Contacts of the helix formed by residues 314 - 322 (chain B) in PDB entry 1W1J
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312B ARG 3.8 0.4 + - - -
313B HIS* 1.3 84.5 - - + +
315B LEU* 1.3 58.2 + - + +
316B LEU 3.2 0.2 - - - -
317B ASP* 3.7 3.2 + - - +
318B ALA* 3.1 24.5 + - - +
339B LEU* 4.4 14.8 - - + +
342B ILE* 4.1 19.3 - - + +
343B ALA* 4.0 18.6 - - + +
346B LEU* 4.5 4.5 - - + -
348B LEU* 3.7 30.1 - - + -
349B GLY 3.2 21.5 - - - +
350B ARG* 3.0 41.8 + - - +
352B ASN* 4.3 4.7 - - - +
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Residues in contact with LEU 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313B HIS* 3.0 16.9 + - + +
314B ILE* 1.3 76.7 - - + +
316B LEU* 1.3 59.3 + - - +
318B ALA* 3.8 11.6 - - + +
319B ALA* 3.1 30.3 + - - +
334B LEU* 4.2 2.2 - - + -
339B LEU* 3.5 36.1 - - + -
342B ILE* 4.3 5.6 - - + -
416B TRP* 3.6 35.1 - - + -
453B ASP* 3.7 35.0 - - + +
454B PHE 3.8 9.0 - - - +
455B ILE* 4.0 18.1 - - + +
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Residues in contact with LEU 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B ARG* 3.5 31.2 - - + +
313B HIS* 2.8 17.9 + - - +
315B LEU* 1.3 78.9 - - - +
317B ASP* 1.3 62.5 + - - +
319B ALA* 4.0 2.0 - - - +
320B VAL* 3.3 25.5 + - - +
413B TRP* 3.7 40.5 - - + +
455B ILE* 3.8 22.1 - - + +
456B GLY* 3.8 18.6 - - - +
457B THR* 3.3 26.2 - - - +
470B CYS* 4.5 7.0 - - - -
1562B EUG 5.6 2.7 - - + -
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Residues in contact with ASP 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B ARG* 2.7 32.6 + - - +
313B HIS 3.7 6.5 + - - +
314B ILE* 3.7 4.5 + - - +
315B LEU 3.5 0.2 - - - -
316B LEU* 1.3 75.2 - - - +
318B ALA* 1.3 64.6 + - - +
320B VAL* 3.3 5.5 + - - +
321B LEU* 3.2 27.1 + - + +
346B LEU* 4.7 2.0 - - - -
348B LEU* 3.5 29.3 - - + +
352B ASN* 3.7 13.2 - - - +
354B TYR* 2.9 29.0 + - - -
394B VAL* 3.8 16.7 - - + +
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Residues in contact with ALA 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314B ILE 3.1 20.1 + - - +
315B LEU* 3.9 16.6 - - + +
316B LEU 3.4 0.2 - - - -
317B ASP* 1.3 75.7 - - - +
319B ALA* 1.3 57.7 + - - +
321B LEU 3.4 0.3 + - - -
322B GLY 2.9 19.9 + - - +
327B TYR* 2.6 38.1 + - + +
342B ILE* 3.8 21.5 - - + -
346B LEU* 4.0 6.7 - - + +
416B TRP* 4.6 0.9 - - + -
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Residues in contact with ALA 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315B LEU 3.1 20.2 + - - +
317B ASP 3.2 0.2 - - - -
318B ALA* 1.3 76.1 - - - +
320B VAL* 1.3 63.4 + - - +
321B LEU 3.2 0.6 + - - -
322B GLY* 3.7 16.5 + - - +
323B ASP* 4.6 1.6 + - - +
412B LYS* 3.2 18.9 - - - +
413B TRP* 3.4 25.4 - - + -
416B TRP* 3.7 29.0 + - + -
455B ILE* 5.9 2.2 - - + -
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Residues in contact with VAL 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312B ARG* 4.2 12.1 - - - +
316B LEU 3.3 14.5 + - - +
317B ASP* 3.3 10.0 + - - +
319B ALA* 1.3 77.4 - - - +
321B LEU* 1.3 69.9 + - + +
392B ASN 5.3 2.9 - - - +
394B VAL* 4.4 18.4 - - + -
397B VAL* 6.0 2.2 - - + -
409B ASP* 4.2 20.2 - - + +
410B GLU* 4.2 15.7 - - + +
412B LYS* 3.3 26.7 - - - +
413B TRP* 3.9 22.4 - - + +
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Residues in contact with LEU 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317B ASP* 3.2 17.3 + - + +
320B VAL* 1.3 88.9 - - + +
322B GLY* 1.3 58.3 + - - +
327B TYR* 3.9 10.5 - - - +
346B LEU* 3.8 31.9 - - + -
348B LEU* 5.8 2.5 - - + -
392B ASN* 3.4 55.3 + - + +
393B SER* 5.2 4.7 - - - -
394B VAL* 5.1 8.3 - - + -
412B LYS* 5.4 2.1 - - - +
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Residues in contact with GLY 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318B ALA 2.9 18.5 + - - +
319B ALA* 3.7 11.8 - - - -
320B VAL 3.7 0.6 - - - -
321B LEU* 1.3 80.0 - - - +
323B ASP* 1.3 70.4 + - - +
326B SER* 4.1 9.0 - - - -
327B TYR* 3.0 11.6 + - - -
412B LYS* 5.7 3.4 - - - -
416B TRP* 4.2 0.2 - - - -
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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