Contacts of the helix formed by residues 305 - 318 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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300B GLU* 3.0 30.1 + - - -
301B SER* 4.2 1.6 - - - -
302B ASP* 3.1 20.9 + - - -
303B ALA 3.2 1.4 + - - -
304B GLY* 1.3 76.7 - - - +
306B GLN* 1.3 70.7 + - - +
308B ARG* 3.2 29.7 + - - +
309B HIS* 3.0 33.2 + - - -
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Residues in contact with GLN 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300B GLU 5.2 1.4 - - - +
304B GLY* 3.2 1.4 - - - -
305B SER* 1.3 87.5 + - - +
307B ILE* 1.3 60.6 + - + +
309B HIS* 3.3 7.0 + - - +
310B TRP* 2.9 28.2 + - - +
349B GLU* 2.8 25.9 + - - +
364B ASN* 3.4 20.0 - - - +
365B HIS* 2.9 65.5 + - + +
366B SER 4.6 0.8 - - - +
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Residues in contact with ILE 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B PRO* 3.4 36.6 - - + +
11B TYR* 3.8 49.6 - - + +
304B GLY* 3.0 20.6 + - - +
306B GLN* 1.3 76.5 - - + +
308B ARG* 1.3 60.9 + - + +
310B TRP* 3.3 6.7 + - + +
311B HIS* 2.9 27.8 + - + +
365B HIS* 3.8 10.5 - - + +
435B SER* 4.0 16.4 - - - +
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Residues in contact with ARG 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B GLU* 3.2 30.9 + - - -
302B ASP* 2.8 43.3 + - - -
303B ALA 3.5 15.2 + - - -
304B GLY 3.1 8.6 + - - +
305B SER* 3.2 19.7 + - - +
307B ILE* 1.3 78.3 - - + +
309B HIS* 1.3 61.0 + - + +
311B HIS* 3.2 9.1 + - - +
312B THR* 2.9 32.3 + - - +
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Residues in contact with HIS 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B VAL* 3.5 24.7 - - + +
298B PRO 3.5 21.8 + - - -
300B GLU* 2.7 44.2 + - + +
305B SER 3.0 17.3 + - - +
306B GLN* 3.6 12.3 + - - +
307B ILE 3.2 0.2 - - - -
308B ARG* 1.3 78.9 - - + +
310B TRP* 1.3 65.5 + - - +
312B THR* 3.3 6.6 + - - +
313B TYR* 3.2 31.3 + - - -
349B GLU* 3.0 38.4 + - - +
366B SER* 5.1 6.7 - - - +
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Residues in contact with TRP 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B SER* 3.6 24.9 - - - -
10B PRO* 3.5 25.5 - - + +
15B PHE* 3.6 25.4 - + - -
306B GLN 2.9 18.6 + - - +
307B ILE* 3.3 10.3 - - + +
309B HIS* 1.3 76.8 - - - +
311B HIS* 1.3 64.4 + - - +
313B TYR* 3.5 2.4 + - - +
314B LEU* 3.1 50.1 + - + +
365B HIS* 3.5 26.8 - - + +
366B SER* 4.9 5.8 - - - +
368B TYR 3.9 1.1 - - - -
369B GLY* 3.5 27.8 - - - -
372B HIS* 4.0 11.7 - + - -
410B TYR* 3.7 8.6 - + - -
435B SER* 2.7 30.6 + - - -
437B ALA* 3.6 14.1 - - + -
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Residues in contact with HIS 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B ILE* 2.9 13.8 + - + +
308B ARG* 3.4 12.8 - - - +
310B TRP* 1.3 78.4 - - - +
312B THR* 1.3 72.5 + - - +
315B HIS* 2.8 57.8 + + + +
410B TYR* 2.7 37.1 + + - +
412B ARG* 3.7 38.2 + - + +
435B SER* 6.1 0.2 - - - +
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Residues in contact with THR 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B TRP* 3.9 32.5 - - + +
297B VAL* 3.9 16.9 - - + +
308B ARG* 2.9 23.0 + - - +
309B HIS* 3.3 6.2 + - - -
311B HIS* 1.3 81.0 - - - +
313B TYR* 1.3 64.5 + - - +
315B HIS* 4.1 2.6 - - - +
316B ASP* 3.1 25.2 + - + +
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Residues in contact with TYR 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269B TRP* 3.6 28.7 - + - -
295B GLY 3.7 5.8 + - - -
296B CYS* 3.8 8.3 - - - +
297B VAL* 4.1 22.7 + - + +
309B HIS 3.2 24.6 + - - +
310B TRP* 3.9 3.4 - - - +
312B THR* 1.3 79.1 - - - +
314B LEU* 1.3 65.4 + - + +
316B ASP* 4.0 0.9 - - - +
317B MET* 3.0 35.3 + - - +
328B PHE* 4.1 12.6 - + - -
330B ASP* 2.6 33.8 + - - -
349B GLU* 5.2 2.3 + - - -
351B PRO* 4.2 7.2 - - + +
366B SER* 3.6 29.6 - - - +
369B GLY* 5.7 0.7 - - - -
370B ILE* 3.7 34.1 - - + +
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Residues in contact with LEU 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310B TRP* 3.1 59.5 + - + +
311B HIS 4.1 1.3 - - - +
313B TYR* 1.3 78.9 - - - +
315B HIS* 1.3 63.1 + - - +
317B MET* 4.5 2.7 - - - -
318B ILE* 3.0 37.3 + - + +
369B GLY* 3.5 31.4 - - - +
372B HIS* 4.6 7.6 - - + -
373B PHE* 4.1 18.2 - - + -
408B VAL* 5.1 2.5 - - + -
410B TYR* 3.9 25.4 - - + -
437B ALA* 4.0 8.5 - - + -
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Residues in contact with HIS 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A ASP* 5.6 0.8 + - - -
391A ASN* 4.0 17.6 + - + +
273B ASP* 2.7 41.4 + - - -
275B PHE* 3.6 11.7 - + - -
311B HIS* 2.8 47.0 + + + +
312B THR* 4.1 2.5 - - - +
314B LEU* 1.3 74.7 - - - +
316B ASP* 1.3 62.6 + - + +
319B GLY* 3.1 17.5 + - - -
394B GLU* 2.8 38.0 + - - +
410B TYR* 4.5 1.7 - - + -
412B ARG* 3.4 23.2 + - - -
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Residues in contact with ASP 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242B LYS* 2.7 26.9 + - - -
269B TRP* 3.3 42.2 - - + +
272B GLY 4.3 4.2 - - - +
273B ASP* 4.5 4.5 - - - +
275B PHE* 3.8 8.3 - - - -
292B PHE* 3.7 3.6 - - - -
312B THR* 3.1 17.7 + - + +
315B HIS* 1.3 79.5 - - + +
317B MET* 1.3 61.8 + - - +
319B GLY 3.5 0.2 + - - -
320B ASN* 2.9 56.7 + - - +
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Residues in contact with MET 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B PHE* 4.0 6.7 - - + -
269B TRP* 5.4 0.9 - - + -
313B TYR* 3.0 32.3 + - - +
314B LEU* 3.9 3.6 - - - +
316B ASP* 1.3 78.8 - - + +
318B ILE* 1.3 63.9 + - - +
320B ASN* 3.4 4.6 + - - +
321B PHE* 3.1 35.0 + - + -
328B PHE* 3.6 57.4 - - + -
369B GLY 4.9 1.3 - - - +
370B ILE* 4.2 23.3 - - + +
373B PHE* 3.6 47.1 - - + -
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Residues in contact with ILE 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B LEU* 3.0 25.5 + - + +
315B HIS 4.2 2.7 - - - +
317B MET* 1.3 75.4 - - - +
319B GLY* 1.3 64.9 + - - +
321B PHE* 3.9 1.0 - - - +
322B LYS* 3.0 26.6 + - + +
373B PHE* 3.7 22.4 - - + -
394B GLU* 3.9 22.9 - - + +
395B GLU* 3.7 36.1 - - - +
396B VAL* 4.1 7.7 - - + +
408B VAL* 4.5 10.5 - - + -
410B TYR* 3.5 34.1 - - + +
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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