Contacts of the helix formed by residues 302 - 311 (chain A) in PDB entry 1WLZ
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 LYS 302 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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263A ASN 3.9 8.7 - - - +
264A THR* 4.2 7.4 - - + -
294A PRO* 2.9 38.6 + - - +
295A VAL 4.1 9.3 + - - -
296A ASN* 4.0 28.4 - - + +
301A LEU* 1.3 69.4 - - - +
303A TYR* 1.3 62.9 + - - +
304A PRO* 3.4 4.3 - - + -
305A ASP* 3.2 32.7 + - + +
306A PHE 3.2 15.6 + - - -
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Residues in contact with TYR 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A THR* 5.2 1.3 - - + -
254A PHE* 3.7 48.0 - + + -
255A GLU* 3.4 28.9 + - + -
258A ASP* 2.7 35.4 + - + +
261A LYS* 5.2 0.9 - - - +
263A ASN* 3.2 23.1 + - - -
264A THR* 3.2 30.5 - - - -
265A ILE* 3.8 11.9 - - + -
301A LEU* 3.1 10.5 + - + -
302A LYS* 1.3 70.6 - - - +
304A PRO* 1.3 83.7 - - + +
306A PHE* 3.4 8.0 - - - +
307A LEU* 2.8 38.4 + - + +
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Residues in contact with PRO 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A ASN* 3.2 40.6 - - + +
302A LYS* 3.4 4.7 - - + -
303A TYR* 1.3 104.3 - - + +
305A ASP* 1.3 67.7 + - - +
307A LEU* 3.5 8.4 + - + +
308A SER* 3.1 23.9 + - - -
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Residues in contact with ASP 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A PRO* 4.0 16.3 - - + +
302A LYS* 3.2 41.9 + - - +
303A TYR 3.1 0.4 - - - -
304A PRO* 1.3 83.7 - - - +
306A PHE* 1.3 64.2 + - - +
308A SER* 3.4 6.4 + - - -
309A ARG* 3.1 23.9 + - - +
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Residues in contact with PHE 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A LEU* 3.9 14.4 - - + -
243A VAL* 3.7 32.1 - - + -
250A ILE* 5.1 2.0 - - + -
254A PHE* 3.7 33.4 - + - -
270A PHE* 3.8 20.2 - + - -
293A MET* 3.6 27.1 - - - -
294A PRO* 3.8 13.8 - - + +
301A LEU* 4.3 8.1 - - + -
302A LYS 3.2 4.6 + - - +
303A TYR* 3.1 16.1 + - - +
305A ASP* 1.3 79.5 - - - +
307A LEU* 1.3 62.9 + - + +
309A ARG* 3.3 2.7 + - - -
310A PHE* 2.9 60.6 + + - +
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Residues in contact with LEU 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A VAL* 4.2 14.4 - - + -
247A TYR* 3.9 26.0 - - + +
250A ILE* 4.5 6.7 - - + -
251A THR* 3.7 34.3 - - + +
254A PHE* 3.7 34.3 - - + -
303A TYR* 2.8 34.5 + - + +
304A PRO* 3.8 7.2 - - + +
306A PHE* 1.3 75.7 - - + +
308A SER* 1.3 57.1 + - - +
311A SER* 2.6 38.7 + - - -
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Residues in contact with SER 308 (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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247A TYR* 5.3 0.4 + - - -
304A PRO 3.1 18.1 + - - -
305A ASP* 3.7 6.7 - - - -
307A LEU* 1.3 77.8 - - - +
309A ARG* 1.3 64.3 + - - +
311A SER* 3.5 15.8 + - - -
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Residues in contact with ARG 309 (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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227A HIS* 5.9 2.2 + - - -
236A LEU* 4.4 15.4 - - - +
240A HIS* 3.1 23.3 + - + -
292A GLU* 2.6 39.4 + - - +
293A MET* 4.3 1.4 - - - +
294A PRO* 5.1 5.7 - - - +
305A ASP 3.1 15.3 + - - +
306A PHE* 3.7 3.8 - - - +
308A SER* 1.3 81.3 - - - +
310A PHE* 1.3 95.4 + - + +
311A SER 3.4 2.8 + - - -
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Residues in contact with PHE 310 (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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236A LEU* 4.0 15.7 - - + -
239A LEU* 3.8 17.9 - - + -
240A HIS* 3.3 71.9 + + - +
243A VAL* 3.6 25.3 - - + +
244A THR* 3.6 3.3 - - - +
293A MET* 3.6 26.9 - - + -
294A PRO* 5.6 1.1 - - + -
306A PHE* 2.9 51.0 + + - +
307A LEU 3.8 0.4 - - - -
309A ARG* 1.3 107.6 - - + +
311A SER* 1.3 57.3 + - - +
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Residues in contact with SER 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A HIS* 5.5 1.3 - - - -
243A VAL* 4.1 1.8 - - - -
244A THR* 3.8 19.7 - - - +
247A TYR* 3.5 32.4 + - - -
307A LEU 2.6 24.4 + - - -
308A SER* 3.5 14.6 + - - -
309A ARG 3.3 3.6 - - - -
310A PHE* 1.3 80.3 - - - +
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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
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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