Contacts of the helix formed by residues 350 - 364 (chain B) in PDB entry 4WMJ
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 ARG 350 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350A ARG* 3.6 24.5 - - - +
385A GLU* 3.0 35.8 + - - -
166B LEU* 5.1 9.0 - - + +
169B LEU* 3.7 32.5 - - + +
170B MET* 3.4 22.0 + - + +
173B GLU* 4.7 1.1 - - + -
347B TYR 4.7 0.8 + - - -
348B LEU* 3.1 1.4 - - - +
349B HIS* 1.3 119.2 + - + +
351B PHE* 1.3 59.2 + - - +
352B ALA 3.4 2.0 - - - -
353B ALA* 3.3 26.0 + - + +
354B TYR* 3.0 23.2 + - - +
385B GLU* 5.0 4.8 + - - -
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Residues in contact with PHE 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B MET* 3.8 25.4 - - + +
341B LEU* 4.5 16.2 - - + -
343B PRO* 4.3 12.3 - - + -
348B LEU* 3.0 34.9 + - + +
349B HIS 3.5 0.2 - - - -
350B ARG* 1.3 77.4 - - - +
352B ALA* 1.3 64.0 + - - +
354B TYR* 3.2 11.8 + - - +
355B PHE* 3.2 42.7 + + - -
410B LEU* 4.4 19.7 - - + -
490B LEU* 4.3 20.4 - - + -
493B LEU* 4.9 9.2 - - + -
494B ILE* 4.5 7.4 - - + -
497B TYR* 3.9 28.9 - + - -
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Residues in contact with ALA 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B LEU* 3.8 36.1 - - + +
343B PRO* 5.3 3.7 - - + +
348B LEU 4.8 0.4 + - - -
349B HIS 5.1 2.4 + - - +
350B ARG 3.4 0.4 - - - -
351B PHE* 1.3 79.2 - - - +
353B ALA* 1.4 57.1 + - - +
355B PHE* 3.2 2.4 + - - +
356B GLN* 2.8 33.0 + - - +
382B VAL* 4.3 3.3 - - - +
383B TRP* 4.2 2.6 + - - -
384B GLY 3.7 33.4 - - - +
385B GLU* 4.7 0.9 - - - +
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Residues in contact with ALA 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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385A GLU* 4.2 8.1 - - + +
393A ALA* 5.3 0.9 - - - +
166B LEU* 3.6 21.6 - - + +
349B HIS 5.4 0.8 + - - +
350B ARG* 3.3 49.4 + - - +
351B PHE 3.3 0.4 - - - -
352B ALA* 1.4 77.8 - - - +
354B TYR* 1.3 62.1 + - - +
356B GLN* 3.1 28.1 - - - +
357B GLN 3.6 0.2 + - - -
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Residues in contact with TYR 354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B GLY* 6.5 0.9 - - - -
166B LEU* 3.9 14.8 - - + +
167B GLY* 3.3 40.6 - - - -
170B MET* 3.7 21.5 - - + -
276B ARG* 3.3 26.2 + - - -
277B TYR* 4.7 1.7 - - - -
278B SER 5.2 0.3 + - - -
279B LEU* 3.3 22.4 - - + +
350B ARG 3.0 13.0 + - - +
351B PHE 3.2 8.9 + - - +
353B ALA* 1.3 76.5 - - - +
355B PHE* 1.3 95.0 + + - +
357B GLN* 3.2 11.5 + - + +
358B GLY* 3.0 21.9 + - - -
494B ILE* 4.0 8.6 - - + +
498B GLU* 4.3 10.8 + - + -
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Residues in contact with PHE 355 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B LEU* 3.6 24.5 - - + -
351B PHE* 3.2 48.6 + + - +
352B ALA 3.2 2.4 + - - -
354B TYR* 1.3 94.7 - + - +
356B GLN* 1.3 60.3 + - - +
357B GLN 3.3 0.7 - - - -
358B GLY* 3.7 5.4 - - - +
359B ASP* 2.8 39.3 + - + +
382B VAL* 4.1 4.6 - - + +
494B ILE* 3.6 28.7 - - + -
497B TYR* 3.3 31.2 - + + -
498B GLU* 4.3 9.0 - - + -
501B ILE* 4.0 24.7 - - + -
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Residues in contact with GLN 356 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A TRP* 3.5 22.8 - - - +
384A GLY 5.1 2.6 + - - +
385A GLU* 4.0 14.9 - - - +
393A ALA* 4.6 2.3 - - + +
394A PHE* 3.7 31.6 - - + +
352B ALA 2.8 13.8 + - - +
353B ALA* 3.1 19.0 - - - +
355B PHE* 1.3 73.9 - - - +
357B GLN* 1.3 56.9 + - - +
360B MET* 2.9 43.6 + - - +
382B VAL* 2.7 37.6 + - - +
383B TRP* 4.0 10.5 - - - +
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Residues in contact with GLN 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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392A HIS 3.3 18.2 + - - +
393A ALA* 3.4 27.2 - - - +
162B GLY* 3.4 18.8 - - - +
163B GLY* 3.4 18.9 + - - +
166B LEU* 3.6 21.7 - - + +
276B ARG* 3.8 23.3 - - + +
353B ALA 3.6 1.2 + - - -
354B TYR* 3.2 11.4 + - + +
356B GLN* 1.3 76.3 - - - +
358B GLY* 1.3 69.6 - - - +
361B GLU* 2.8 50.0 + - - +
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Residues in contact with GLY 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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276B ARG* 4.2 23.5 - - - +
277B TYR* 4.0 4.4 + - - -
354B TYR* 3.0 16.8 + - - -
355B PHE* 3.4 11.4 + - - -
357B GLN* 1.3 75.9 - - - +
359B ASP* 1.3 55.9 + - - +
362B SER* 2.6 30.8 + - - -
501B ILE* 3.8 12.1 - - - +
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Residues in contact with ASP 359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B HIS* 5.7 0.5 - - - -
355B PHE* 2.8 21.6 + - + +
358B GLY* 1.3 75.6 - - - +
360B MET* 1.3 59.5 + - - +
362B SER* 3.2 2.1 + - - -
363B ASN* 2.9 38.5 + - - +
379B GLY* 4.8 0.3 - - - -
380B PRO* 4.1 19.4 - - - +
382B VAL* 3.5 26.5 - - + +
500B LYS* 4.6 13.9 + - - +
501B ILE* 3.7 30.1 - - + +
504B GLN* 4.7 5.9 - - - +
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Residues in contact with MET 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A TRP* 3.8 24.7 - - + -
393A ALA 5.0 0.2 - - - -
394A PHE* 3.9 23.6 - - + +
397A LEU* 3.5 40.7 + - + +
356B GLN* 2.9 39.1 + - - +
359B ASP* 1.3 74.2 - - - +
361B GLU* 1.3 58.1 + - - +
363B ASN 5.2 0.2 - - - -
364B GLY* 2.9 28.5 + - - +
379B GLY* 6.1 0.2 - - - -
380B PRO 3.5 15.0 - - - +
381B VAL* 3.7 20.4 - - + -
382B VAL* 3.4 26.0 - - + +
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Residues in contact with GLU 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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391A GLN 5.3 0.7 - - - +
392A HIS* 3.8 18.0 - - - +
393A ALA 3.4 14.7 + - - +
394A PHE* 5.2 0.2 - - - +
396A GLN* 3.4 35.0 + - + +
276B ARG* 3.0 32.6 + - - +
356B GLN 3.9 0.2 + - - -
357B GLN* 2.8 44.2 + - + +
360B MET* 1.3 75.5 - - - +
362B SER* 1.3 60.7 + - - +
365B LYS* 3.4 13.3 + - - -
514B ASP 3.9 0.5 - - - +
515B GLN* 4.2 13.8 - - + +
518B VAL* 4.8 9.0 - - - +
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Residues in contact with SER 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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276B ARG* 2.9 14.3 + - - +
277B TYR* 2.7 16.9 + - - -
358B GLY 2.6 26.0 + - - -
359B ASP 3.2 2.8 + - - -
361B GLU* 1.3 78.8 - - - +
363B ASN* 1.3 66.8 + - - +
365B LYS* 2.8 27.0 + - - +
501B ILE* 3.6 16.8 - - - -
512B SER* 3.2 23.7 + - - -
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Residues in contact with ASN 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 ASP* 2.9 19.6 + - - +
360B MET 4.0 0.2 - - - -
362B SER* 1.3 75.0 - - - +
364B GLY* 1.3 58.9 + - - +
365B LYS* 2.9 9.7 + - - -
378B THR* 3.3 6.1 + - - -
379B GLY* 3.1 27.4 + - - -
501B ILE* 3.0 39.4 + - - +
504B GLN* 3.9 5.9 + - - +
505B GLY 3.9 2.2 - - - +
508B TRP* 3.7 26.7 - - + -
510B ILE* 3.5 16.8 - - + +
512B SER* 2.7 25.7 + - - -
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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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396A GLN* 3.0 34.3 + - - +
397A LEU* 3.6 25.5 - - - +
400A GLN 3.5 7.9 - - - +
401A GLY* 3.8 5.8 - - - -
360B MET 2.9 19.7 + - - -
361B GLU 4.5 0.4 - - - -
362B SER 3.5 1.2 - - - -
363B ASN* 1.3 72.7 - - - +
365B LYS* 1.3 59.1 + - - +
378B THR* 4.8 0.7 - - - -
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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