Contacts of the helix formed by residues 430 - 447 (chain A) in PDB entry 3WAJ
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 TYR 430 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A GLU* 2.5 54.2 + - + +
167A ALA* 4.8 5.6 - - - -
170A GLN* 3.5 36.2 + - - -
211A TYR* 2.7 22.6 + - - -
215A TRP* 3.4 9.9 - + - -
413A TRP* 4.6 3.8 - - - -
417A MET* 4.0 11.8 - - + +
421A LEU* 3.7 27.1 - - + -
427A PHE* 3.1 27.8 + + - +
428A ALA 3.0 1.0 + - - -
429A TYR* 1.3 98.3 - + - +
431A PHE* 1.3 62.4 + - - +
432A ALA 3.5 0.5 + - - -
433A ALA* 4.1 6.5 + - - +
434A VAL* 3.8 13.7 + - - +
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Residues in contact with PHE 431 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381A PHE* 3.5 27.4 - + + -
417A MET* 3.7 34.8 - - + -
418A PHE* 3.8 41.5 - + - -
421A LEU* 3.7 31.0 - - + -
422A TRP* 5.1 10.8 - + - -
427A PHE 4.9 0.9 - - - -
428A ALA* 2.8 26.2 + - + +
430A TYR* 1.3 77.3 - - + +
432A ALA* 1.3 55.8 + - - +
433A ALA 3.4 0.2 - - - -
434A VAL* 2.9 13.5 + - + +
435A SER* 2.7 35.9 + - - -
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Residues in contact with ALA 432 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A ILE* 3.9 7.2 - - + +
147A VAL* 4.3 13.8 - - + +
151A PHE* 3.4 38.8 - - + -
381A PHE* 4.2 5.3 - - + -
428A ALA 3.9 1.8 + - - +
429A TYR* 3.2 16.2 + - - +
431A PHE* 1.3 77.7 - - - +
433A ALA* 1.3 63.6 + - - +
435A SER* 3.2 9.0 + - - -
436A ALA* 3.0 23.9 + - - +
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Residues in contact with ALA 433 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A VAL* 4.8 8.7 - - + -
144A ILE* 3.8 15.5 - - + +
151A PHE* 5.4 1.9 - - + -
167A ALA* 5.9 4.0 - - + -
171A VAL* 3.5 33.4 - - + -
413A TRP* 3.9 12.1 - - + -
429A TYR 4.5 1.0 + - - -
430A TYR 4.1 4.1 + - - +
431A PHE 3.4 0.4 - - - -
432A ALA* 1.3 77.9 - - - +
434A VAL* 1.3 62.4 + - - +
436A ALA* 3.4 1.7 + - - +
437A VAL* 3.1 31.3 + - + +
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Residues in contact with VAL 434 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392A ILE* 4.5 7.4 - - + -
413A TRP* 3.4 37.0 - - + -
414A ALA* 4.3 13.5 - - + +
417A MET* 4.4 12.3 - - + -
418A PHE* 6.0 4.9 - - + -
430A TYR 3.8 12.1 + - - +
431A PHE* 2.9 20.0 + - + +
433A ALA* 1.3 77.1 - - - +
435A SER* 1.3 63.6 + - - +
436A ALA 3.2 0.2 + - - -
437A VAL* 3.3 2.1 + - - +
438A TYR* 3.2 48.3 + - + +
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Residues in contact with SER 435 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A VAL* 4.3 5.7 - - - +
381A PHE* 4.0 21.1 - - - -
384A LEU* 3.5 32.2 - - - +
385A PHE* 4.7 2.9 - - - -
388A GLY* 4.0 7.1 - - - -
431A PHE* 2.7 16.4 + - - -
432A ALA* 3.3 8.7 + - - -
434A VAL* 1.3 75.1 - - - +
436A ALA* 1.3 58.4 + - - +
439A SER* 2.7 33.5 + - - -
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Residues in contact with ALA 436 (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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124A VAL* 5.2 2.7 - - + -
140A ALA* 4.0 6.7 - - - +
143A LEU* 3.7 16.1 - - + +
144A ILE* 3.9 38.1 - - + +
147A VAL* 5.2 0.9 - - + -
384A LEU* 4.4 4.3 - - + -
432A ALA 3.0 15.8 + - - +
433A ALA* 3.8 4.3 - - - +
435A SER* 1.3 77.8 + - - +
437A VAL* 1.3 61.2 + - + +
439A SER 3.9 0.2 - - - -
440A ALA* 3.2 26.5 + - - +
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Residues in contact with VAL 437 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A VAL* 4.3 9.4 - - + -
127A LEU* 4.4 15.9 - - + -
128A THR* 3.5 42.4 - - + +
132A PHE* 4.2 6.7 - - + -
410A LEU* 3.7 31.4 - - + -
413A TRP* 4.9 4.7 - - + -
433A ALA* 3.1 19.9 + - + +
434A VAL* 4.0 4.0 - - - +
436A ALA* 1.3 73.0 - - - +
438A TYR* 1.3 60.9 + - + +
439A SER 3.1 4.0 - - - -
440A ALA* 3.3 4.5 + - - +
441A LEU* 3.1 26.0 + - - +
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Residues in contact with TYR 438 (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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132A PHE* 4.4 7.0 - + - -
387A PHE 2.9 12.8 - - - +
388A GLY* 3.2 22.4 - - - +
391A GLY* 3.2 29.3 - - - -
392A ILE* 3.5 22.9 - - + +
395A SER* 4.1 21.3 + - - -
407A GLU 4.7 0.3 + - - -
410A LEU* 3.1 57.3 - - + +
411A LEU* 3.1 15.9 + - + +
413A TRP* 5.1 4.0 - + - -
414A ALA* 3.7 23.1 - - + -
434A VAL* 3.2 25.9 + - + +
437A VAL* 1.3 80.6 - - + +
439A SER* 1.3 57.5 + - - +
441A LEU* 4.0 6.7 - - + -
442A ALA* 3.6 4.6 + - - +
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Residues in contact with SER 439 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A LEU* 3.4 21.5 - - - -
384A LEU* 3.2 15.4 + - - -
387A PHE* 3.0 15.0 - - - +
388A GLY 2.9 19.9 + - - -
435A SER 2.7 24.7 + - - -
437A VAL 3.1 0.8 - - - -
438A TYR* 1.3 78.6 - - - +
440A ALA* 1.3 57.0 + - - +
441A LEU 3.0 4.5 - - - -
442A ALA* 3.3 1.2 + - - +
443A LEU* 2.9 37.2 + - - +
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Residues in contact with ALA 440 (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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128A THR* 4.9 0.7 - - - +
136A ALA* 3.1 31.0 - - + +
139A ILE* 3.8 16.0 - - + +
140A ALA* 3.3 21.8 - - + +
143A LEU* 3.7 1.0 - - - +
436A ALA 3.2 16.2 + - - +
437A VAL 3.3 5.6 + - - +
439A SER* 1.3 78.4 - - - +
441A LEU* 1.3 56.9 + - - +
444A SER* 3.0 29.2 + - - -
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Residues in contact with LEU 441 (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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132A PHE* 3.7 40.4 - - + -
136A ALA* 4.7 4.3 - - + -
391A GLY* 3.7 23.1 - - - +
394A TYR* 3.6 26.9 - - + -
395A SER* 4.7 4.3 - - - -
398A ARG* 3.3 27.6 - - - +
437A VAL 3.1 15.5 + - - +
438A TYR* 4.2 7.2 - - + -
439A SER 3.0 0.4 - - - -
440A ALA* 1.3 75.5 - - - +
442A ALA* 1.3 68.5 + - - +
443A LEU 3.1 1.6 - - - -
444A SER* 3.1 26.0 + - - +
445A VAL* 3.3 12.1 - - + +
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Residues in contact with ALA 442 (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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387A PHE* 3.3 31.4 - - + +
390A ALA* 4.8 7.2 - - + -
391A GLY* 4.0 12.8 - - - +
394A TYR* 6.0 1.6 - - - -
438A TYR 3.6 6.0 + - - +
439A SER 3.3 3.3 + - - +
441A LEU* 1.3 84.0 - - - +
443A LEU* 1.3 63.3 + - + +
445A VAL* 3.9 6.0 - - - +
446A VAL* 3.4 27.9 + - - +
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Residues in contact with LEU 443 (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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139A ILE* 3.6 34.1 - - + -
143A LEU* 4.6 10.1 - - + -
387A PHE* 4.4 21.5 - - + -
439A SER* 2.9 19.9 + - - +
442A ALA* 1.3 76.3 - - + +
444A SER* 1.3 51.7 + - - +
445A VAL 2.5 18.6 + - - -
446A VAL* 3.0 2.2 + - + +
447A PHE* 2.8 52.8 + - + -
477A ILE* 4.6 13.2 - - + +
478A ALA* 4.5 16.8 - - + +
481A ALA* 4.5 15.3 - - + -
482A ILE* 5.5 4.7 - - + -
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Residues in contact with SER 444 (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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133A ASP* 3.9 7.1 + - - +
135A ARG* 3.9 6.8 - - - +
136A ALA* 3.6 31.4 + - - +
139A ILE* 3.8 10.0 - - - +
398A ARG* 5.3 0.3 + - - -
440A ALA 3.0 20.1 + - - -
441A LEU* 3.1 11.9 + - - +
443A LEU* 1.3 74.0 - - - +
445A VAL* 1.3 63.4 + - - +
447A PHE* 4.4 6.1 - - - -
448A ASP* 3.6 22.9 + - - +
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Residues in contact with VAL 445 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394A TYR* 3.5 49.4 - - + +
398A ARG* 4.0 11.9 - - - +
441A LEU* 3.3 16.6 - - + +
442A ALA* 3.9 8.3 - - - +
443A LEU 2.5 7.9 + - - -
444A SER* 1.3 81.0 - - - +
446A VAL* 1.3 68.3 + - + +
447A PHE 3.2 1.0 - - - +
448A ASP* 3.4 7.7 + - - +
449A LYS* 3.1 35.9 + - + +
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Residues in contact with VAL 446 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442A ALA 3.4 17.7 + - - +
443A LEU* 3.0 5.0 + - + +
445A VAL* 1.3 81.3 - - + +
447A PHE* 1.3 69.2 + - + +
449A LYS* 3.2 21.3 + - - +
450A LEU* 3.3 26.0 - - + +
473A PHE* 6.4 0.9 - - + -
474A ALA* 5.4 1.3 - - - -
477A ILE* 3.4 34.5 - - + -
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Residues in contact with PHE 447 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A ILE* 4.3 24.2 - - + -
443A LEU* 2.8 41.7 + - + +
444A SER* 4.4 4.3 - - - -
446A VAL* 1.3 83.1 - - + +
448A ASP* 1.3 60.3 + - - +
449A LYS 3.0 4.7 - - - -
450A LEU* 3.1 19.7 + - - +
451A HIS* 3.1 22.6 + - + +
474A ALA* 3.6 32.3 - - + -
475A LEU* 5.6 3.4 - - + -
477A ILE* 5.0 0.7 - - + -
478A ALA* 3.5 26.7 - - + -
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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
------------------------------------------------------------
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