Contacts of the helix formed by residues 346 - 364 (chain B) in PDB entry 3WOO
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 ASP 346 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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342B PHE 2.8 8.3 + - - -
343B LYS* 3.5 7.5 + - - +
344B ARG 3.4 3.6 + - - -
345B ILE* 1.3 77.3 - - - +
347B ALA* 1.3 65.5 + - - +
348B ALA* 3.3 5.7 + - - +
349B GLY* 3.0 29.5 + - - -
350B GLN* 3.0 20.8 + - - +
353B ARG* 3.3 18.7 + - - +
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Residues in contact with ALA 347 (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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285B PHE* 3.5 26.7 - - + -
342B PHE* 2.8 31.2 + - + -
345B ILE* 3.5 8.6 - - + -
346B ASP* 1.3 74.7 - - - +
348B ALA* 1.3 53.7 - - - +
350B GLN* 2.9 9.9 + - - +
351B LYS* 2.8 40.3 + - - +
685B VAL* 4.0 16.6 - - + +
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Residues in contact with ALA 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B PHE* 3.5 26.4 - - + -
286B ASP* 4.5 10.2 - - - +
342B PHE* 5.4 0.4 - - - +
346B ASP* 3.3 5.8 - - - +
347B ALA* 1.3 77.4 - - - +
349B GLY* 1.3 63.8 + - - +
351B LYS* 3.3 2.0 + - - +
352B LEU* 3.2 23.4 + - - +
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Residues in contact with GLY 349 (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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346B ASP* 3.0 27.8 + - - -
347B ALA 3.1 0.6 - - - -
348B ALA* 1.3 80.8 - - - +
350B GLN* 1.3 59.3 + - - +
352B LEU* 3.7 5.9 - - - +
353B ARG* 2.9 42.6 + - - +
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Residues in contact with GLN 350 (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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345B ILE* 2.4 35.7 - - - +
346B ASP 3.0 14.8 - - - +
347B ALA* 2.9 10.4 + - - +
349B GLY* 1.3 72.5 - - - +
351B LYS* 1.3 59.0 + - + +
353B ARG* 3.9 17.4 - - - +
354B GLU* 3.0 30.5 + - - +
685B VAL* 3.7 28.0 - - + +
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Residues in contact with LYS 351 (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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277B ASN 5.1 0.4 + - - -
278B ARG 4.3 9.3 + - - -
280B ALA* 2.8 41.2 + - - +
281B LEU 4.4 0.7 - - - -
282B ALA* 3.9 26.9 - - + +
285B PHE* 3.8 33.0 - - + -
286B ASP* 5.5 0.4 - - - +
347B ALA 2.8 22.0 + - - +
348B ALA* 3.6 6.1 - - - +
349B GLY 3.1 0.2 - - - -
350B GLN* 1.3 74.3 - - - +
352B LEU* 1.3 67.8 + - - +
354B GLU* 3.0 5.6 + - - +
355B GLU* 3.0 23.0 + - - +
684B TRP* 4.8 8.7 + - + +
685B VAL* 4.1 19.1 - - + -
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Residues in contact with LEU 352 (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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282B ALA* 3.9 13.9 - - + +
286B ASP* 6.0 2.5 - - - +
348B ALA 3.2 13.4 + - - +
349B GLY* 3.7 6.7 - - - +
351B LYS* 1.3 76.6 - - - +
353B ARG* 1.3 73.1 + - + +
355B GLU* 3.1 2.8 + - - +
356B ALA* 3.0 25.9 + - + +
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Residues in contact with ARG 353 (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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346B ASP* 3.3 25.7 + - - +
349B GLY* 2.9 38.5 + - - +
350B GLN* 3.9 18.2 - - - +
352B LEU* 1.3 85.1 - - + +
354B GLU* 1.3 60.8 + - - +
356B ALA* 3.8 6.7 - - - +
357B ALA* 3.2 19.8 + - - +
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Residues in contact with GLU 354 (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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350B GLN 3.0 19.2 + - - +
351B LYS* 4.0 2.7 - - - +
353B ARG* 1.3 75.3 - - - +
355B GLU* 1.3 55.9 + - - +
357B ALA* 3.7 5.2 - - + +
358B VAL* 2.8 43.2 + - - +
560B LEU* 6.0 0.7 - - - +
563B TYR* 4.1 27.5 + - + +
564B LYS* 4.3 15.2 + - - +
569B GLU* 3.6 27.4 - - - +
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Residues in contact with GLU 355 (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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280B ALA 4.5 1.2 - - - +
281B LEU* 3.5 11.6 - - - +
282B ALA* 2.9 39.6 + - + +
283B ALA* 5.0 1.6 + - - +
351B LYS 3.0 15.6 + - - +
352B LEU* 3.6 4.9 - - - +
354B GLU* 1.3 74.6 - - - +
356B ALA* 1.3 66.1 + - - +
358B VAL* 2.9 6.9 + - - +
359B LEU* 2.8 43.6 + - + +
376B HIS* 2.7 32.1 + - - +
380B LEU* 5.2 3.5 - - - +
556B TYR* 4.1 8.3 + - - +
560B LEU* 6.5 0.2 - - - -
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Residues in contact with ALA 356 (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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352B LEU* 3.0 17.9 + - + +
353B ARG* 3.8 7.9 - - - +
355B GLU* 1.3 74.3 - - - +
357B ALA* 1.3 58.6 + - - +
359B LEU* 3.8 4.7 - - - -
360B GLY* 2.8 30.1 + - - -
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Residues in contact with ALA 357 (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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353B ARG 3.2 16.0 + - - +
354B GLU* 3.7 8.1 - - + +
356B ALA* 1.3 79.8 - - - +
358B VAL* 1.3 58.0 + - - +
360B GLY* 4.3 1.3 - - - -
361B TRP* 3.2 25.3 + - - +
563B TYR* 3.4 26.0 - - - +
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Residues in contact with VAL 358 (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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354B GLU* 2.8 31.9 + - - +
355B GLU* 2.9 8.5 + - - +
357B ALA* 1.3 75.5 - - - +
359B LEU* 1.3 62.7 + - - +
361B TRP* 3.3 8.0 + - + +
362B LEU* 3.0 41.4 + - + +
556B TYR* 4.2 10.8 - - + +
559B ALA 5.4 0.9 - - - +
560B LEU* 3.8 34.1 - - + +
563B TYR* 3.7 37.7 - - + -
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Residues in contact with LEU 359 (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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355B GLU* 2.8 35.4 + - + +
356B ALA* 3.8 4.7 - - - +
358B VAL* 1.3 70.7 - - - +
360B GLY* 1.3 66.4 + - - +
362B LEU* 3.0 31.2 + - + +
363B LYS* 3.4 30.8 + - - +
373B LEU* 4.4 14.1 - - + -
376B HIS* 3.8 49.1 - - + +
556B TYR* 4.3 5.4 - - - +
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Residues in contact with GLY 360 (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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356B ALA 2.8 19.6 + - - -
357B ALA* 4.3 1.6 - - - -
359B LEU* 1.3 72.4 - - - +
361B TRP* 1.3 61.2 + - - +
362B LEU 3.2 0.2 + - - -
363B LYS* 3.3 24.3 - - - +
364B GLY* 3.4 7.6 + - - -
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Residues in contact with TRP 361 (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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357B ALA 3.2 21.2 + - - +
358B VAL* 3.4 6.3 - - + +
359B LEU 3.1 0.8 - - - -
360B GLY* 1.3 75.7 - - - +
362B LEU* 1.3 83.4 + - + +
364B GLY* 3.6 8.1 + - - -
365B GLN* 2.6 54.0 + - + +
559B ALA* 4.0 11.0 - - + -
562B ASP* 4.1 12.3 - - + -
563B TYR* 3.8 56.1 - + + -
566B SER* 4.4 15.8 + - - -
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Residues in contact with LEU 362 (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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358B VAL* 3.0 26.5 + - + +
359B LEU* 3.0 30.1 + - + +
361B TRP* 1.3 99.4 - - + +
363B LYS* 1.3 61.2 + - - +
365B GLN* 2.9 34.1 + - - +
366B GLY 4.0 0.7 + - - -
369B GLY* 3.9 27.8 - - - +
372B ALA* 3.6 32.5 - - + -
373B LEU* 4.4 12.6 - - + +
556B TYR* 4.4 9.6 - - + -
559B ALA* 4.2 7.2 - - + -
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Residues in contact with LYS 363 (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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359B LEU* 3.4 27.3 + - - +
360B GLY* 3.3 22.1 - - - +
362B LEU* 1.3 70.6 - - - +
364B GLY* 1.3 52.1 + - - +
365B GLN 2.6 17.7 + - - -
366B GLY* 2.7 18.7 + - - +
369B GLY 5.6 0.7 - - - -
373B LEU* 3.7 28.7 - - + +
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Residues in contact with GLY 364 (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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360B GLY 3.4 7.4 + - - -
361B TRP* 3.7 7.0 - - - -
362B LEU 3.2 1.0 - - - -
363B LYS* 1.3 80.2 - - - +
365B GLN* 1.3 65.3 + - - +
366B GLY 3.7 0.4 - - - -
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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