Contacts of the helix formed by residues 518 - 534 (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 VAL 518 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396A GLN* 4.0 3.6 + - + +
399A HIS* 5.9 0.4 - - - -
435A GLN* 5.3 2.3 + - - -
361B GLU* 4.8 9.6 - - - +
515B GLN* 3.3 35.0 - - + +
516B TRP 3.0 1.0 + - - -
517B GLY* 1.3 77.0 - - - +
519B GLU* 1.4 80.4 + - + +
520B LEU 3.5 1.0 + - - -
521B GLY* 3.7 3.6 + - - -
522B LYS* 3.3 52.6 + - + +
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Residues in contact with GLU 519 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443A LYS* 5.2 6.2 + - - +
469A LYS* 2.7 32.4 + - - +
471A PHE* 5.0 3.6 - - + -
516B TRP* 3.2 41.9 + - + +
517B GLY 3.3 0.4 - - - -
518B VAL* 1.4 91.0 - - + +
520B LEU* 1.3 66.6 + - - +
522B LYS* 3.2 6.6 + - + +
523B GLN* 3.0 36.1 + - + +
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Residues in contact with LEU 520 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438A ALA* 3.7 30.1 - - + +
441A LYS* 5.5 2.2 - - - -
442A GLY* 3.5 33.9 - - - +
443A LYS* 3.9 20.2 - - + +
471A PHE* 3.7 40.6 - - + -
518B VAL 3.5 0.6 - - - -
519B GLU* 1.3 77.8 - - - +
521B GLY* 1.3 64.0 + - - +
523B GLN* 3.2 11.1 + - - +
524B LEU* 2.9 49.0 + - + +
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Residues in contact with GLY 521 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399A HIS* 5.2 3.4 - - - -
431A ASN* 5.0 1.4 - - - +
434A ALA* 3.6 8.9 - - - +
435A GLN* 3.7 27.6 + - - -
438A ALA* 4.2 15.5 - - - +
517B GLY 5.2 0.8 + - - -
518B VAL 3.7 3.8 + - - -
519B GLU 3.4 0.4 - - - -
520B LEU* 1.3 79.8 - - - +
522B LYS* 1.3 62.0 + - - +
524B LEU* 4.5 0.4 - - - -
525B ALA* 3.1 24.3 + - - +
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Residues in contact with LYS 522 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391A GLN* 5.8 4.5 - - - +
392A HIS* 5.1 16.6 - - + -
431A ASN* 5.6 4.0 - - - +
435A GLN* 4.8 0.8 - - - +
161B ILE* 5.8 4.7 - - - +
220B GLU* 5.7 3.4 - - - -
518B VAL* 3.3 43.3 + - + +
519B GLU* 3.2 10.3 + - - +
521B GLY* 1.3 76.7 - - - +
523B GLN* 1.3 64.1 + - + +
525B ALA* 3.5 5.2 + - - +
526B LYS* 3.2 39.4 + - - +
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Residues in contact with GLN 523 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443A LYS* 2.9 26.2 + - - +
451A GLU* 3.3 27.4 + - - -
519B GLU* 3.0 27.5 + - + +
520B LEU* 3.4 13.0 - - - +
522B LYS* 1.3 75.9 - - + +
524B LEU* 1.3 69.1 + - + +
526B LYS* 3.4 11.2 + - - +
527B ALA* 3.2 20.4 + - - +
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Residues in contact with LEU 524 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434A ALA* 3.6 11.9 - - + +
437A GLU* 3.6 30.6 - - + +
438A ALA* 3.6 42.2 - - + +
441A LYS* 4.4 18.4 - - + -
520B LEU* 2.9 35.1 + - + +
521B GLY 4.1 0.2 - - - +
523B GLN* 1.3 80.3 - - + +
525B ALA* 1.3 62.6 + - - +
527B ALA* 3.4 8.5 + - + +
528B ILE* 3.2 27.2 + - - +
541B HIS* 5.3 0.4 + - + -
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Residues in contact with ALA 525 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430A ALA* 3.7 22.2 - - + +
431A ASN* 4.0 18.6 - - - +
434A ALA* 3.2 16.0 - - + +
219B GLN* 5.9 1.3 - - - +
521B GLY 3.1 18.3 + - - +
522B LYS* 3.9 4.9 - - - +
524B LEU* 1.3 74.1 - - - +
526B LYS* 1.3 65.9 + - - +
528B ILE* 3.0 11.3 + - - -
529B GLU* 3.1 21.7 + - - +
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Residues in contact with LYS 526 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B GLN* 5.7 9.6 - - - +
522B LYS* 3.2 28.2 + - - +
523B GLN* 3.7 11.2 - - - +
524B LEU 3.3 0.2 - - - -
525B ALA* 1.3 80.6 - - + +
527B ALA* 1.3 59.6 - - - +
529B GLU* 3.6 17.2 + - - +
530B PRO* 3.3 18.9 - - - +
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Residues in contact with ALA 527 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523B GLN 3.2 10.5 + - - +
524B LEU* 3.6 14.4 - - + +
525B ALA 3.1 0.6 - - - -
526B LYS* 1.3 80.5 - - - +
528B ILE* 1.3 62.6 + - + +
530B PRO* 3.4 17.5 - - - +
531B GLU* 3.7 14.3 - - - +
541B HIS* 5.1 7.0 - - - +
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Residues in contact with ILE 528 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430A ALA* 3.9 20.6 - - + -
433A LEU* 3.8 38.1 - - + -
434A ALA* 3.9 11.7 - - + +
437A GLU* 3.7 17.7 - - - +
524B LEU 3.2 17.0 + - - +
525B ALA 3.0 5.4 + - - +
527B ALA* 1.3 76.5 - - - +
529B GLU* 1.3 61.4 + - - +
530B PRO 3.4 0.2 - - - -
531B GLU* 2.8 25.2 + - - +
532B LEU* 3.2 16.9 + - + +
541B HIS* 3.6 24.9 - - + +
545B THR* 4.3 7.9 - - + -
549B ILE* 4.4 6.7 - - + -
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Residues in contact with GLU 529 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426A LYS* 5.1 5.3 - - + +
427A ILE* 4.3 18.4 - - + +
430A ALA* 3.8 17.8 - - + +
219B GLN* 2.9 36.8 + - - +
525B ALA* 3.1 24.6 + - - +
526B LYS* 3.8 16.1 + - - +
528B ILE* 1.3 76.8 - - - +
530B PRO* 1.3 70.2 - - + +
531B GLU 3.2 0.3 + - - -
532B LEU* 3.2 18.5 + - - +
533B GLN* 3.7 11.1 - - - +
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Residues in contact with PRO 530 (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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526B LYS 3.3 13.5 - - - +
527B ALA* 3.4 14.8 - - - +
529B GLU* 1.3 94.3 - - + +
531B GLU* 1.3 63.2 + - + +
533B GLN* 3.2 20.4 + - + +
534B ASP* 3.2 18.2 + - - +
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Residues in contact with GLU 531 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527B ALA* 3.7 16.2 - - - +
528B ILE* 2.8 17.6 + - - +
530B PRO* 1.3 78.5 - - + +
532B LEU* 1.3 58.1 + - - +
533B GLN 3.5 0.2 + - - -
534B ASP* 3.5 8.0 - - - +
536B LYS* 4.6 7.9 + - - +
538B ILE* 3.8 25.0 - - + +
540B SER* 2.8 24.9 + - - -
541B HIS* 2.6 31.5 + - - -
549B ILE* 4.0 6.8 - - + +
553B LYS* 2.6 36.0 + - - +
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Residues in contact with LEU 532 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426A LYS* 3.5 49.6 + - + +
429A LEU* 4.0 11.4 - - + -
430A ALA* 3.8 21.5 - - + +
433A LEU* 4.1 18.6 - - + -
528B ILE* 3.7 16.2 - - + +
529B GLU* 3.2 9.5 + - - +
531B GLU* 1.3 76.3 - - - +
533B GLN* 1.3 60.4 + - + +
549B ILE* 4.1 20.9 - - + +
552B LEU* 5.1 3.1 - - + -
553B LYS* 4.1 8.7 - - + +
556B PHE* 3.5 33.7 - - + -
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Residues in contact with GLN 533 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A ALA* 6.1 0.2 - - - -
426A LYS* 3.7 34.6 - - - +
529B GLU 3.7 14.9 - - - +
530B PRO* 3.2 11.8 + - + +
532B LEU* 1.3 75.3 - - - +
534B ASP* 1.4 67.5 + - - +
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Residues in contact with ASP 534 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530B PRO 3.2 12.1 + - - +
531B GLU* 3.8 11.0 - - - +
532B LEU 3.6 0.4 - - - +
533B GLN* 1.4 83.6 - - + +
535B GLY* 1.3 59.4 + - - +
536B LYS* 2.7 45.1 + - - +
538B ILE* 3.8 0.5 - - - +
553B LYS* 2.8 40.2 + - - -
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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
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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