Contacts of the helix formed by residues 314 - 322 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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312A ARG 3.8 0.9 + - - -
313A HIS* 1.3 82.4 - - + +
315A LEU* 1.3 69.1 + - + +
316A LEU 3.0 1.0 + - - -
317A ASP* 3.1 7.8 + - - +
318A ALA* 2.9 17.7 + - + -
339A LEU* 4.0 15.5 - - + +
342A ILE* 4.1 17.5 - - + -
343A ALA* 3.8 22.2 - - - +
346A LEU* 4.2 10.5 - - + -
348A LEU* 3.7 25.6 - - + -
349A GLY 3.6 26.0 - - - +
350A ARG* 3.5 38.4 + - - +
352A ASN* 4.6 2.9 - - - +
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Residues in contact with LEU 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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313A HIS* 3.1 19.0 + - + +
314A ILE* 1.3 80.3 - - + +
316A LEU* 1.3 54.1 + - - +
318A ALA* 3.6 15.4 - - + +
319A ALA* 2.7 37.1 + - - +
334A LEU* 4.2 1.6 - - + -
339A LEU* 3.6 33.4 - - + -
342A ILE* 4.1 10.8 - - + -
416A TRP* 4.0 23.7 - - + -
453A ASP* 3.6 38.6 - - + +
454A PHE 4.4 5.8 - - - +
455A ILE* 4.1 15.7 - - + -
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Residues in contact with LEU 316 (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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312A ARG* 3.7 36.1 - - + +
313A HIS 3.3 12.3 + - - +
314A ILE 3.0 0.6 + - - -
315A LEU* 1.3 77.3 - - - +
317A ASP* 1.3 64.7 + - - +
319A ALA* 3.1 3.7 + - - +
320A VAL* 2.9 23.9 + - - +
413A TRP* 3.5 42.9 - - + +
455A ILE* 3.7 26.7 - - + +
456A GLY* 4.3 10.1 - - - +
457A THR* 2.9 29.4 - - - +
470A CYS* 4.5 7.0 - - - -
1562A EUG 5.2 4.0 - - + -
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Residues in contact with ASP 317 (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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312A ARG* 3.2 34.2 + - - +
313A HIS 3.8 2.1 + - - +
314A ILE* 3.1 9.5 + - - +
316A LEU* 1.3 77.8 - - - +
318A ALA* 1.3 63.4 + - - +
320A VAL* 2.9 15.1 + - - +
321A LEU* 3.2 19.0 + - + +
348A LEU* 3.4 29.2 - - + +
352A ASN* 3.9 9.0 - - - +
354A TYR* 2.4 32.8 + - - -
394A VAL* 3.3 16.3 - - + +
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Residues in contact with ALA 318 (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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314A ILE* 2.9 13.3 + - - +
315A LEU* 3.6 19.5 - - + +
317A ASP* 1.3 75.3 - - - +
319A ALA* 1.3 52.9 + - - +
321A LEU* 2.9 19.7 + - - -
322A GLY 3.0 9.7 + - - +
327A TYR* 2.9 38.8 + - + +
342A ILE* 3.9 20.6 - - + -
346A LEU* 4.6 5.8 - - + -
416A TRP* 4.4 2.2 - - + -
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Residues in contact with ALA 319 (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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315A LEU 2.7 22.7 + - - +
316A LEU* 3.4 2.2 - - - +
318A ALA* 1.3 67.8 - - - +
320A VAL* 1.3 65.6 + - - +
322A GLY 3.5 17.8 + - - +
323A ASP* 5.3 0.5 - - - -
412A LYS* 3.7 5.5 - - - +
413A TRP* 3.3 42.0 + - + +
416A TRP* 3.4 24.8 + - + -
455A ILE* 4.9 5.2 - - + -
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Residues in contact with VAL 320 (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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312A ARG* 3.7 21.3 - - - +
316A LEU 2.9 18.7 + - - +
317A ASP 2.9 8.2 + - - +
319A ALA* 1.3 79.2 - - - +
321A LEU* 1.3 68.7 + - + +
392A ASN 5.4 1.3 - - - +
394A VAL* 3.9 19.3 - - + -
397A VAL* 5.5 3.8 - - + -
409A ASP* 4.4 22.4 - - + +
410A GLU* 4.2 15.3 - - + +
412A LYS* 3.6 19.7 - - - +
413A TRP* 4.0 19.5 - - + +
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Residues in contact with LEU 321 (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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317A ASP* 3.2 15.9 + - + +
318A ALA 2.9 11.0 + - - +
320A VAL* 1.3 93.4 - - + +
322A GLY* 1.3 54.4 + - - +
327A TYR* 4.0 9.2 - - - +
346A LEU* 4.1 27.8 - - + -
348A LEU* 5.7 3.6 - - + -
392A ASN* 3.3 51.6 - - + +
393A SER* 5.3 1.1 - - - -
394A VAL* 4.7 12.6 - - + +
412A LYS* 5.7 1.1 - - - -
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Residues in contact with GLY 322 (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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318A ALA 3.0 15.8 + - - +
319A ALA* 3.5 16.2 - - - -
320A VAL 3.7 1.0 - - - -
321A LEU* 1.3 77.3 - - - +
323A ASP* 1.3 70.0 + - - +
326A SER* 3.4 13.9 - - - -
327A TYR* 3.6 5.0 + - - -
412A LYS* 5.6 6.1 - - - -
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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