Contacts of the helix formed by residues 305 - 326 (chain A) in PDB entry 2WMN
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 ASN 305 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A GLN 3.8 0.4 - - - -
275A CYS* 4.4 4.3 - - - -
304A LEU* 1.3 72.0 - - - +
306A PRO* 1.3 66.0 - - + +
307A ILE* 3.9 13.8 - - + +
308A GLU* 2.7 36.9 + - + +
309A VAL* 2.8 37.5 + - - +
371A LYS* 6.1 1.2 - - - +
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Residues in contact with PRO 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A VAL 3.1 25.7 - - - +
272A GLU 3.3 20.0 - - - +
273A GLU* 3.4 14.8 - - - +
274A GLN 2.8 20.6 - - - +
275A CYS* 4.0 9.2 - - - -
305A ASN* 1.3 90.3 - - + +
307A ILE* 1.3 56.9 + - + +
309A VAL* 3.3 3.6 - - + +
310A ALA* 2.9 25.1 + - - +
354A TYR* 5.2 1.2 - - - -
358A PHE* 3.6 11.4 - - + -
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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
----------------------------------------------------------
305A ASN* 4.2 14.6 - - + +
306A PRO* 1.3 76.2 - - + +
308A GLU* 1.3 66.6 + - + +
309A VAL 3.1 0.9 - - - -
310A ALA* 3.1 2.1 + - - +
311A ILE* 2.7 49.4 + - + +
358A PHE* 3.6 29.4 - - + +
368A PRO* 6.0 2.0 - - + -
369A ASP* 5.3 7.6 - - + +
371A LYS* 4.8 15.5 - - + -
372A VAL* 4.0 21.5 - - + -
375A LEU* 3.8 31.0 - - + -
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Residues in contact with GLU 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A ASP 4.1 2.6 - - - +
304A LEU* 3.3 28.8 - - + +
305A ASN* 2.7 52.8 + - + +
307A ILE* 1.3 81.5 - - + +
309A VAL* 1.3 57.8 + - - +
311A ILE* 3.5 10.7 - - - +
312A ASP* 2.8 32.7 + - - +
371A LYS* 3.5 26.1 + - + +
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Residues in contact with VAL 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A GLN* 3.4 29.4 - - + +
275A CYS 4.1 0.7 - - - -
276A LYS* 3.9 27.1 - - + +
304A LEU* 3.9 13.7 - - + +
305A ASN 2.8 27.5 + - - +
306A PRO 3.3 7.2 - - - +
308A GLU* 1.3 77.0 - - - +
310A ALA* 1.3 54.2 + - - +
312A ASP* 3.2 5.0 + - - +
313A GLU* 2.7 59.2 + - + +
354A TYR* 4.9 5.6 - - + +
33B VAL* 5.4 4.9 - - + -
34B PRO 5.9 1.6 - - - +
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Residues in contact with ALA 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A PRO 2.9 15.5 + - - +
307A ILE* 3.3 11.9 - - - +
309A VAL* 1.3 74.9 - - - +
311A ILE* 1.3 64.9 + - - +
313A GLU* 3.0 3.3 + - - +
314A MET* 2.8 29.0 + - - +
354A TYR* 3.5 42.6 - - + -
358A PHE* 4.2 8.5 - - + -
375A LEU* 4.4 8.3 - - + -
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Residues in contact with ILE 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A ILE* 2.7 39.4 + - + +
308A GLU* 3.5 7.9 - - - +
310A ALA* 1.3 72.8 - - - +
312A ASP* 1.3 61.5 + - - +
314A MET* 3.2 4.0 + - - +
315A SER* 2.9 39.6 + - - +
371A LYS* 4.0 30.3 - - + -
374A LEU* 3.6 36.8 - - + -
375A LEU* 3.9 32.7 - - + +
378A VAL* 4.5 5.6 - - + +
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Residues in contact with ASP 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A LYS* 2.8 27.3 + - - +
278A ARG* 3.4 15.7 + - - -
304A LEU* 4.5 4.7 - - + +
308A GLU 2.8 21.2 + - - +
309A VAL* 3.5 4.5 - - - +
311A ILE* 1.3 75.1 - - - +
313A GLU* 1.3 61.8 + - - +
315A SER* 3.3 7.8 + - - -
316A LYS* 3.0 46.6 + - - +
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Residues in contact with GLU 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A LYS* 2.9 34.0 + - - +
309A VAL* 2.7 39.1 + - + +
310A ALA 3.5 3.4 - - - +
312A ASP* 1.3 72.1 - - - +
314A MET* 1.3 63.5 + - - +
316A LYS* 3.4 25.8 + - - +
317A LYS* 3.4 11.8 + - - +
354A TYR* 3.7 27.6 - - + +
33B VAL* 4.2 11.5 - - - +
34B PRO 5.4 4.9 - - - +
35B THR* 6.3 0.9 - - - -
37B PHE* 4.3 10.7 - - + -
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Residues in contact with MET 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A ALA 2.8 20.9 + - - +
311A ILE* 3.5 3.8 - - - +
313A GLU* 1.3 74.2 - - - +
315A SER* 1.3 66.6 + - - +
317A LYS* 3.0 15.7 + - - +
318A VAL* 3.3 14.9 + - - +
351A PRO* 4.3 4.7 - - + -
354A TYR* 3.6 28.9 - - + -
375A LEU* 4.6 3.4 - - + -
378A VAL* 3.4 18.8 - - + -
379A PHE* 3.6 41.7 - - + -
382A PHE* 3.7 38.1 - - + -
37B PHE* 3.9 16.4 - - - -
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Residues in contact with SER 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A ILE* 2.9 24.0 + - - +
312A ASP* 3.5 9.9 - - - -
314A MET* 1.3 75.9 - - - +
316A LYS* 1.3 64.8 + - - +
318A VAL* 3.0 27.5 - - - +
319A ALA* 3.2 10.2 + - - +
374A LEU* 5.9 0.5 - - - +
378A VAL* 3.7 18.9 - - - +
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Residues in contact with LYS 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A GLU* 3.8 15.6 + - - -
276A LYS* 3.6 13.1 - - - +
278A ARG* 4.8 1.5 - - - +
312A ASP* 3.0 46.8 + - - +
313A GLU* 3.8 19.2 + - - +
314A MET 3.2 0.4 - - - -
315A SER* 1.3 76.9 - - - +
317A LYS* 1.3 56.4 + - - +
319A ALA* 4.0 4.5 - - - +
320A GLU* 3.0 32.2 + - - +
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Residues in contact with LYS 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A GLU 3.4 5.5 + - - +
314A MET 3.0 10.1 + - - +
316A LYS* 1.3 77.9 - - - +
318A VAL* 1.3 60.2 + - - +
320A GLU* 3.1 31.8 + - + +
321A LEU* 2.9 32.6 + - + +
338A LYS* 4.5 18.2 + - + +
342A SER* 4.0 15.7 - - - +
382A PHE* 4.0 14.6 - - + -
37B PHE* 3.4 62.2 - - + +
38B ASP 5.5 2.2 + - - -
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Residues in contact with VAL 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A MET 3.8 7.2 - - - +
315A SER* 3.0 26.9 - - - +
317A LYS* 1.3 73.5 - - - +
319A ALA* 1.3 65.7 + - + +
321A LEU* 3.1 9.6 + - - +
322A ARG* 2.8 47.0 + - + +
378A VAL* 4.0 12.1 - - + +
381A GLN* 4.0 15.7 - - + +
382A PHE* 3.4 50.5 - - + +
385A ALA* 4.5 3.3 - - + +
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Residues in contact with ALA 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A SER 3.2 11.8 + - - +
316A LYS* 4.1 5.2 - - - +
318A VAL* 1.3 79.9 - - + +
320A GLU* 1.3 65.0 + - - +
322A ARG* 3.9 9.5 - - - +
323A GLN* 2.9 27.7 + - - +
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Residues in contact with GLU 320 (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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316A LYS* 3.0 19.4 + - - +
317A LYS* 3.1 35.5 + - + +
318A VAL 3.2 0.2 - - - -
319A ALA* 1.3 77.8 - - - +
321A LEU* 1.3 59.2 + - + +
323A GLN* 3.7 3.2 + - - +
324A LEU* 3.0 36.8 + - + +
334A LYS* 6.4 0.4 - - - -
338A LYS* 2.7 51.5 + - + -
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Residues in contact with LEU 321 (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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317A LYS* 2.9 27.6 + - + +
318A VAL* 3.1 5.4 + - - +
320A GLU* 1.3 74.5 - - - +
322A ARG* 1.3 54.3 + - - +
324A LEU* 2.8 11.2 + - + +
325A CYS* 2.7 39.8 + - - -
335A LEU* 4.9 6.1 - - + +
338A LYS* 4.0 35.9 - - + +
339A LEU* 4.2 11.7 - - + -
342A SER* 4.0 14.8 - - - +
382A PHE* 4.4 4.5 - - + -
385A ALA* 3.9 28.3 - - + +
386A CYS* 4.2 17.9 - - - +
389A ALA* 4.6 10.1 - - + -
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Residues in contact with ARG 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A VAL* 2.8 32.5 + - - +
319A ALA* 3.9 7.5 - - - +
321A LEU* 1.3 71.8 - - - +
323A GLN* 1.3 57.0 + - - +
325A CYS* 3.0 7.8 + - - -
326A SER* 2.7 40.9 + - - +
381A GLN* 3.2 59.7 + - - +
384A GLU* 4.9 7.3 - - - +
385A ALA* 4.8 12.7 - - + +
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Residues in contact with GLN 323 (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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319A ALA 2.9 18.9 + - - +
320A GLU* 3.9 3.8 - - - +
322A ARG* 1.3 76.5 - - - +
324A LEU* 1.3 77.9 + - - +
326A SER* 3.6 9.7 - - - +
327A SER* 2.7 30.6 + - - -
334A LYS* 5.5 1.7 + - - -
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Residues in contact with LEU 324 (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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320A GLU* 3.0 27.8 + - + +
321A LEU* 2.8 13.3 + - - +
323A GLN* 1.3 97.6 - - - +
325A CYS* 1.3 66.5 + - - +
327A SER* 3.5 12.7 - - - -
330A VAL* 4.1 13.0 - - - +
331A ASP* 5.4 4.7 + - + +
334A LYS* 3.0 55.4 - - + +
335A LEU* 3.7 21.8 - - + -
338A LYS* 3.6 19.7 - - + -
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Residues in contact with CYS 325 (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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321A LEU 2.7 23.7 + - - +
322A ARG* 3.5 9.2 - - - +
324A LEU* 1.3 73.7 - - - +
326A SER* 1.3 54.2 + - - +
327A SER* 2.6 21.8 + - - +
330A VAL* 3.9 6.9 - - - +
335A LEU* 4.7 6.7 - - - -
385A ALA* 4.2 6.3 - - - -
388A GLN* 4.0 15.5 - - + -
389A ALA* 3.8 36.3 - - - -
392A VAL* 4.3 22.9 - - + +
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Residues in contact with SER 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A ARG* 2.7 26.7 + - - +
323A GLN* 3.6 7.8 - - - +
325A CYS* 1.3 69.4 - - - +
327A SER* 1.3 64.3 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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