Contacts of the helix formed by residues 330 - 338 (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 LEU 330 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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288A HIS* 4.3 9.0 - - + -
293A TYR* 3.6 29.8 - - + -
296A LEU* 4.5 7.0 - - + -
297A HIS* 4.5 7.4 - - - +
307A LEU* 5.0 11.9 - - + -
311A ALA* 3.9 24.0 - - + -
315A HIS* 4.1 16.4 - - + -
328A THR* 2.9 9.0 + - - +
329A TYR* 1.3 77.9 - - - +
331A ALA* 1.3 62.2 + - - +
332A PRO* 3.3 2.9 - - - -
333A GLU* 3.0 35.1 + - + +
334A PHE* 3.0 34.5 + - + -
337A TRP* 4.5 9.6 - - + -
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Residues in contact with ALA 331 (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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41A LEU* 4.2 22.6 - - + +
43A PHE* 3.8 22.0 - - + +
83A LEU* 4.8 6.1 - - + -
328A THR* 3.5 26.3 + - + +
330A LEU* 1.3 76.8 - - - +
332A PRO* 1.3 73.5 - - + +
334A PHE* 3.0 3.9 + - - +
335A LEU* 2.8 28.5 + - + +
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Residues in contact with PRO 332 (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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43A PHE* 3.6 31.4 - - + -
63A ILE* 5.9 0.4 - - + -
74A TYR* 5.6 0.4 - - - +
78A LEU* 4.1 25.8 - - + -
81A LYS* 4.7 5.9 + - - +
329A TYR 3.4 12.6 - - - +
330A LEU 3.4 4.3 - - - -
331A ALA* 1.3 96.1 - - + +
333A GLU* 1.3 69.8 + - - +
335A LEU* 3.4 16.3 + - + +
336A ASP* 3.7 12.2 + - - +
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Residues in contact with GLU 333 (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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62A ASN* 4.5 17.5 + - - +
293A TYR* 4.7 3.6 + - - -
297A HIS* 5.1 3.1 - - - -
307A LEU* 5.6 4.0 - - + +
329A TYR 3.8 2.6 - - - +
330A LEU* 3.0 38.5 + - + +
332A PRO* 1.3 82.1 - - - +
334A PHE* 1.3 60.2 + - - +
336A ASP* 2.8 26.5 + - - +
337A TRP* 3.0 51.1 + - + -
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Residues in contact with PHE 334 (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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36A LEU* 3.6 26.5 - - + -
41A LEU* 3.6 27.1 - - + -
311A ALA* 3.5 29.6 - - + -
312A PHE* 3.7 30.1 - + - -
315A HIS* 3.3 36.3 - + + -
328A THR* 5.0 0.2 - - + -
330A LEU* 3.0 33.6 + - + -
331A ALA 3.7 2.5 - - - +
333A GLU* 1.3 76.9 - - - +
335A LEU* 1.3 58.5 + - - +
337A TRP* 3.8 19.3 - + - -
338A LEU* 2.8 42.5 + - + +
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Residues in contact with LEU 335 (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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38A LYS* 3.2 44.4 + - + +
41A LEU* 4.3 9.4 - - + -
78A LEU* 3.4 41.1 - - + +
81A LYS* 3.6 33.4 - - + +
82A GLY 3.8 1.6 - - - +
83A LEU* 3.7 34.5 - - + +
331A ALA 2.8 17.0 + - - +
332A PRO* 3.5 11.0 - - + +
333A GLU 3.1 0.2 - - - -
334A PHE* 1.3 76.8 - - - +
336A ASP* 1.3 59.3 + - - +
339A ASP* 3.5 9.9 - - - +
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Residues in contact with ASP 336 (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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81A LYS* 3.4 35.0 + - - +
332A PRO 3.8 8.7 - - - +
333A GLU* 2.8 13.4 + - - +
335A LEU* 1.3 77.6 - - - +
337A TRP* 1.3 66.2 + - + +
338A LEU 3.3 1.1 - - - -
339A ASP* 3.0 31.7 + - - +
340A GLU* 3.9 10.7 + - - +
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Residues in contact with TRP 337 (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 LEU* 4.6 6.7 - - + -
308A LYS* 3.7 53.6 + - + +
311A ALA* 3.7 25.6 - - + -
312A PHE* 3.4 38.6 - + + -
330A LEU* 4.5 6.5 - - + -
333A GLU* 3.4 40.9 + - + +
334A PHE* 3.8 28.5 - + - +
336A ASP* 1.3 81.0 - - + +
338A LEU* 1.3 58.8 + - - +
339A ASP 2.9 10.1 + - - -
340A GLU* 3.0 33.1 + - - +
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Residues in contact with LEU 338 (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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36A LEU* 3.7 43.1 - - + +
37A THR* 3.9 6.7 - - - +
38A LYS* 3.8 46.2 - - + +
41A LEU* 4.1 12.3 - - + -
312A PHE* 4.5 12.6 - - + -
334A PHE* 2.8 33.5 + - + +
337A TRP* 1.3 71.1 - - - +
339A ASP* 1.3 62.5 + - - +
340A GLU 3.4 6.0 - - - +
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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