Contacts of the helix formed by residues 350 - 364 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A LEU* 5.1 7.8 - - + +
169A LEU* 4.7 23.7 - - + +
170A MET* 3.4 30.5 - - + +
173A GLU* 4.8 3.8 - - + +
347A TYR 4.7 1.2 + - - -
348A LEU 3.1 1.2 - - - -
349A HIS* 1.3 116.8 + - + +
351A PHE* 1.3 63.9 + - - +
352A ALA 3.4 2.0 - - - -
353A ALA* 3.4 24.5 + - + +
354A TYR* 3.0 18.7 + - - +
385A GLU* 5.0 4.6 + - - -
350B ARG* 3.6 24.9 - - - +
385B GLU* 3.0 35.0 + - - -
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Residues in contact with PHE 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A MET* 3.6 20.9 - - + +
341A LEU* 4.5 15.0 - - + -
343A PRO* 4.4 13.9 - - + -
348A LEU* 3.1 44.8 + - + +
350A ARG* 1.3 75.9 - - - +
352A ALA* 1.3 64.9 + - - +
354A TYR* 3.2 4.3 + - - +
355A PHE* 3.1 51.9 + + - -
410A LEU* 4.6 19.3 - - + -
490A LEU* 4.4 7.6 - - + -
493A LEU* 4.9 9.2 - - + -
494A ILE* 4.4 15.7 - - + -
497A TYR* 3.8 27.6 - + - -
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Residues in contact with ALA 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A LEU* 3.7 40.8 - - + +
343A PRO* 5.3 3.1 - - + +
348A LEU 4.7 0.6 + - - -
349A HIS 5.0 3.0 + - - +
350A ARG 3.4 0.4 - - - -
351A PHE* 1.3 80.5 - - - +
353A ALA* 1.3 58.7 + - - +
355A PHE* 3.3 2.6 + - - +
356A GLN* 2.9 29.9 + - - +
382A VAL* 4.4 3.6 - - - +
383A TRP* 4.1 2.7 - - - -
384A GLY* 3.8 29.8 - - - +
385A GLU* 4.7 1.1 - - - +
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Residues in contact with ALA 353 (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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166A LEU* 3.7 19.0 - - + +
349A HIS 5.4 0.6 + - - -
350A ARG* 3.4 46.2 + - - +
351A PHE 3.3 0.2 - - - -
352A ALA* 1.3 76.6 - - - +
354A TYR* 1.3 64.3 + - - +
356A GLN* 3.3 21.7 + - - +
357A GLN 3.4 8.0 + - - -
384A GLY 5.5 0.4 + - - -
385B GLU* 4.0 10.1 - - + +
393B ALA* 5.3 1.0 - - - +
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Residues in contact with TYR 354 (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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163A GLY* 6.4 1.8 - - - -
166A LEU* 3.8 16.5 - - + +
167A GLY* 3.4 39.9 - - - -
170A MET* 3.7 25.1 - - + -
276A ARG* 3.3 27.9 + - - -
277A TYR* 4.7 1.4 - - - -
278A SER 5.2 0.5 + - - -
279A LEU* 3.5 19.9 + - + +
350A ARG 3.0 13.3 + - - +
351A PHE 3.4 7.6 - - - +
353A ALA* 1.3 77.5 - - - +
355A PHE* 1.3 91.7 + + - +
357A GLN* 3.2 13.0 + - - +
358A GLY* 3.0 21.2 + - - -
494A ILE* 4.1 9.7 - - + +
498A GLU* 4.2 11.4 + - + +
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Residues in contact with PHE 355 (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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341A LEU* 3.6 23.3 - - + -
351A PHE* 3.1 46.8 + + - +
352A ALA 3.7 0.2 - - - -
354A TYR* 1.3 106.6 - + - +
356A GLN* 1.3 60.6 + - - +
357A GLN 3.2 0.7 - - - -
358A GLY* 3.9 7.0 - - - +
359A ASP* 2.7 38.6 + - + +
382A VAL* 4.2 3.8 - - + -
494A ILE* 3.6 21.3 - - + -
497A TYR* 3.3 33.9 - + + -
498A GLU* 4.2 8.3 - - + -
501A ILE* 3.9 26.0 - - + -
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Residues in contact with GLN 356 (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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352A ALA 2.9 16.4 + - - +
353A ALA* 3.4 14.4 - - - +
354A TYR 3.3 0.2 - - - -
355A PHE* 1.3 74.7 - - - +
357A GLN* 1.3 55.8 + - - +
360A MET* 2.9 48.8 + - - +
382A VAL* 2.8 35.8 + - - +
383A TRP* 4.0 10.1 - - - +
383B TRP* 3.5 20.6 - - - +
384B GLY 5.2 2.4 + - - +
385B GLU* 3.8 16.8 - - - +
393B ALA* 4.7 2.3 - - - +
394B PHE* 3.7 30.9 - - + +
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Residues in contact with GLN 357 (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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162A GLY* 3.3 14.2 - - - +
163A GLY* 3.2 22.0 + - - +
166A LEU* 3.1 33.0 - - + +
276A ARG* 3.7 21.3 - - + +
353A ALA 3.4 2.0 + - - -
354A TYR* 3.2 12.9 + - + +
356A GLN* 1.3 73.2 - - - +
358A GLY* 1.3 65.4 + - - +
359A ASP 3.2 2.5 - - - -
361A GLU* 3.1 38.8 + - + +
392B HIS 3.3 19.0 + - - -
393B ALA* 3.4 23.3 - - - +
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Residues in contact with GLY 358 (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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276A ARG* 4.2 21.8 - - - -
277A TYR* 3.9 4.3 + - - -
354A TYR* 3.0 19.0 + - - -
355A PHE* 3.4 12.3 + - - -
357A GLN* 1.3 72.9 - - - +
359A ASP* 1.3 56.4 - - - +
362A SER* 2.6 30.3 + - - -
501A ILE* 3.6 11.5 - - - +
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Residues in contact with ASP 359 (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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339A HIS* 5.5 0.5 - - - -
355A PHE* 2.7 21.1 + - + +
358A GLY* 1.3 77.4 - - - +
360A MET* 1.3 60.1 + - - +
362A SER* 3.2 2.6 + - - -
363A ASN* 2.9 36.9 + - - +
379A GLY* 4.7 0.3 - - - -
380A PRO* 4.1 20.4 - - - +
382A VAL* 3.5 25.3 - - + +
500A LYS* 4.5 12.3 + - - +
501A ILE* 3.6 28.0 - - + +
504A GLN* 4.4 8.9 - - - +
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Residues in contact with MET 360 (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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356A GLN* 2.9 38.9 + - - +
359A ASP* 1.3 80.0 - - - +
361A GLU* 1.3 56.6 + - - +
363A ASN 5.2 0.2 - - - -
364A GLY* 2.9 29.3 + - - +
380A PRO 3.5 14.8 - - - +
381A VAL* 3.7 19.5 - - + -
382A VAL* 3.5 24.5 - - + +
383B TRP* 3.7 26.5 - - + -
394B PHE* 3.8 17.7 - - + +
396B GLN* 4.2 0.2 - - - +
397B LEU* 3.6 39.4 + - + +
398B VAL* 5.6 0.2 - - + -
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Residues in contact with GLU 361 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A ARG* 2.9 36.7 + - - +
357A GLN* 3.1 29.4 + - + +
360A MET* 1.3 77.7 - - - +
362A SER* 1.3 59.5 + - - +
365A LYS* 3.4 13.9 + - - -
514A ASP 3.8 0.5 - - - +
515A GLN* 4.1 13.6 - - + +
518A VAL* 4.1 17.5 - - - +
391B GLN 5.1 0.3 - - - +
392B HIS* 3.7 19.0 - - - +
393B ALA 3.4 17.6 + - - +
394B PHE* 5.3 0.2 - - - +
396B GLN* 3.5 28.9 + - + +
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Residues in contact with SER 362 (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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276A ARG* 2.9 16.1 + - - +
277A TYR* 2.7 16.5 + - - -
358A GLY 2.6 25.3 + - - -
359A ASP 3.2 3.5 + - - -
360A MET 3.2 0.6 - - - -
361A GLU* 1.3 78.6 - - - +
363A ASN* 1.3 64.6 + - - +
365A LYS* 2.8 26.3 + - - +
501A ILE* 3.5 17.3 - - - -
510A ILE* 4.4 0.2 - - - +
512A SER* 3.2 24.2 + - - -
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Residues in contact with ASN 363 (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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359A ASP* 2.9 18.8 + - - +
362A SER* 1.3 77.0 - - - +
364A GLY* 1.3 57.0 + - - +
365A LYS* 2.8 13.4 + - - -
378A THR* 3.3 6.6 + - - -
379A GLY* 3.0 26.3 + - - -
501A ILE* 2.9 37.8 + - - +
504A GLN* 3.8 6.9 + - - +
505A GLY 3.8 3.0 - - - +
508A TRP* 3.8 26.5 - - + -
510A ILE* 3.7 13.9 - - + +
512A SER* 2.6 26.9 + - - -
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Residues in contact with GLY 364 (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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360A MET 2.9 20.1 + - - -
361A GLU 4.5 0.2 - - - -
362A SER 3.6 1.8 - - - -
363A ASN* 1.3 72.4 - - - +
365A LYS* 1.3 58.4 - - - -
378A THR* 4.6 1.3 - - - -
379A GLY 5.3 0.2 - - - -
396B GLN* 3.0 35.0 + - - +
397B LEU* 3.6 26.0 - - - +
400B GLN 3.6 3.3 - - - +
401B GLY* 3.7 9.6 - - - -
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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