Contacts of the helix formed by residues 289 - 302 (chain A) in PDB entry 1W31
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 VAL 289 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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215A LEU* 3.2 37.7 - - + +
216A TYR* 3.8 6.5 - - + -
263A LYS* 3.3 46.7 - - + -
264A PRO* 4.1 7.9 - - + -
287A TYR* 2.9 14.7 + - + +
288A HIS* 1.3 75.3 - - - +
290A SER* 1.3 66.1 + - - +
292A GLU* 3.0 21.1 + - + +
293A TYR* 2.9 20.3 + - - +
329A TYR* 4.2 0.2 - - - -
363A SHO 3.7 12.3 - - + +
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Residues in contact with SER 290 (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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60A LEU* 3.8 12.6 - - - -
215A LEU 3.6 5.2 + - - -
216A TYR 3.6 2.6 - - - -
218A PRO* 3.1 30.9 - - - +
219A PHE* 3.1 16.6 + - - -
289A VAL* 1.3 70.5 - - - +
291A GLY* 1.3 60.2 + - - +
293A TYR* 3.3 3.2 + - - +
294A ALA* 2.7 38.5 + - - +
329A TYR* 3.8 11.8 - - - -
363A SHO 2.7 29.8 + - - -
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Residues in contact with GLY 291 (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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214A ASN 5.3 0.4 - - - -
215A LEU* 2.8 44.2 + - - +
217A GLY 4.9 0.2 - - - -
218A PRO* 4.1 10.1 - - - -
290A SER* 1.3 76.9 + - - +
292A GLU* 1.3 56.8 + - - +
294A ALA* 3.9 2.5 - - - +
295A MET* 2.9 29.1 + - - +
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Residues in contact with GLU 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A LEU* 3.9 15.9 - - + +
264A PRO* 3.4 10.6 - - - +
265A SER* 3.0 31.9 + - - -
266A THR* 3.0 26.4 + - - +
267A PHE* 3.3 23.0 + - + -
288A HIS* 3.5 15.8 - - - +
289A VAL* 3.0 29.9 + - + +
291A GLY* 1.3 72.4 - - - +
293A TYR* 1.3 67.1 + - - +
295A MET* 3.2 8.7 + - - +
296A LEU* 3.0 28.2 + - - +
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Residues in contact with TYR 293 (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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60A LEU* 3.8 23.1 - - + -
61A PRO* 2.7 42.8 + - + -
62A ASN* 3.8 8.8 + - - +
63A ILE* 4.2 1.9 - - + +
288A HIS* 3.6 17.4 - - - +
289A VAL 2.9 16.0 + - - +
290A SER 3.5 2.9 - - - +
292A GLU* 1.3 76.9 - - - +
294A ALA* 1.3 62.4 + - - +
296A LEU* 3.3 4.9 + - - +
297A HIS* 3.2 50.5 + + - -
329A TYR* 3.7 39.8 + - + +
330A LEU* 3.6 34.8 - - + -
333A GLU* 4.7 3.5 + - - -
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Residues in contact with ALA 294 (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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59A SER 4.0 9.2 - - - +
61A PRO* 4.6 8.5 - - + -
218A PRO* 3.9 17.7 - - + -
290A SER 2.7 21.7 + - - +
291A GLY* 4.0 3.4 - - - +
293A TYR* 1.3 74.6 - - + +
295A MET* 1.3 59.7 + - - +
297A HIS* 3.3 7.4 + - - +
298A ALA* 2.9 31.3 + - - +
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Residues in contact with MET 295 (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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215A LEU* 3.7 26.9 - - + -
267A PHE* 3.8 28.7 - - + -
291A GLY 2.9 16.7 + - - +
292A GLU* 3.2 8.3 + - - +
294A ALA* 1.3 77.4 - - - +
296A LEU* 1.3 68.6 + - + +
298A ALA* 3.5 6.5 + - - +
299A ALA* 3.1 26.0 + - + +
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Residues in contact with LEU 296 (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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288A HIS* 3.7 26.0 - - + +
292A GLU 3.0 17.8 + - - +
293A TYR 3.7 6.3 - - - +
294A ALA 3.2 0.2 - - - -
295A MET* 1.3 82.4 - - + +
297A HIS* 1.3 60.3 + - - +
299A ALA* 3.4 5.3 + - + +
300A ALA* 2.9 30.7 + - - +
305A VAL* 4.6 4.0 - - + +
307A LEU* 4.1 13.3 - - + +
310A ILE* 4.1 35.4 - - + +
311A ALA* 4.3 8.3 - - + -
314A SER* 3.9 20.6 - - - +
330A LEU* 4.5 7.4 - - + -
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Residues in contact with HIS 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A PRO* 4.3 17.1 - - + +
62A ASN* 3.8 19.2 + - - -
293A TYR* 3.2 62.0 + + - -
294A ALA* 3.3 9.2 + - - +
296A LEU* 1.3 79.7 - - - +
298A ALA* 1.3 56.1 + - - +
300A ALA* 3.2 3.0 + - - +
301A GLU* 2.9 48.6 + - - +
307A LEU* 3.4 38.1 - - + +
330A LEU* 4.5 5.2 - - + +
333A GLU* 5.1 2.7 - - - -
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Residues in contact with ALA 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A ALA 2.9 17.5 + - - +
295A MET* 3.7 7.9 - - - +
297A HIS* 1.3 76.8 - - - +
299A ALA* 1.3 63.1 + - - +
301A GLU* 3.2 16.7 + - - +
302A LYS* 3.0 22.7 + - - +
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Residues in contact with ALA 299 (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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295A MET* 3.1 17.8 + - + +
296A LEU* 3.9 5.2 - - + +
298A ALA* 1.3 78.3 - - - +
300A ALA* 1.3 60.6 + - - +
302A LYS* 3.3 2.6 + - - +
303A GLY 3.3 2.8 + - - -
304A VAL* 2.8 48.8 + - + +
305A VAL* 3.9 16.6 - - + -
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Residues in contact with ALA 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A LEU 2.9 18.9 + - - +
297A HIS* 3.5 5.8 - - - +
299A ALA* 1.3 77.7 - - - +
301A GLU* 1.3 59.3 + - + +
303A GLY* 2.9 20.8 + - - -
305A VAL* 3.2 23.9 - - + +
307A LEU* 4.0 30.5 - - + +
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Residues in contact with GLU 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A PRO* 5.6 3.3 - - - +
297A HIS* 2.9 37.3 + - - +
298A ALA* 3.4 13.2 - - - +
300A ALA* 1.3 77.8 - - + +
302A LYS* 1.3 56.6 + - - +
303A GLY* 3.0 4.7 + - - -
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Residues in contact with LYS 302 (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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298A ALA 3.0 15.2 + - - +
299A ALA* 3.3 4.0 + - - +
300A ALA 3.2 0.6 - - - -
301A GLU* 1.3 74.4 - - - +
303A GLY* 1.3 61.4 + - - +
304A VAL* 3.0 24.5 - - + +
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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