Contacts of the helix formed by residues 351 - 360 (chain B) in PDB entry 2W8D
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 351 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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481A LYS* 5.6 3.2 - - - +
317B PHE* 2.7 26.7 + - - +
318B VAL* 3.7 25.0 + - + +
321B ALA* 3.5 18.4 - - - +
348B THR 2.9 15.8 + - - -
350B TRP* 1.3 77.1 - - - +
352B ARG* 1.3 63.2 + - - +
353B ASN* 3.3 9.8 - - - +
354B GLU* 3.1 31.4 + - - +
355B MSE 3.2 16.3 + - - +
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Residues in contact with ARG 352 (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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297B TPO 4.0 19.6 + - - +
298B SER 4.9 0.2 - - - +
301B GLU* 2.9 30.5 + - - -
317B PHE* 3.5 25.6 - - + -
343B HIS* 2.9 40.1 + - - -
346B THR 5.5 0.8 + - - -
347B GLN 3.5 8.7 + - - +
349B PHE* 3.2 40.9 + - - +
350B TRP* 2.9 17.5 + - + +
351B ASN* 1.3 76.8 - - - +
353B ASN* 1.3 57.3 + - - +
356B TYR* 2.9 64.5 + - + +
364B PHE* 3.9 14.9 - - + -
407B ILE* 4.1 8.0 - - - +
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Residues in contact with ASN 353 (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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347B GLN* 3.0 50.7 + - + +
348B THR* 3.7 21.3 - - - +
351B ASN* 3.8 12.1 - - - +
352B ARG* 1.3 71.4 - - - +
354B GLU* 1.3 61.4 + - - +
357B LYS* 3.1 40.4 + - - +
364B PHE* 4.3 2.7 - - - -
632B TYR* 3.5 13.7 - - + -
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Residues in contact with GLU 354 (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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481A LYS* 3.8 25.1 + - - -
318B VAL 5.2 1.6 - - - +
321B ALA* 3.5 16.6 - - + +
322B GLN* 2.9 31.5 + - - +
351B ASN* 3.1 33.4 + - - +
352B ARG 3.2 0.4 - - - -
353B ASN* 1.3 84.0 + - - +
355B MSE 1.3 64.7 + - - +
356B TYR 3.4 0.2 - - - -
357B LYS* 3.4 19.2 + - + +
358B ALA* 3.6 8.8 + - - +
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Residues in contact with MSE 355 (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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302B PHE* 4.1 17.7 - - + -
316B VAL* 3.3 29.8 - - + +
317B PHE* 3.6 57.9 - - + +
320B LYS 3.5 22.2 - - - +
321B ALA* 3.7 14.5 - - - +
325B LEU* 3.6 26.5 - - + -
351B ASN 3.2 8.5 + - - +
354B GLU* 1.3 80.4 - - - +
356B TYR* 1.3 61.6 + - - +
358B ALA* 3.0 16.0 + - - +
359B GLU* 3.2 20.4 + - - +
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Residues in contact with TYR 356 (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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301B GLU* 2.4 33.7 + - - -
317B PHE* 3.9 15.3 - + - -
341B THR* 3.3 38.2 - - - +
352B ARG* 2.9 32.3 + - + +
355B MSE 1.3 76.9 - - - +
357B LYS* 1.3 57.1 + - - +
359B GLU* 3.1 18.5 + - - -
360B GLY 2.9 22.9 + - - -
361B ILE* 3.1 27.1 + - + -
364B PHE* 3.6 39.3 - + + -
405B LYS* 3.3 12.5 + - - -
407B ILE* 4.4 1.2 - - - +
632B TYR* 3.1 17.0 - - + +
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Residues in contact with LYS 357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347B GLN* 5.8 0.6 - - - +
353B ASN* 3.1 37.6 + - - +
354B GLU* 3.4 12.1 + - + +
355B MSE 3.2 0.8 - - - -
356B TYR* 1.3 77.1 - - - +
358B ALA* 1.3 61.5 + - - +
360B GLY* 3.1 11.5 + - - +
625B VAL* 3.4 14.4 - - - +
627B PRO* 3.6 33.0 - - + +
628B SER* 5.7 0.7 - - - -
630B TYR* 3.2 35.1 - - + +
631B ASP* 4.9 2.0 - - - +
632B TYR* 3.2 28.4 + - + +
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Residues in contact with ALA 358 (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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321B ALA 3.5 24.2 - - - +
323B ASN 3.9 15.0 - - - +
325B LEU* 3.5 33.3 + - + +
327B SER* 4.2 0.2 + - - -
354B GLU 3.6 3.4 + - - +
355B MSE 3.0 13.2 + - - +
357B LYS* 1.3 80.1 - - - +
359B GLU* 1.3 59.5 + - - +
360B GLY 3.3 0.2 - - - -
625B VAL* 3.9 13.4 - - - +
627B PRO* 4.7 11.8 - - + +
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Residues in contact with GLU 359 (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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302B PHE* 3.9 14.0 - - - -
305B GLU* 3.5 21.3 - - + +
306B ASN* 2.7 26.4 + - - -
317B PHE* 4.2 3.4 - - - -
325B LEU* 4.1 9.0 - - + -
327B SER* 3.3 27.2 - - - +
329B PRO* 3.4 16.6 - - - +
330B ALA* 3.7 10.9 + - - +
355B MSE 3.4 20.0 - - - +
356B TYR* 3.1 33.1 + - - +
358B ALA* 1.3 78.1 - - - +
360B GLY* 1.3 61.5 + - - +
361B ILE* 3.4 9.2 - - + +
625B VAL* 4.8 0.2 - - - -
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Residues in contact with GLY 360 (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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329B PRO* 4.2 4.1 - - - +
330B ALA* 4.8 1.3 - - - -
333B LYS* 2.8 28.4 + - - -
339B SER* 3.2 4.0 + - - -
356B TYR 2.9 3.2 + - - -
357B LYS 3.1 12.5 + - - -
358B ALA 3.3 0.8 - - - -
359B GLU* 1.3 79.9 - - - +
361B ILE* 1.3 63.0 + - - +
625B VAL* 4.3 9.1 - - - +
630B TYR* 3.7 20.9 - - - -
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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