Contacts of the helix formed by residues 508 - 519 (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 SER 508 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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506B PHE* 4.1 2.1 - - - -
507B PHE* 1.3 75.3 - - - +
509B GLU* 1.3 66.7 + - - +
510B ARG* 3.1 9.5 + - - +
511B GLU* 2.5 28.3 + - - +
512B ALA* 3.1 19.8 + - - +
683B GLN* 3.3 31.8 + - - +
684B SER 2.9 24.7 - - - -
686B LEU* 3.6 9.4 - - - +
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Residues in contact with GLU 509 (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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508B SER* 1.3 75.1 - - - +
510B ARG* 1.3 57.4 + - - +
512B ALA* 3.2 8.9 + - - +
513B SER* 2.9 31.4 + - - -
608B LEU* 4.3 13.9 - - + -
643B THR 4.5 0.5 - - - +
644B VAL* 3.5 16.9 - - + +
645B SER* 2.6 48.4 + - - -
648B ALA* 3.9 0.6 - - - +
674B TRP* 2.9 22.6 + - - +
681B LEU* 3.6 3.8 - - + +
682B PRO* 3.6 35.6 + - + +
684B SER 4.5 0.6 + - - -
686B LEU* 3.7 15.2 - - + +
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Residues in contact with ARG 510 (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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506B PHE* 4.2 16.6 - - - -
508B SER* 3.1 8.1 + - - +
509B GLU* 1.3 80.8 - - - +
511B GLU* 1.3 89.3 + - - +
513B SER* 3.4 3.6 + - - -
514B PHE* 3.1 42.4 + - + -
678B LYS* 4.6 12.7 - - + +
681B LEU* 4.0 13.9 - - + +
682B PRO 3.5 9.1 + - - +
683B GLN* 3.1 47.5 + - + +
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Residues in contact with GLU 511 (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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505B LYS* 4.4 16.1 - - - +
506B PHE* 3.7 23.6 - - - +
507B PHE* 3.8 19.9 - - + -
508B SER* 2.5 41.8 + - - +
510B ARG* 1.3 108.6 + - - +
512B ALA* 1.3 64.9 + - - +
514B PHE* 3.3 12.0 + - + +
515B VAL* 3.2 25.1 + - - +
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Residues in contact with ALA 512 (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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507B PHE* 3.6 27.3 - - + -
508B SER 3.1 11.0 + - - +
509B GLU* 3.2 11.9 + - - +
511B GLU* 1.3 75.1 - - - +
513B SER* 1.3 65.9 + - - +
515B VAL* 3.0 6.2 + - - +
516B LEU* 3.0 22.9 + - - +
607B MET* 4.0 16.1 - - + +
608B LEU* 4.7 5.6 - - + -
674B TRP* 3.6 15.5 - - + -
686B LEU* 4.9 0.7 - - + -
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Residues in contact with SER 513 (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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509B GLU 2.9 7.5 + - - -
510B ARG 3.7 3.8 - - - -
511B GLU 3.4 0.2 - - - -
512B ALA* 1.3 75.8 - - - +
514B PHE* 1.3 57.9 + - - +
516B LEU* 3.9 1.7 - - - +
517B HIS* 2.9 30.5 + - - +
674B TRP* 2.9 37.4 + - - -
675B VAL* 3.5 8.1 - - - +
678B LYS* 3.4 18.5 - - - +
681B LEU* 3.4 28.7 - - - -
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Residues in contact with PHE 514 (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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510B ARG* 3.1 39.3 + - + -
511B GLU* 3.3 11.8 + - + +
512B ALA 3.2 0.6 - - - -
513B SER* 1.3 76.4 - - - +
515B VAL* 1.3 58.4 + - - +
517B HIS* 3.6 6.1 - - - +
518B THR* 2.7 39.5 + - - -
550B PRO* 4.0 30.1 - - + -
678B LYS* 3.5 32.5 - - + +
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Residues in contact with VAL 515 (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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497B LEU* 4.4 20.6 - - + -
505B LYS* 5.8 3.1 - - - -
507B PHE* 4.4 15.3 - - + -
511B GLU 3.2 12.3 + - - +
512B ALA 3.0 8.6 + - - +
514B PHE* 1.3 79.4 - - + +
516B LEU* 1.3 64.8 + - - +
518B THR* 3.3 1.0 + - - -
519B ILE* 3.0 30.2 + - + +
543B TYR* 4.4 14.4 - - - +
550B PRO* 5.6 4.7 - - + -
553B LEU* 4.1 22.0 - - + -
603B LEU* 4.8 4.0 - - + -
607B MET* 3.8 22.7 - - + -
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Residues in contact with LEU 516 (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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512B ALA 3.0 15.2 + - - +
513B SER 3.9 4.0 - - - +
515B VAL* 1.3 77.7 - - - +
517B HIS* 1.3 53.9 + - - +
519B ILE* 4.8 2.5 - - + -
520B GLY* 2.5 36.6 + - - +
600B LEU* 4.3 24.2 - - + +
603B LEU* 6.2 3.4 - - + -
604B LEU* 4.0 13.5 - - + -
607B MET* 4.8 7.9 - - + -
651B LEU* 3.7 30.1 - - + -
655B MET* 4.3 19.1 - - + -
669B VAL* 4.0 18.4 - - + -
670B LEU* 4.7 0.7 - - - +
674B TRP* 3.7 16.4 - - + -
675B VAL* 4.1 6.7 - - + -
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Residues in contact with HIS 517 (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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513B SER 2.9 20.0 + - - +
514B PHE* 3.6 10.4 - - + +
516B LEU* 1.3 74.7 - - - +
518B THR* 1.3 67.7 + - - +
521B LYS* 2.9 42.9 + - + +
670B LEU* 3.7 27.3 + - + +
675B VAL* 3.8 16.3 - - + +
678B LYS* 3.3 25.2 + - - +
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Residues in contact with THR 518 (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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471B ASN* 3.4 28.7 - - + +
514B PHE* 2.7 23.1 + - - -
515B VAL 3.8 3.1 - - - -
517B HIS* 1.3 79.3 + - - +
519B ILE* 1.3 60.5 + - - +
521B LYS* 3.7 14.7 + - - +
522B THR* 3.0 25.7 + - - -
550B PRO* 3.4 36.4 - - - +
551B GLU* 5.0 1.6 - - - -
553B LEU* 3.9 14.4 - - + -
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Residues in contact with ILE 519 (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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471B ASN* 5.5 2.2 - - + -
515B VAL* 3.0 25.6 + - + +
516B LEU* 4.0 4.3 - - + +
518B THR* 1.3 76.2 - - + +
520B GLY* 1.3 66.7 + - - +
522B THR* 3.1 7.8 + - - +
523B VAL* 3.1 23.2 + - + +
536B LEU* 5.2 0.7 - - + -
541B ILE* 4.1 36.6 - - + -
553B LEU* 4.0 29.6 - - + -
555B ILE* 4.2 24.9 - - + +
600B LEU* 3.8 29.2 - - + -
603B LEU* 5.4 3.6 - - + -
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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