Contacts of the helix formed by residues 508 - 519 (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 SER 508 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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506A PHE* 4.1 1.9 - - - -
507A PHE* 1.3 75.5 - - - +
509A GLU* 1.3 65.6 + - - +
510A ARG* 3.1 9.9 + - - +
511A GLU* 2.5 27.1 + - - +
512A ALA* 3.0 20.1 + - - +
682A PRO 3.9 0.2 - - - -
683A GLN* 3.3 31.4 + - - +
684A SER 2.9 26.0 - - - -
686A LEU* 3.5 10.7 - - - +
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Residues in contact with GLU 509 (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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508A SER* 1.3 74.8 - - - +
510A ARG* 1.3 56.6 + - - +
512A ALA* 3.5 8.6 - - - +
513A SER* 2.8 26.7 + - - -
608A LEU* 4.2 13.9 - - + -
643A THR 4.3 1.0 - - - +
644A VAL* 3.4 15.8 - - - -
645A SER* 2.5 51.4 + - - -
648A ALA* 3.8 1.1 - - - +
674A TRP* 2.8 24.9 + - - +
681A LEU* 3.5 10.6 - - + +
682A PRO* 3.7 33.7 + - + +
684A SER 4.5 0.4 + - - -
686A LEU* 3.8 15.4 - - + +
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Residues in contact with ARG 510 (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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506A PHE* 4.2 16.2 - - - -
508A SER* 3.1 8.1 + - - +
509A GLU* 1.3 80.7 - - - +
511A GLU* 1.3 90.0 + - - +
513A SER* 3.3 3.5 + - - -
514A PHE* 3.2 43.2 + - + -
678A LYS* 4.6 12.3 - - + +
681A LEU* 3.5 16.3 - - + +
682A PRO 3.4 9.8 + - - +
683A GLN* 3.0 47.7 + - + +
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Residues in contact with GLU 511 (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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505A LYS* 4.3 16.7 - - - +
506A PHE* 3.7 24.0 - - - +
507A PHE* 3.8 21.5 - - + -
508A SER* 2.5 43.2 + - - +
510A ARG* 1.3 108.2 + - - +
512A ALA* 1.3 65.7 + - - +
514A PHE* 3.4 11.3 + - + +
515A VAL* 3.2 24.9 + - - +
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Residues in contact with ALA 512 (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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507A PHE* 3.7 25.3 - - + -
508A SER 3.0 13.4 + - - +
509A GLU* 3.5 10.8 - - - +
511A GLU* 1.3 75.2 - - - +
513A SER* 1.3 64.9 + - - +
515A VAL* 3.0 4.7 + - - +
516A LEU* 3.0 23.2 + - - +
607A MET* 3.9 17.6 - - + +
608A LEU* 4.6 5.8 - - + -
674A TRP* 3.7 16.8 - - + -
686A LEU* 4.8 0.7 - - + -
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Residues in contact with SER 513 (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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509A GLU 2.8 7.7 + - - -
510A ARG 3.7 2.0 - - - -
512A ALA* 1.3 75.6 - - - +
514A PHE* 1.3 57.0 + - - +
516A LEU* 3.9 1.4 - - - +
517A HIS* 2.9 30.8 + - - +
674A TRP* 2.8 38.8 + - - -
675A VAL* 3.4 9.4 - - - +
678A LYS* 3.4 17.0 - - - +
681A LEU* 3.3 28.7 - - - -
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Residues in contact with PHE 514 (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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510A ARG* 3.2 39.4 + - + -
511A GLU* 3.6 11.4 - - - +
512A ALA 3.1 0.6 - - - -
513A SER* 1.3 77.3 - - - +
515A VAL* 1.3 57.3 + - - +
517A HIS* 3.7 6.6 - - - +
518A THR* 2.7 38.5 + - - -
550A PRO* 4.0 29.6 - - + -
678A LYS* 3.4 33.2 - - + +
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Residues in contact with VAL 515 (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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497A LEU* 4.3 19.5 - - + -
501A ILE* 4.8 0.2 - - + -
505A LYS* 5.7 2.7 - - - -
507A PHE* 4.4 14.8 - - + -
511A GLU 3.2 12.7 + - - +
512A ALA 3.0 8.6 + - - +
514A PHE* 1.3 76.3 - - + +
516A LEU* 1.3 67.0 + - - +
518A THR* 3.8 1.0 - - - -
519A ILE* 3.0 31.0 + - + +
543A TYR* 4.4 13.7 - - - +
550A PRO* 5.7 3.8 - - + -
553A LEU* 4.1 24.0 - - + -
603A LEU* 4.7 4.3 - - + -
607A MET* 3.7 23.6 - - + -
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Residues in contact with LEU 516 (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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512A ALA 3.0 14.1 + - - +
513A SER 3.9 3.8 - - - +
515A VAL* 1.3 79.0 - - - +
517A HIS* 1.3 54.0 + - - +
519A ILE* 4.8 2.7 - - + -
520A GLY* 2.5 37.3 + - - +
600A LEU* 4.1 33.4 - - + +
603A LEU* 6.0 4.5 - - + -
604A LEU* 4.1 13.0 - - + -
607A MET* 4.7 7.9 - - + -
651A LEU* 3.8 29.4 - - + -
655A MET* 4.3 11.2 - - + -
669A VAL* 3.9 18.8 - - + -
670A LEU* 4.6 0.8 - - + +
674A TRP* 3.8 16.4 - - + -
675A VAL* 4.1 7.2 - - + -
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Residues in contact with HIS 517 (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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513A SER 2.9 20.0 + - - +
514A PHE* 3.7 9.5 - - - +
516A LEU* 1.3 74.0 - - - +
518A THR* 1.3 65.9 + - - +
521A LYS* 2.9 44.4 + - + +
670A LEU* 3.7 26.9 + - + +
675A VAL* 3.8 15.7 - - + +
678A LYS* 3.4 25.7 + - - +
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Residues in contact with THR 518 (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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471A ASN* 3.5 29.4 - - + +
514A PHE* 2.7 24.1 + - - -
515A VAL 3.8 3.1 - - - -
517A HIS* 1.3 78.7 + - - +
519A ILE* 1.3 61.0 + - + +
521A LYS* 3.6 14.1 + - - +
522A THR* 2.8 24.8 + - - -
550A PRO* 3.5 37.0 - - - +
551A GLU* 5.0 1.1 - - - -
553A LEU* 3.9 14.1 - - + -
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Residues in contact with ILE 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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471A ASN* 5.6 1.8 - - + -
515A VAL* 3.0 27.9 + - + +
516A LEU* 4.0 3.4 - - + +
518A THR* 1.3 76.3 - - + +
520A GLY* 1.3 64.6 + - - +
522A THR* 3.2 6.7 + - - +
523A VAL* 3.0 22.7 + - + +
536A LEU* 5.1 0.7 - - + -
541A ILE* 4.0 40.4 - - + -
553A LEU* 4.1 24.5 - - + -
555A ILE* 4.2 28.0 - - + -
600A LEU* 3.8 28.7 - - + -
603A LEU* 5.3 3.8 - - + -
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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