Contacts of the helix formed by residues 308 - 315 (chain A) in PDB entry 1WDR
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 HIS 308 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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301A TRP 5.4 0.2 - - - -
302A TRP* 3.4 14.1 + - - -
303A TYR* 3.0 41.3 + + - -
305A VAL 3.2 22.2 + - - -
306A GLU 3.5 13.0 - - - -
307A ASN* 1.3 77.8 - - - +
309A ALA* 1.3 65.0 + - - +
310A ALA 3.3 2.2 - - - -
311A GLU* 2.7 30.1 + - - +
312A LEU* 3.0 19.7 + - + +
318A ASN* 3.0 35.8 + - - +
319A LEU* 3.7 8.3 - - - -
320A ASN* 2.7 29.2 + - - -
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Residues in contact with ALA 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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203A ILE* 3.7 26.9 - - + -
242A PRO* 4.3 1.8 - - + -
248A PHE* 3.6 31.1 - - + -
302A TRP* 3.8 5.5 - - + +
307A ASN* 3.1 24.3 - - - +
308A HIS* 1.3 75.7 - - - +
310A ALA* 1.3 58.1 + - - +
312A LEU* 3.2 2.9 + - - +
313A THR* 2.9 31.4 + - - +
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Residues in contact with ALA 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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191A SER* 4.5 1.0 + - - -
192A TYR* 5.9 0.3 - - - -
203A ILE 3.4 17.5 + - - +
299A ILE* 3.5 14.1 - - + +
301A TRP* 3.4 45.5 - - + +
302A TRP* 3.9 7.8 - - + +
308A HIS 3.3 0.6 - - - -
309A ALA* 1.3 75.3 - - - +
311A GLU* 1.3 66.6 + - - +
313A THR* 3.4 2.6 + - - -
314A ALA* 3.1 23.2 + - - +
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Residues in contact with GLU 311 (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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299A ILE* 3.3 31.4 - - + +
301A TRP 4.8 1.2 + - - +
303A TYR* 3.5 21.9 + - - -
308A HIS* 2.7 39.1 + - + +
310A ALA* 1.3 78.2 - - - +
312A LEU* 1.4 63.1 + - + +
314A ALA* 3.1 5.7 + - - +
315A GLY 3.1 5.7 + - - -
316A TYR* 2.9 35.2 + - + +
318A ASN* 2.9 23.5 + - + +
325A TYR* 2.7 30.9 + - - +
362A LEU* 4.0 0.4 - - - +
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Residues in contact with LEU 312 (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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206A PHE* 3.6 4.4 - - - -
248A PHE* 3.9 18.4 - - + -
254A TYR* 4.5 6.7 - - + -
263A LEU* 3.8 38.6 - - + +
266A TYR* 3.4 13.3 - - - -
307A ASN 3.5 17.7 - - - +
308A HIS 3.0 17.4 + - - +
309A ALA 3.5 8.3 - - - +
311A GLU* 1.4 76.5 - - - +
313A THR* 1.3 61.8 + - - +
315A GLY* 3.1 12.3 + - - -
316A TYR 3.6 13.7 - - - +
317A TYR* 4.1 9.2 - - + +
318A ASN 3.5 27.4 - - - +
319A LEU* 4.0 12.6 - - + -
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Residues in contact with THR 313 (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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189A TYR* 4.0 0.5 - - - +
191A SER* 3.2 18.1 + - - -
203A ILE 2.7 26.4 + - - +
204A GLY* 3.8 8.4 - - - +
205A GLU* 3.8 14.6 - - - -
206A PHE* 3.7 27.8 - - + +
235A ALA* 5.9 0.4 - - + -
248A PHE* 3.8 22.9 - - + -
266A TYR* 2.7 25.3 + - - -
309A ALA 2.9 16.2 + - - +
310A ALA 3.4 5.4 + - - -
312A LEU* 1.3 74.9 - - - +
314A ALA* 1.3 58.9 + - - +
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Residues in contact with ALA 314 (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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188A ARG* 3.6 10.7 - - + +
189A TYR* 2.9 31.5 + - - +
191A SER* 3.2 16.9 + - - +
192A TYR* 4.8 2.0 - - + -
270A LEU* 3.7 0.2 - - - +
299A ILE* 4.0 25.8 - - + -
310A ALA 3.1 18.5 + - - +
311A GLU 3.1 5.6 + - - +
313A THR* 1.3 76.1 - - - +
315A GLY* 1.3 58.7 + - - +
316A TYR* 4.2 9.5 - - + -
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Residues in contact with GLY 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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189A TYR* 3.7 17.5 - - - -
266A TYR* 3.8 8.5 - - - -
267A SER* 3.3 26.4 - - - +
270A LEU* 3.7 10.8 - - - +
312A LEU 3.1 13.5 + - - -
313A THR 3.2 1.4 - - - -
314A ALA* 1.3 80.0 - - - +
316A TYR* 1.3 65.7 + - - +
317A TYR 3.7 0.8 + - - -
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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