253A ILE* 3.5 31.4 - - + -
280A LEU* 4.7 9.0 - - + -
285A LEU* 4.0 25.1 - - + -
301A SER* 1.3 74.7 - - - +
303A TYR* 1.3 62.4 + - - +
323A GLY 3.6 4.1 + - - -
324A ILE* 2.8 46.1 + - + +
326A ILE* 3.6 30.7 - - + -
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Residues in contact with TYR 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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250A ILE* 3.9 2.4 - - + +
251A PHE* 3.4 12.4 - - - +
252A GLY* 3.1 49.9 + - - -
253A ILE 3.7 10.5 - - - -
254A GLN* 4.4 5.6 - - + +
259A ARG* 3.7 48.1 - - + +
261A SER* 3.7 28.4 + - - -
302A LEU* 1.3 76.0 - - - +
304A VAL* 1.3 66.0 + - - +
305A SER* 5.0 8.5 - - - -
320A GLU* 4.0 16.4 - - - +
321A ARG 3.2 11.0 - - - +
322A SER* 3.8 19.3 - - - -
323A GLY 4.8 0.4 - - - +
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Residues in contact with VAL 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A VAL* 4.5 10.9 - - + +
216A PRO* 5.3 0.2 - - + -
229A LEU* 4.8 0.9 - - + -
231A VAL* 3.9 28.3 - - + -
233A ILE* 5.1 0.2 - - + -
249A VAL* 3.5 28.5 - - + -
250A ILE 3.5 3.8 - - - +
251A PHE* 3.5 27.8 - - + -
303A TYR* 1.3 73.9 - - - +
305A SER* 1.3 64.9 + - - +
306A ALA 4.0 0.2 - - - -
320A GLU* 3.1 8.5 - - - +
321A ARG* 2.7 44.4 + - + +
324A ILE* 4.1 18.2 - - + -
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Residues in contact with SER 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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248A PHE 3.4 5.7 - - - +
249A VAL* 4.3 0.7 - - - -
250A ILE* 2.9 50.4 + - - +
303A TYR* 4.1 8.7 + - - -
304A VAL* 1.3 73.8 - - - +
306A ALA* 1.3 62.6 + - - +
307A THR* 4.8 3.3 + - - -
318A GLN* 6.0 1.0 - - - +
319A ALA 3.7 10.4 + - - -
320A GLU* 4.4 12.1 + - - +
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Residues in contact with ALA 306 (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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212A VAL* 4.6 8.7 - - + -
214A VAL* 3.8 27.1 - - + +
233A ILE* 4.3 21.8 - - + -
247A ALA* 5.4 1.3 - - + -
248A PHE 3.4 5.6 - - - +
249A VAL* 4.1 7.9 - - + +
304A VAL 4.0 1.6 + - - -
305A SER* 1.3 74.4 + - - +
307A THR* 1.3 70.9 + - - +
308A VAL* 4.3 0.9 - - + -
318A GLN* 3.5 2.3 - - - +
319A ALA* 3.1 31.9 + - + +
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Residues in contact with THR 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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247A ALA* 3.3 1.6 - - - -
248A PHE* 2.8 55.8 + - + +
305A SER* 4.8 4.2 + - - -
306A ALA* 1.3 83.1 + - - +
308A VAL* 1.3 60.4 + - - +
309A ILE* 4.7 5.4 - - + -
316A MET* 3.5 37.7 - - + -
317A VAL 3.4 6.7 - - - +
318A GLN* 3.6 18.9 + - + +
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Residues in contact with VAL 308 (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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210A PHE* 3.8 26.7 - - + -
212A VAL* 3.7 31.0 - - + -
233A ILE* 4.3 7.0 - - + -
235A ALA* 4.4 13.0 - - + -
243A VAL* 4.7 8.7 - - + -
245A GLY* 5.0 1.3 - - - -
246A THR 3.6 11.9 - - - +
247A ALA* 3.7 18.8 - - + +
271A ILE* 4.6 8.3 - - + -
307A THR* 1.3 74.5 - - - +
309A ILE* 1.3 72.9 + - - +
316A MET* 3.6 2.3 - - - +
317A VAL 3.0 29.6 + - - -
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Residues in contact with ILE 309 (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* 4.3 0.9 - - - -
246A THR* 2.8 37.5 + - - +
248A PHE* 4.2 24.5 - - + -
307A THR* 4.6 5.8 - - + +
308A VAL* 1.3 81.2 - - - +
310A LEU* 1.3 77.3 + - - +
313A GLY* 4.2 13.0 - - - -
315A ASP 4.0 11.0 - - - +
316A MET* 4.0 29.4 - - + -
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Residues in contact with LEU 310 (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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209A SER* 4.4 5.8 - - - +
210A PHE* 3.8 27.1 - - + -
237A PHE* 4.4 17.5 - - + -
243A VAL* 3.5 31.9 - - + -
244A GLU 3.8 8.3 - - - +
245A GLY* 4.1 0.2 - - - -
308A VAL* 4.3 0.4 - - + -
309A ILE* 1.3 85.7 - - - +
311A HIS* 1.3 60.3 + - - +
312A SER* 2.9 22.4 - - - +
313A GLY* 3.0 17.2 + - - +
314A SER* 5.1 2.0 - - - -
315A ASP* 3.7 32.4 + - + +
828B VAL* 6.1 0.7 - - + -
830B TYR* 4.5 7.9 - - - +
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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