Contacts of the helix formed by residues 518 - 529 (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 VAL 518 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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361A GLU* 4.1 19.7 - - - +
515A GLN* 3.3 25.6 - - + +
517A GLY* 1.3 81.7 - - - +
519A GLU* 1.3 64.4 + - + +
520A LEU 3.5 1.1 + - - -
521A GLY* 3.8 3.7 + - - -
522A LYS* 3.3 46.2 + - + +
391B GLN 4.9 10.5 - - - +
392B HIS* 6.1 0.9 - - - +
395B TYR* 5.4 2.2 - - + -
396B GLN* 4.5 17.7 - - + +
399B HIS* 5.6 1.1 - - - -
435B GLN* 5.3 3.1 + - - +
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Residues in contact with GLU 519 (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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516A TRP* 3.3 32.0 + - + +
517A GLY 3.4 0.4 - - - -
518A VAL* 1.3 80.4 - - + +
520A LEU* 1.3 63.3 + - - +
522A LYS* 3.1 10.3 + - + +
523A GLN* 2.9 59.7 + - + +
443B LYS* 3.7 11.5 + - - -
451B GLU* 3.8 5.7 - - - +
469B LYS* 2.8 39.3 + - - +
471B PHE* 4.8 3.4 - - + -
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Residues in contact with LEU 520 (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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518A VAL 3.5 0.6 - - - -
519A GLU* 1.3 77.4 - - - +
521A GLY* 1.3 64.5 + - - +
522A LYS 3.2 0.3 + - - -
523A GLN* 3.2 13.4 + - + +
524A LEU* 3.0 45.3 + - + +
438B ALA* 3.6 35.9 - - + +
441B LYS* 5.5 2.5 - - + +
442B GLY* 3.6 30.3 - - - +
443B LYS* 3.9 21.1 - - - +
471B PHE* 3.7 39.4 - - + -
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Residues in contact with GLY 521 (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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517A GLY 5.4 0.8 + - - -
518A VAL 3.8 4.0 + - - -
519A GLU 3.4 0.2 - - - -
520A LEU* 1.3 78.6 - - - +
522A LYS* 1.3 61.2 + - - +
524A LEU* 4.5 0.7 - - - -
525A ALA* 3.0 25.5 + - - +
399B HIS* 5.1 3.8 + - - -
431B ASN* 4.9 1.2 - - - +
434B ALA* 3.7 8.9 - - - +
435B GLN* 3.6 28.5 + - - -
438B ALA* 4.2 16.8 - - - +
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Residues in contact with LYS 522 (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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218A THR* 6.4 0.6 - - - +
220A GLU* 5.8 2.2 - - - -
518A VAL* 3.3 37.0 + - + +
519A GLU* 3.1 11.8 + - - +
521A GLY* 1.3 76.3 - - - +
523A GLN* 1.3 63.3 + - + +
525A ALA* 3.3 5.8 + - - +
526A LYS* 3.1 26.8 + - - +
391B GLN* 5.9 5.4 - - - +
392B HIS* 5.1 17.3 - - + -
431B ASN* 5.6 3.1 - - - +
435B GLN* 5.9 0.9 - - - +
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Residues in contact with GLN 523 (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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519A GLU* 2.9 48.6 + - + +
520A LEU* 3.5 11.4 - - + +
522A LYS* 1.3 75.9 - - + +
524A LEU* 1.3 69.0 + - + +
526A LYS* 3.3 11.4 + - - +
527A ALA* 3.2 18.9 + - - +
443B LYS* 2.8 27.0 + - - +
451B GLU* 4.0 11.1 + - - +
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Residues in contact with LEU 524 (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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520A LEU* 3.0 31.5 + - + +
523A GLN* 1.3 83.1 - - + +
525A ALA* 1.3 61.3 + - - +
527A ALA* 3.3 10.0 + - + +
528A ILE* 3.2 27.5 + - - +
541A HIS* 5.4 0.8 + - + -
434B ALA* 3.6 15.3 - - + +
437B GLU* 3.7 27.1 - - + +
438B ALA* 3.6 40.4 - - + +
441B LYS* 4.2 25.1 - - + +
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Residues in contact with ALA 525 (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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219A GLN* 5.9 2.0 - - - +
521A GLY 3.0 19.4 + - - +
522A LYS* 3.7 5.6 - - - +
524A LEU* 1.3 75.1 - - - +
526A LYS* 1.3 65.3 + - - +
528A ILE* 3.2 1.5 + - - +
529A GLU* 3.1 29.5 + - - +
430B ALA* 3.7 19.6 - - + +
431B ASN* 4.0 21.8 - - - +
434B ALA* 3.3 14.3 - - + +
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Residues in contact with LYS 526 (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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219A GLN* 5.7 4.3 - - - +
522A LYS 3.1 15.9 + - - +
523A GLN* 3.3 11.9 + - - +
525A ALA* 1.3 76.3 - - - +
527A ALA* 1.3 61.4 + - - +
529A GLU* 3.6 16.5 + - - +
530A PRO* 3.2 20.1 - - - +
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Residues in contact with ALA 527 (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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523A GLN 3.2 9.9 + - - +
524A LEU* 3.6 14.8 - - + +
525A ALA 3.1 0.6 - - - -
526A LYS* 1.3 77.9 - - - +
528A ILE* 1.3 63.2 + - + +
530A PRO* 3.5 16.3 - - - +
531A GLU* 3.8 13.3 - - - +
541A HIS* 5.1 6.5 - - - +
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Residues in contact with ILE 528 (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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524A LEU 3.2 14.1 + - - +
525A ALA 3.2 4.7 + - - +
527A ALA* 1.3 76.3 - - - +
529A GLU* 1.3 66.9 + - - +
530A PRO 3.3 0.7 - - - -
531A GLU* 2.8 19.1 + - - +
532A LEU* 3.3 25.6 + - + +
541A HIS* 3.6 24.5 - - + +
545A THR* 4.3 6.5 - - + -
549A ILE* 4.5 5.4 - - + -
430B ALA* 4.0 11.2 - - + +
433B LEU* 3.9 38.6 - - + -
434B ALA* 3.9 10.3 - - + +
437B GLU* 3.5 23.3 - - - +
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Residues in contact with GLU 529 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A GLN* 3.0 34.4 + - - +
525A ALA* 3.1 16.9 + - - +
526A LYS* 3.7 22.7 + - - +
528A ILE* 1.3 75.9 - - - +
530A PRO* 1.4 71.3 - - + +
532A LEU* 3.0 19.2 + - - +
533A GLN* 3.9 11.8 + - - +
426B LYS* 5.1 5.1 - - + +
427B ILE* 3.7 21.2 - - + +
430B ALA* 3.8 16.6 - - + -
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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