Contacts of the helix formed by residues 521 - 529 (chain B) in PDB entry 2WNT
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 LYS 521 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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576A TYR* 4.2 12.2 + - - +
469B HIS* 4.7 9.4 + - - +
470B PRO* 6.3 0.8 - - - +
471B ASN* 4.0 16.6 + - - -
517B HIS* 2.9 31.3 + - + +
518B THR* 3.7 19.6 - - - +
520B GLY* 1.3 78.4 - - - +
522B THR* 1.3 56.2 + - - +
524B GLU* 3.4 4.7 + - - +
525B TYR* 3.1 26.2 + - - +
670B LEU* 3.7 19.7 - - + +
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Residues in contact with THR 522 (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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469B HIS* 3.2 32.1 - - + +
471B ASN* 3.2 15.4 + - - +
472B ILE* 3.5 32.3 - - + -
518B THR 3.0 13.2 + - - -
519B ILE* 3.1 9.2 + - - -
521B LYS* 1.3 78.3 - - - +
523B VAL* 1.3 58.1 + - - +
525B TYR* 3.6 2.4 + - - +
526B LEU* 3.2 26.6 + - + +
555B ILE* 4.0 19.7 - - + -
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Residues in contact with VAL 523 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519B ILE* 3.1 20.4 + - + +
520B GLY 3.8 4.7 - - - +
522B THR* 1.3 75.6 - - - +
524B GLU* 1.3 61.1 + - - +
526B LEU* 3.2 9.2 + - + +
527B HIS* 2.8 61.9 + - + +
533B HIS* 6.1 1.6 - - + -
536B LEU* 3.6 27.4 - - + -
555B ILE* 4.3 12.6 - - + -
596B ASP* 4.4 8.3 - - + +
597B ILE* 4.6 6.1 - - + -
600B LEU* 4.2 11.0 - - + -
666B ALA* 4.3 8.1 - - + -
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Residues in contact with GLU 524 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576A TYR* 3.8 25.6 + - + -
520B GLY 3.0 18.1 + - - +
521B LYS* 3.6 6.1 - - - +
523B VAL* 1.3 77.7 - - - +
525B TYR* 1.3 62.2 + - - +
527B HIS* 3.9 3.7 - - - +
528B SER* 3.1 23.7 + - - -
666B ALA* 3.8 15.3 - - + -
667B LYS* 3.2 38.8 + - + +
670B LEU* 3.1 23.5 - - + +
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Residues in contact with TYR 525 (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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570A LEU* 3.2 37.3 - - + +
571A LEU 2.7 31.3 + - - -
572A MET* 4.4 9.2 - - + -
576A TYR* 3.8 32.5 - + - +
466B TYR* 3.5 33.8 - + + -
469B HIS* 3.7 25.8 - + + +
472B ILE* 5.1 0.4 - - + -
521B LYS 3.1 14.4 + - - +
522B THR 3.8 8.5 - - - +
523B VAL 3.2 0.2 - - - -
524B GLU* 1.3 77.6 - - - +
526B LEU* 1.3 70.4 + - + +
528B SER* 2.6 23.5 + - - -
529B GLN* 3.2 23.9 + - + +
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Residues in contact with LEU 526 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462B ILE* 5.2 0.4 - - + -
466B TYR* 4.3 19.5 - - + -
472B ILE* 3.7 25.6 - - + -
522B THR* 3.2 22.5 + - + +
523B VAL* 3.2 11.9 + - + +
525B TYR* 1.3 81.8 - - + +
527B HIS* 1.3 66.3 + - + +
529B GLN* 3.0 15.8 + - - +
531B VAL* 3.0 47.6 + - + +
533B HIS* 5.3 9.2 - - + +
555B ILE* 4.9 6.1 - - + -
558B PHE* 3.9 28.7 - - + -
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Residues in contact with HIS 527 (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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523B VAL* 2.8 43.7 + - + +
524B GLU* 3.9 5.2 - - - +
526B LEU* 1.3 72.5 - - + +
528B SER* 1.3 58.0 + - - +
530B GLY* 2.9 18.2 + - - -
531B VAL 3.4 17.9 - - - +
532B VAL* 4.2 1.1 - - + -
574B PRO* 3.0 17.5 - - - +
593B GLU* 3.4 59.7 - - + +
596B ASP* 2.9 25.2 + - + -
597B ILE* 4.3 8.3 - - + -
666B ALA* 4.4 11.0 + - + +
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Residues in contact with SER 528 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573A THR* 4.0 10.2 + - - +
575A CYS* 5.9 1.7 - - - +
576A TYR* 3.7 39.2 - - - +
524B GLU* 3.1 15.1 + - - -
525B TYR* 2.6 20.8 + - - -
527B HIS* 1.3 74.7 - - - +
529B GLN* 1.3 64.7 + - - +
530B GLY 3.3 0.9 - - - -
573B THR* 3.4 11.4 - - - -
574B PRO* 3.4 18.3 - - - +
575B CYS* 5.0 0.9 + - - +
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Residues in contact with GLN 529 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529A GLN* 5.7 1.0 - - - +
571A LEU* 3.8 20.2 + - - +
572A MET* 3.7 7.9 - - - +
573A THR* 3.2 41.8 - - - +
576A TYR* 5.3 0.4 - - - +
466B TYR* 3.5 42.6 + - + +
525B TYR* 3.5 24.6 - - + +
526B LEU* 3.0 10.7 + - - +
528B SER* 1.3 85.4 + - - +
530B GLY* 1.3 58.5 + - - +
531B VAL* 4.6 0.7 - - + -
563B GLN* 2.9 20.1 - - - +
572B MET 3.8 5.6 - - - +
573B THR* 4.4 4.8 - - - -
574B PRO* 4.4 0.7 - - - -
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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
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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