Contacts of the helix formed by residues 314 - 320 (chain A) in PDB entry 2WWA
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 ILE 314 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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306A ILE 4.2 0.2 - - - +
307A HIS 3.1 31.6 - - - +
308A ILE 3.6 7.9 - - - +
309A PHE* 3.6 2.5 - - - -
310A ALA 3.2 35.0 - - - +
311A PHE 3.8 0.4 + - - -
312A VAL 3.3 0.2 - - - -
313A LEU* 1.4 74.7 - - - +
315A GLN* 1.4 63.5 + - - +
316A LEU 3.1 2.0 - - - -
317A VAL* 3.4 6.9 + - + +
318A ALA* 3.2 22.2 + - - +
330A MET* 3.5 21.5 - - + +
331A GLY* 3.4 36.3 - - - +
333A TYR* 3.6 14.7 - - + -
348A SER* 3.7 6.5 - - - +
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Residues in contact with GLN 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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65A ILE* 4.9 17.0 - - - +
67A PHE* 4.5 16.3 - - - -
68A LEU* 5.9 1.0 - - - +
138A ALA* 3.7 31.5 + - + +
139A GLY 5.8 0.2 - - - -
140A TYR* 5.6 7.5 - - - +
311A PHE 3.4 20.2 + - - +
312A VAL* 3.8 10.7 - - - +
314A ILE* 1.4 77.6 - - - +
316A LEU* 1.4 60.1 + - - +
318A ALA* 4.0 2.9 - - - +
319A LYS* 3.3 21.7 + - - +
333A TYR* 4.2 31.3 - - + +
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Residues in contact with LEU 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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134A ILE* 3.0 50.3 - - + +
137A PHE* 3.6 19.5 - - + +
138A ALA* 3.6 17.7 - - + +
312A VAL 3.2 22.2 - - - +
313A LEU* 3.6 33.0 - - + +
314A ILE 3.1 0.2 - - - -
315A GLN* 1.4 78.5 - - - +
317A VAL* 1.4 57.6 + - + +
318A ALA 3.3 1.1 - - - -
319A LYS* 3.4 2.4 + - - +
320A ASN* 2.9 41.5 + - - +
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Residues in contact with VAL 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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307A HIS* 4.5 8.3 - - + -
313A LEU 4.4 3.1 - - - +
314A ILE* 3.4 21.5 + - + +
316A LEU* 1.4 75.0 - - + +
318A ALA* 1.4 60.9 + - - +
320A ASN* 3.0 25.4 - - + +
322A PRO 5.3 3.8 - - - +
326A ILE* 3.9 23.8 - - + +
327A CYS* 3.3 42.8 - - - +
328A LYS* 3.8 15.5 + - - +
330A MET* 4.2 14.1 - - + -
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Residues in contact with ALA 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 ILE 3.2 17.0 + - - +
315A GLN 4.0 3.1 - - - +
317A VAL* 1.4 77.5 - - - +
319A LYS* 1.4 63.7 + - - +
320A ASN 3.8 2.8 - - - +
321A GLU* 5.4 0.7 - - - -
328A LYS* 3.7 30.6 + - + +
331A GLY 4.2 4.9 - - - +
333A TYR* 3.7 43.6 - - + +
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Residues in contact with LYS 319 (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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136A ILE 6.0 0.7 - - - -
137A PHE* 3.3 28.7 - - - +
138A ALA 3.8 9.0 - - - +
139A GLY* 4.4 17.3 - - - -
143A ASP 5.9 0.4 - - - -
144A ASP* 3.2 39.7 + - - -
315A GLN 3.3 12.7 + - - +
316A LEU 3.6 0.4 - - - +
318A ALA* 1.4 77.9 - - - +
320A ASN* 1.4 67.5 + - - +
321A GLU* 3.6 6.6 + - - +
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Residues in contact with ASN 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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137A PHE* 4.2 27.8 + - - +
316A LEU* 2.9 30.6 + - - +
317A VAL* 3.0 27.9 - - + +
318A ALA 3.8 2.8 - - - +
319A LYS* 1.4 82.2 + - - +
321A GLU* 1.4 60.9 + - - +
322A PRO* 3.6 15.0 - - + +
323A THR* 5.9 0.5 - - - +
328A LYS* 5.4 1.6 - - - -
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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