Contacts of the helix formed by residues 305 - 318 (chain A) in PDB entry 2WNW
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 305 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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300A GLU* 3.1 42.9 + - - -
301A SER 4.2 0.9 - - - -
302A ASP* 2.8 23.2 + - - -
303A ALA 3.3 1.1 + - - -
304A GLY* 1.3 76.5 - - - +
306A GLN* 1.3 74.5 + - - +
308A ARG* 3.2 15.9 + - - +
309A HIS* 2.9 36.2 + - - -
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Residues in contact with GLN 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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300A GLU 5.4 1.4 - - - +
303A ALA 4.6 4.3 + - - +
304A GLY 3.4 0.8 - - - -
305A SER* 1.3 88.6 + - - +
307A ILE* 1.3 58.5 + - + +
309A HIS* 3.3 6.2 + - - +
310A TRP* 2.9 28.4 + - - +
349A GLU* 2.9 24.9 + - - +
364A ASN* 3.5 18.4 - - - +
365A HIS* 2.9 65.0 + - + +
366A SER 4.7 0.4 - - - +
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Residues in contact with ILE 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A PRO* 3.7 37.2 - - + -
11A TYR* 3.7 49.6 - - + +
303A ALA 5.4 1.1 + - - +
304A GLY* 3.3 13.6 + - - +
306A GLN* 1.3 77.7 - - + +
308A ARG* 1.3 61.3 + - + +
310A TRP* 3.3 8.2 + - + +
311A HIS* 2.9 28.6 + - + +
365A HIS* 4.4 6.5 - - + +
435A SER* 4.2 13.7 - - - +
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Residues in contact with ARG 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A GLU* 3.0 37.6 + - - -
302A ASP* 2.7 27.7 + - - -
304A GLY* 3.0 14.6 + - - +
305A SER* 3.6 13.0 - - - +
307A ILE* 1.3 81.0 - - + +
309A HIS* 1.3 61.3 + - + +
311A HIS* 3.3 9.0 + - - +
312A THR* 2.9 32.1 + - - +
1447A PO4 2.3 37.2 + - - +
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Residues in contact with HIS 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A VAL* 3.5 22.4 - - + +
298A PRO* 3.2 23.5 + - + -
300A GLU* 2.7 33.9 + - + +
305A SER* 2.9 35.3 + - - +
306A GLN* 3.7 11.3 + - - +
308A ARG* 1.3 78.1 - - + +
310A TRP* 1.3 66.9 + - - +
312A THR* 3.3 6.9 + - - -
313A TYR* 3.1 31.0 + - - -
349A GLU* 3.0 38.5 + - - +
366A SER* 5.2 7.9 - - - +
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Residues in contact with TRP 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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8A SER* 3.6 23.3 - - - -
10A PRO* 3.7 25.5 - - + +
15A PHE* 3.6 23.3 - + - -
306A GLN 2.9 13.5 + - - +
307A ILE* 3.3 16.4 - - + +
309A HIS* 1.3 77.4 - - - +
311A HIS* 1.3 64.3 + - - +
313A TYR* 3.5 1.7 + - - +
314A LEU* 3.1 40.3 + - + +
365A HIS* 3.5 26.6 - - + +
366A SER* 5.0 5.4 - - - +
368A TYR 3.9 1.1 - - - -
369A GLY* 3.5 27.8 - - - -
372A HIS* 4.0 7.0 - + - -
410A TYR* 3.8 9.9 - + - -
435A SER* 2.7 32.9 + - - -
437A ALA* 3.6 26.7 - - + -
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Residues in contact with HIS 311 (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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307A ILE* 2.9 16.4 + - + +
308A ARG* 3.5 11.7 - - - +
310A TRP* 1.3 78.4 - - + +
312A THR* 1.3 65.8 + - - +
315A HIS* 2.8 63.3 + + + +
410A TYR* 2.7 38.4 + + - +
412A ARG* 3.6 41.6 + - + +
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Residues in contact with THR 312 (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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269A TRP* 3.8 31.9 - - + +
297A VAL* 3.9 17.7 - - + +
308A ARG* 2.9 19.0 + - - +
309A HIS* 3.7 5.1 - - - -
311A HIS* 1.3 84.0 - - - +
313A TYR* 1.3 64.2 + - - +
315A HIS* 4.2 2.4 - - - +
316A ASP* 3.2 24.9 + - + +
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Residues in contact with TYR 313 (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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269A TRP* 3.7 28.7 - + - -
295A GLY 3.7 6.3 + - - -
296A CYS* 3.7 8.0 - - - +
297A VAL* 4.1 23.4 + - + +
309A HIS 3.1 22.4 + - - +
310A TRP* 4.0 3.4 - - - +
312A THR* 1.3 80.4 - - - +
314A LEU* 1.3 63.9 + - + +
316A ASP* 4.1 0.5 - - - +
317A MET* 3.0 36.7 + - - +
328A PHE* 4.1 12.1 - + - -
330A ASP* 2.6 33.4 + - - -
349A GLU 5.2 2.4 + - - -
351A PRO* 4.3 6.6 - - - +
366A SER* 3.6 30.5 - - - +
369A GLY* 5.5 0.9 - - - -
370A ILE* 3.7 34.5 - - + +
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Residues in contact with LEU 314 (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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310A TRP* 3.1 59.6 + - + +
311A HIS 4.1 0.7 - - - +
313A TYR* 1.3 79.7 - - - +
315A HIS* 1.3 63.7 + - - +
317A MET* 3.9 3.0 - - - +
318A ILE* 3.0 35.3 + - + +
369A GLY* 3.5 31.9 - - - +
372A HIS* 4.7 8.3 - - + -
373A PHE* 4.2 17.0 - - + -
408A VAL* 5.1 4.5 - - + -
410A TYR* 3.8 28.5 - - + -
437A ALA* 4.0 8.5 - - + -
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Residues in contact with HIS 315 (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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273A ASP* 2.8 38.9 + - - -
275A PHE* 3.6 13.8 - + - -
311A HIS* 2.8 46.3 + + + +
312A THR* 4.2 2.2 - - - +
314A LEU* 1.3 72.7 - - - +
316A ASP* 1.3 64.0 + - + +
319A GLY 3.2 17.8 + - - -
394A GLU* 2.8 37.7 + - - +
410A TYR* 4.5 1.0 - - - -
412A ARG* 3.5 11.0 + - - -
390B ASP* 5.6 0.4 + - - -
391B ASN* 3.1 33.7 + - - -
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Residues in contact with ASP 316 (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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242A LYS* 2.7 27.5 + - - -
269A TRP* 3.4 37.2 - - + +
272A GLY 4.3 3.6 - - - +
273A ASP* 4.5 4.2 - - - +
275A PHE* 3.8 9.5 - - - -
292A PHE* 3.7 8.1 - - - -
312A THR* 3.2 17.2 + - + +
315A HIS* 1.3 79.2 - - + +
317A MET* 1.3 62.0 + - - +
319A GLY 3.4 0.3 + - - -
320A ASN* 2.7 57.2 + - - +
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Residues in contact with MET 317 (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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48A PHE* 4.0 6.7 - - + -
269A TRP* 5.4 0.7 - - + -
313A TYR* 3.0 33.6 + - - +
314A LEU* 3.9 3.1 - - - +
316A ASP* 1.3 78.6 - - + +
318A ILE* 1.3 62.7 + - - +
320A ASN* 3.7 5.5 - - - +
321A PHE* 3.1 36.1 + - + -
328A PHE* 3.7 59.2 - - + -
369A GLY 4.8 1.6 - - - +
370A ILE* 4.3 21.3 - - + -
373A PHE* 3.7 45.3 - - + -
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Residues in contact with ILE 318 (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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314A LEU* 3.0 25.3 + - + +
315A HIS 4.2 2.5 - - - +
317A MET* 1.3 75.0 - - - +
319A GLY* 1.3 65.1 + - - +
321A PHE* 3.9 1.2 - - - +
322A LYS* 3.0 31.0 + - + +
373A PHE* 3.7 22.9 - - + -
394A GLU* 3.8 26.2 - - + +
395A GLU* 3.7 35.0 - - - +
396A VAL* 4.2 7.6 - - + +
408A VAL* 4.5 11.2 - - + -
410A TYR* 3.6 32.1 - - + +
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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