Contacts of the helix formed by residues 521 - 529 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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469A HIS* 4.6 8.8 + - - +
470A PRO* 6.2 1.4 - - - +
471A ASN* 3.9 17.3 + - - -
517A HIS* 2.9 32.7 + - + +
518A THR* 3.6 19.1 + - - +
520A GLY* 1.3 78.8 - - - +
522A THR* 1.3 56.5 + - - +
524A GLU* 3.4 3.6 + - - +
525A TYR* 3.1 27.7 + - - +
670A LEU* 3.8 18.8 - - + +
576B TYR* 4.2 15.9 + - - +
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Residues in contact with THR 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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469A HIS* 3.4 29.8 - - + +
471A ASN* 3.3 24.3 + - - +
472A ILE* 3.5 29.4 - - + -
518A THR 2.8 15.4 + - - -
519A ILE* 3.2 8.5 + - - +
521A LYS* 1.3 77.3 - - - +
523A VAL* 1.3 58.6 + - - +
525A TYR* 3.8 2.3 + - - +
526A LEU* 3.2 27.7 + - + +
555A ILE* 4.1 15.3 - - + -
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Residues in contact with VAL 523 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519A ILE* 3.0 20.1 + - + +
520A GLY* 3.8 6.3 - - - +
521A LYS 3.3 0.2 - - - -
522A THR* 1.3 76.3 - - - +
524A GLU* 1.3 60.1 + - - +
525A TYR 3.2 0.2 - - - -
526A LEU* 3.2 9.3 + - + +
527A HIS* 2.8 61.0 + - + +
533A HIS* 6.1 1.6 - - + -
536A LEU* 3.6 28.0 - - + -
555A ILE* 4.3 11.7 - - + -
596A ASP* 4.3 9.2 - - + +
597A ILE* 4.6 0.9 - - + -
600A LEU* 4.2 13.0 - - + -
666A ALA* 4.3 8.3 - - + -
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Residues in contact with GLU 524 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520A GLY 2.9 18.5 + - - +
521A LYS* 3.7 4.5 - - - +
522A THR 3.4 0.2 - - - -
523A VAL* 1.3 78.2 - - - +
525A TYR* 1.3 61.7 + - - +
527A HIS* 3.9 3.4 - - - +
528A SER* 3.1 23.4 + - - -
666A ALA* 3.7 15.7 - - + +
667A LYS* 3.1 40.0 + - + +
670A LEU* 3.0 24.5 - - + +
576B TYR* 4.0 22.0 + - + -
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Residues in contact with TYR 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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465A ARG 5.3 0.2 + - - -
466A TYR* 3.6 35.1 - + + -
469A HIS* 3.7 30.1 - + + +
472A ILE* 5.2 0.2 - - + -
521A LYS 3.1 16.3 + - - +
522A THR 3.9 6.1 - - - +
523A VAL 3.2 0.2 - - - -
524A GLU* 1.3 77.6 - - - +
526A LEU* 1.3 69.2 + - + +
528A SER* 2.6 21.5 + - - -
529A GLN* 3.2 27.5 + - + +
570B LEU* 3.7 25.4 - - + +
571B LEU* 2.5 31.5 + - - +
572B MET* 4.3 10.8 - - + -
576B TYR* 3.5 36.9 - + + +
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Residues in contact with LEU 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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462A ILE* 5.2 0.4 - - + -
466A TYR* 4.3 20.0 - - + -
472A ILE* 3.7 30.3 - - + -
522A THR* 3.2 22.1 + - + +
523A VAL* 3.2 12.9 + - + +
525A TYR* 1.3 83.1 - - + +
527A HIS* 1.3 65.6 + - + +
529A GLN* 2.9 16.2 + - - +
531A VAL* 3.0 47.3 + - + +
533A HIS* 5.3 9.2 - - + +
555A ILE* 4.9 7.2 - - + -
558A PHE* 4.1 21.8 - - + -
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Residues in contact with HIS 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 VAL* 2.8 42.0 + - + +
524A GLU* 3.9 5.6 - - - +
526A LEU* 1.3 73.1 - - + +
528A SER* 1.3 58.5 + - - +
530A GLY* 2.9 18.8 + - - -
531A VAL 3.4 17.7 - - - +
532A VAL* 4.2 2.4 - - + +
533A HIS 5.4 0.2 - - - -
574A PRO* 3.4 13.9 - - - +
589A GLN* 5.4 0.3 - - - +
593A GLU* 3.4 57.0 - - + +
596A ASP* 2.6 33.4 + - + +
597A ILE* 4.3 7.3 - - + +
666A ALA* 4.4 10.4 + - + +
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Residues in contact with SER 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 GLU* 3.1 15.1 + - - -
525A TYR 2.6 19.9 + - - -
527A HIS* 1.3 77.9 - - - +
529A GLN* 1.3 62.5 + - - +
530A GLY 3.3 0.7 - - - -
573A THR* 3.4 24.3 - - - +
574A PRO* 3.4 5.0 - - - +
575B CYS* 3.4 18.4 - - - +
576B TYR* 3.5 41.9 - - - +
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Residues in contact with GLN 529 (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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466A TYR* 3.5 42.6 + - + +
525A TYR* 3.5 32.7 + - + +
526A LEU* 2.9 12.0 + - - +
528A SER* 1.3 86.6 + - - +
530A GLY* 1.3 58.8 + - - +
531A VAL 3.4 0.2 - - - -
563A GLN* 3.1 19.4 - - - +
572A MET 3.8 7.1 - - - +
573A THR* 4.5 9.2 - - - +
574A PRO* 4.4 0.2 - - - -
529B GLN* 5.7 1.2 - - - +
571B LEU* 4.3 8.8 - - - +
572B MET* 3.9 5.8 - - - +
573B THR* 3.3 39.5 + - - +
576B TYR* 4.8 0.8 - - - +
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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