Contacts of the helix formed by residues 407 - 422 (chain A) in PDB entry 1W6J
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 PHE 407 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A LEU* 4.0 14.8 - - + -
81A MET* 3.6 25.1 - - + -
82A THR* 3.7 36.8 - - + -
85A VAL* 3.7 32.1 - - + -
396A LEU* 5.4 3.4 - - + -
401A GLY* 3.6 24.7 - - - +
404A ARG* 3.0 26.8 + - + -
406A GLU* 1.3 101.9 - - + +
408A SER* 1.3 62.2 + - - +
409A SER 3.3 2.7 - - - -
410A CYS* 3.4 9.8 + - + +
411A LEU* 3.1 28.4 + - + +
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Residues in contact with SER 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402A HIS* 6.0 2.5 - - - +
404A ARG 3.6 5.1 + - - -
405A PRO* 2.7 28.9 + - - +
406A GLU 3.5 0.2 - - - -
407A PHE* 1.3 78.1 - - - +
409A SER* 1.3 57.5 + - - +
411A LEU* 3.4 10.2 + - - +
412A GLN* 3.0 30.0 + - - +
473A HIS* 5.6 12.6 - - - -
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Residues in contact with SER 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405A PRO 4.8 0.4 + - - -
406A GLU 5.0 4.4 + - - -
407A PHE 3.3 0.2 - - - -
408A SER* 1.3 81.2 + - - +
410A CYS* 1.3 56.6 + - - +
412A GLN* 3.4 6.8 + - - +
413A LYS* 3.0 34.7 + - - +
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Residues in contact with CYS 410 (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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85A VAL* 3.9 32.8 - - + -
88A GLN* 3.0 35.3 + - - +
94A TRP* 3.6 28.9 - - - -
396A LEU* 4.1 10.5 - - - -
406A GLU 5.5 0.6 + - - +
407A PHE* 3.4 12.2 + - - +
409A SER* 1.3 78.2 - - - +
411A LEU* 1.3 58.9 + - - +
413A LYS* 3.2 1.3 + - - -
414A ALA* 2.8 26.3 + - - +
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Residues in contact with LEU 411 (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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94A TRP* 5.8 0.4 - - + -
393A ILE* 5.1 12.6 - - + -
396A LEU* 3.7 34.3 - - + -
397A LEU* 4.4 5.4 - - + -
401A GLY* 4.0 6.5 - - - +
402A HIS* 3.7 39.3 - - + +
407A PHE* 3.1 21.0 + - + +
408A SER* 3.8 7.6 - - - +
410A CYS* 1.3 76.9 - - - +
412A GLN* 1.3 60.7 + - - +
414A ALA* 3.7 4.8 - - + +
415A HIS* 2.9 29.6 + - - +
467A LEU* 3.9 28.4 - - + +
471A CYS* 4.5 6.5 - - - -
474A VAL* 5.0 2.7 - - + -
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Residues in contact with GLN 412 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A SER 3.0 17.4 + - - +
409A SER* 3.7 6.7 - - - +
411A LEU* 1.3 76.0 - - - +
413A LYS* 1.3 60.6 + - + +
415A HIS* 3.5 8.1 + - - +
416A GLU* 3.0 33.7 + - - +
419A ARG* 6.0 1.2 - - - +
473A HIS* 3.3 7.8 - - + +
474A VAL* 3.2 20.7 - - + +
475A THR* 2.8 50.4 + - - +
476A GLU* 5.6 0.4 + - - -
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Residues in contact with LYS 413 (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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88A GLN* 4.0 5.2 - - - +
90A GLU 3.4 26.0 + - - +
91A ASP* 4.0 13.5 + - - +
92A GLY* 3.6 19.9 - - - -
409A SER* 3.0 22.0 + - - +
410A CYS* 3.2 4.2 + - - +
412A GLN* 1.3 76.1 - - + +
414A ALA* 1.3 60.3 + - - +
416A GLU* 3.3 36.4 + - - +
417A PHE 2.9 24.8 + - - -
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Residues in contact with ALA 414 (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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88A GLN* 3.6 4.2 - - - +
92A GLY 3.5 18.2 - - - +
94A TRP* 4.0 11.4 - - + -
389A THR* 4.3 2.4 - - + +
393A ILE* 3.8 27.8 - - + -
410A CYS 2.8 17.4 + - - +
411A LEU* 3.7 7.6 - - + +
413A LYS* 1.3 73.0 - - - +
415A HIS* 1.3 64.7 + - - +
417A PHE* 3.3 3.9 + - - +
418A LEU* 3.1 27.4 + - - +
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Residues in contact with HIS 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393A ILE* 4.9 0.2 - - - -
411A LEU 2.9 18.7 + - - +
412A GLN* 3.6 7.6 - - - +
413A LYS 3.3 0.2 - - - -
414A ALA* 1.3 77.2 - - - +
416A GLU* 1.3 60.0 - - - +
418A LEU* 3.2 7.5 + - - +
419A ARG* 2.9 27.8 + - + +
464A VAL* 4.1 15.6 + - + +
467A LEU* 3.7 28.9 - - + +
468A GLN* 3.0 43.1 + - + -
474A VAL* 3.8 27.2 - - + +
475A THR 4.2 3.6 - - - -
476A GLU 3.5 21.6 + - - -
477A HIS* 3.9 0.6 - - - -
478A ILE* 4.1 7.5 + - + +
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Residues in contact with GLU 416 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A ASP 5.5 1.7 - - - +
412A GLN* 3.0 26.1 + - - +
413A LYS* 3.4 39.9 + - - +
415A HIS* 1.3 77.6 - - - +
417A PHE* 1.3 65.9 + - - +
419A ARG* 3.3 24.9 + - - +
420A LEU* 3.0 47.1 + - + +
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Residues in contact with PHE 417 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A ARG* 3.9 7.0 - - - -
32A GLY* 3.5 34.5 - - - -
91A ASP* 3.5 28.0 + - + +
92A GLY 4.0 6.5 - - - +
93A HIS* 3.5 32.5 - + + -
385A GLN* 4.1 9.6 - - + -
386A ILE* 3.9 29.6 - - + -
389A THR* 4.1 5.2 - - + -
413A LYS 2.9 10.3 + - - +
414A ALA 3.6 7.2 - - - +
416A GLU* 1.3 77.3 - - - +
418A LEU* 1.3 69.4 + - + +
420A LEU* 3.4 5.0 + - + +
421A SER* 2.7 51.2 + - - -
445A SER 4.7 1.1 - - - -
446A THR* 5.5 1.8 - - + -
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Residues in contact with LEU 418 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A ILE* 4.3 27.6 - - + +
389A THR* 4.2 12.1 - - + -
390A ALA* 4.3 5.4 - - - -
393A ILE* 3.4 27.6 - - + -
414A ALA 3.1 15.3 + - - +
415A HIS* 3.7 6.3 - - - +
417A PHE* 1.3 89.1 - - + +
419A ARG* 1.3 66.2 + - - +
421A SER* 3.1 11.2 + - - -
422A GLN* 3.1 10.9 + - - +
442A PHE* 3.3 15.4 - - + -
460A ALA* 4.2 10.8 - - + +
463A ALA* 4.0 17.9 - - + -
464A VAL* 4.1 21.5 - - + -
467A LEU* 5.7 0.2 - - + -
478A ILE* 4.7 1.3 - - - -
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Residues in contact with ARG 419 (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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412A GLN* 6.0 1.2 - - - +
415A HIS* 2.9 18.2 + - + +
416A GLU* 3.6 31.1 - - - +
418A LEU* 1.3 79.2 - - - +
420A LEU* 1.3 85.2 + - + +
421A SER 3.4 0.3 + - - -
422A GLN* 3.6 14.6 + - - +
475A THR 5.0 0.6 + - - -
476A GLU* 3.0 52.8 + - - +
477A HIS 4.3 3.6 - - - -
478A ILE* 3.8 27.0 - - + +
482A ARG* 3.8 28.9 + - - +
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Residues in contact with LEU 420 (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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31A ARG* 3.5 36.8 + - + +
416A GLU* 3.0 46.0 + - + +
417A PHE* 4.1 4.7 - - + +
419A ARG* 1.3 102.4 - - + +
421A SER* 1.3 58.7 + - - +
422A GLN 3.5 1.5 - - - +
447A LEU* 3.3 23.2 - - - +
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Residues in contact with SER 421 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A ARG 5.0 2.6 + - - -
386A ILE* 4.0 28.5 - - - +
417A PHE* 2.7 44.2 + - - -
418A LEU* 3.1 7.1 + - - -
420A LEU* 1.3 77.1 - - - +
422A GLN* 1.3 65.0 + - - +
423A VAL* 3.5 4.5 + - - +
441A GLY 4.7 0.2 - - - +
442A PHE* 4.4 7.5 - - - -
443A SER 5.5 0.3 + - - -
447A LEU* 3.5 29.4 + - - +
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Residues in contact with GLN 422 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418A LEU 3.1 5.2 + - - +
419A ARG* 3.8 12.0 - - - +
420A LEU 3.5 4.5 - - - +
421A SER* 1.3 78.4 - - - +
423A VAL* 1.3 66.9 + - - +
424A PRO* 3.3 9.7 - - - +
440A GLY* 2.9 37.6 + - - +
441A GLY 3.8 1.6 - - - +
442A PHE* 3.7 29.1 - - + -
447A LEU* 3.6 3.8 - - - +
478A ILE* 3.7 14.5 - - - +
482A ARG* 3.1 55.8 + - - +
483A LEU* 5.1 1.2 - - - +
486A ALA* 4.1 5.5 - - - +
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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
------------------------------------------------------------
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