Contacts of the helix formed by residues 514 - 524 (chain B) in PDB entry 2W93
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 THR 514 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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361B ALA 3.2 15.3 + - - -
362B SER* 3.5 23.8 - - - +
363B THR 3.2 8.1 - - - +
364B PRO* 4.6 2.0 - - + -
365B LEU* 3.5 9.1 - - - +
513B ALA* 1.3 88.3 - - + +
515B THR* 1.3 60.1 + - - +
517B GLU* 3.0 38.7 + - - +
518B TRP* 2.9 28.1 + - - +
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Residues in contact with THR 515 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359B VAL* 3.7 11.1 - - + +
360B PRO 3.3 14.6 - - - +
361B ALA* 3.7 2.7 - - - +
363B THR* 2.3 44.9 + - - +
364B PRO 4.5 3.8 + - - -
365B LEU* 3.8 5.2 - - - +
369B TRP* 3.6 45.4 + - - -
514B THR* 1.3 71.4 - - - +
516B GLY* 1.3 65.7 + - - +
518B TRP* 3.3 1.7 + - - +
519B ASP* 3.0 29.0 + - - +
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Residues in contact with GLY 516 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361B ALA* 2.9 36.3 + - - -
515B THR* 1.3 79.3 - - - +
517B GLU* 1.3 55.9 + - - +
519B ASP* 3.4 4.3 + - - +
520B LYS* 2.9 47.1 + - - +
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Residues in contact with GLU 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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511B ARG* 3.9 7.3 - - - +
512B VAL* 3.5 20.4 - - + +
513B ALA* 2.8 33.6 + - - +
514B THR* 3.0 34.0 + - - +
516B GLY* 1.3 74.4 - - - +
518B TRP* 1.3 61.9 + - - +
520B LYS* 4.1 5.7 - - + +
521B LEU* 3.1 25.8 + - - +
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Residues in contact with TRP 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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365B LEU* 3.8 10.1 - - + -
369B TRP* 3.6 30.7 - + + -
370B MET* 3.7 38.6 - - + -
373B GLN* 3.8 18.2 + - + +
374B LEU* 4.0 24.4 - - + +
377B PHE* 5.6 1.2 - - + +
441B PHE* 3.9 20.9 - + - -
467B PHE* 3.9 18.8 - + - -
512B VAL* 3.9 23.1 - - + +
514B THR 2.9 13.4 + - - +
515B THR 3.5 7.6 - - - +
517B GLU* 1.3 77.7 - - - +
519B ASP* 1.3 71.6 + - - +
521B LEU* 3.9 0.7 - - - +
522B THR* 2.9 53.0 + - + +
538B VAL* 4.2 12.6 - - + -
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Residues in contact with ASP 519 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369B TRP* 3.8 5.0 - - - -
373B GLN* 2.8 40.5 + - - +
376B ASN* 5.1 0.5 + - - -
515B THR* 3.0 19.6 + - - +
516B GLY* 3.9 5.3 - - - +
518B TRP* 1.3 79.3 - - - +
520B LYS* 1.3 65.8 + - + +
522B THR* 3.9 4.7 + - - -
523B GLN* 3.0 53.0 + - - +
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Residues in contact with LYS 520 (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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361B ALA* 4.2 12.9 - - - +
516B GLY* 2.9 35.6 + - - +
517B GLU* 4.2 4.5 - - - +
519B ASP* 1.3 78.8 - - + +
521B LEU* 1.3 63.4 + - - +
523B GLN* 4.3 4.2 - - - +
524B ASP* 3.5 18.9 + - - +
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Residues in contact with LEU 521 (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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467B PHE* 5.4 0.4 - - + -
510B HIS* 3.3 53.8 - - + +
512B VAL* 3.9 11.2 - - + -
517B GLU 3.1 18.1 + - - +
518B TRP 3.9 2.0 - - - +
520B LYS* 1.3 76.8 - - - +
522B THR* 1.3 68.9 + - + +
524B ASP* 3.2 20.2 + - + +
527B PHE* 3.4 44.2 - - + +
536B ILE* 3.8 20.9 - - + -
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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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376B ASN* 6.1 1.4 - - - +
377B PHE* 3.6 30.1 - - + +
467B PHE* 4.7 10.1 - - + -
518B TRP* 2.9 57.7 + - + +
519B ASP* 3.7 4.9 + - - -
521B LEU* 1.3 81.7 - - + +
523B GLN* 1.3 56.8 + - - +
524B ASP 3.4 0.2 - - - -
527B PHE* 3.9 19.1 - - + -
528B ASN* 2.7 27.1 + - - +
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Residues in contact with GLN 523 (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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373B GLN* 5.6 0.4 - - - +
376B ASN* 5.5 10.9 - - + +
519B ASP* 3.0 47.0 + - - +
520B LYS* 4.5 3.8 - - - +
522B THR* 1.3 81.7 - - - +
524B ASP* 1.3 63.6 + - - +
525B LYS* 3.3 11.6 + - - +
528B ASN* 4.0 2.9 + - - +
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Residues in contact with ASP 524 (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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520B LYS 3.5 13.7 + - - +
521B LEU* 3.2 17.3 + - + +
523B GLN* 1.3 75.7 - - - +
525B LYS* 1.3 67.0 + - - +
526B SER* 3.1 15.4 - - - -
527B PHE* 2.9 34.8 + - + +
528B ASN* 2.9 19.1 + - - -
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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