Contacts of the helix formed by residues 352 - 361 (chain B) in PDB entry 2WZJ
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 352 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117B GLU* 3.5 14.4 - - - +
118B VAL 4.9 3.4 - - - -
345B SER* 3.2 26.8 + - - +
350B ARG* 3.8 24.6 - - + +
351B TYR* 1.3 80.6 - - - +
353B GLU* 1.3 67.8 + - + +
354B VAL* 3.1 9.3 + - - +
355B MET* 3.0 20.8 + - - +
356B ALA* 3.3 15.4 + - - +
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Residues in contact with GLU 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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52B ASN* 3.6 29.4 + - - +
72B HIS* 5.1 0.3 + - - -
117B GLU* 3.7 20.6 + - - +
337B TYR* 3.6 16.3 + - - -
341B GLU* 5.8 0.2 - - - +
352B ASN* 1.3 77.7 - - + +
354B VAL* 1.3 72.0 + - + +
356B ALA* 3.8 1.8 - - - +
357B THR* 3.2 26.2 + - - -
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Residues in contact with VAL 354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332B MET* 3.4 23.8 - - + +
337B TYR* 4.0 22.9 - - + -
341B GLU* 4.3 15.5 - - + +
342B ILE* 3.6 24.7 - - + +
345B SER* 3.1 30.5 - - - +
346B LEU* 5.7 1.6 - - + -
352B ASN* 3.1 8.4 + - - +
353B GLU* 1.3 84.1 - - + +
355B MET* 1.3 64.8 + - - +
357B THR* 3.3 4.3 + - - -
358B TYR* 3.1 21.4 + - + +
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Residues in contact with MET 355 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B LYS* 5.5 1.1 - - - +
116B PHE 4.8 1.8 - - - +
322B ASP 6.1 0.9 - - - +
345B SER* 4.2 7.1 - - - +
346B LEU* 3.9 25.1 - - + -
349B GLN* 3.5 37.7 - - - +
350B ARG 3.7 11.7 - - - -
351B TYR* 3.4 51.6 - - + +
352B ASN* 3.0 15.2 + - - +
354B VAL* 1.3 76.4 - - - +
356B ALA* 1.3 62.9 + - - +
358B TYR* 3.4 1.4 + - - +
359B LEU* 3.0 47.3 + - + +
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Residues in contact with ALA 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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53B TYR* 3.5 11.4 - - - +
72B HIS* 4.9 3.8 - - - +
116B PHE* 3.7 22.4 + - + +
117B GLU* 3.4 25.1 - - + +
352B ASN 3.3 10.4 + - - +
353B GLU* 3.8 5.4 - - - +
354B VAL 3.2 0.2 - - - -
355B MET* 1.3 79.7 - - - +
357B THR* 1.3 63.4 + - - +
359B LEU* 3.2 4.6 + - - +
360B LEU* 2.8 32.9 + - + +
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Residues in contact with THR 357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B HIS* 3.3 31.3 + - + -
74B LEU* 4.0 1.9 - - + +
75B THR* 4.4 2.9 - - + -
332B MET* 4.0 5.4 - - + -
335B MET* 4.2 10.8 - - - -
337B TYR* 2.9 39.8 + - + -
353B GLU 3.2 5.9 + - - -
354B VAL 3.3 8.6 + - - -
356B ALA* 1.3 77.0 - - - +
358B TYR* 1.3 66.7 + - - +
360B LEU* 3.8 1.3 - - - +
361B LEU* 3.1 40.6 + - + +
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Residues in contact with TYR 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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322B ASP* 2.8 48.2 + - - -
323B TYR* 3.9 7.9 - - - -
324B LYS 3.3 5.0 + - - -
325B ASP* 3.0 21.6 + - - +
328B ARG* 3.0 53.5 + - + -
329B THR* 4.3 15.9 - - - -
332B MET* 3.7 21.6 - - - -
342B ILE* 4.9 2.2 - - + -
346B LEU* 3.4 30.7 - - + -
354B VAL* 3.1 13.8 + - + +
355B MET 3.5 8.3 - - - +
356B ALA 3.2 0.2 - - - -
357B THR* 1.3 79.8 - - - +
359B LEU* 1.3 71.1 + - + +
361B LEU* 3.3 7.3 + - - -
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Residues in contact with LEU 359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B LYS* 4.7 14.8 - - - +
115B LEU 4.3 10.5 - - - +
116B PHE* 4.1 32.3 - - + +
322B ASP* 4.5 15.5 - - + +
328B ARG* 4.1 3.7 + - - +
346B LEU* 5.5 0.2 - - + -
351B TYR* 4.9 0.4 - - + -
355B MET* 3.0 48.8 + - + +
356B ALA 3.8 2.9 - - - +
358B TYR* 1.3 91.3 - - + +
360B LEU* 1.3 66.0 + - - +
362B GLY* 3.2 10.2 + - - -
363B TYR* 3.3 19.1 - - + -
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Residues in contact with LEU 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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53B TYR* 4.6 6.1 - - + +
72B HIS* 3.3 45.3 - - + +
75B THR* 4.1 13.9 - - + +
77B LYS* 3.3 32.9 + - + +
78B GLU 5.5 0.4 - - - +
79B VAL* 3.8 15.7 - - + -
116B PHE* 3.5 43.5 - - + -
356B ALA* 2.8 22.2 + - + +
357B THR 3.9 3.1 - - - +
359B LEU* 1.3 77.3 - - - +
361B LEU* 1.3 59.7 + - - +
362B GLY 3.1 4.9 + - - -
363B TYR* 3.3 13.5 + - + +
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Residues in contact with LEU 361 (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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75B THR* 3.9 22.9 - - + -
77B LYS* 4.7 5.0 + - - +
327B ARG* 3.7 17.2 + - - +
328B ARG* 3.5 32.3 - - + +
331B LEU* 4.4 18.8 - - + -
332B MET* 3.6 30.7 - - + -
335B MET* 4.1 17.3 - - + -
357B THR* 3.1 26.5 + - + +
358B TYR 4.5 0.4 - - - +
359B LEU 3.3 0.4 - - - -
360B LEU* 1.3 74.3 - - - +
362B GLY* 1.3 55.0 + - - +
363B TYR 3.2 7.1 + - - -
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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