Contacts of the helix formed by residues 514 - 523 (chain A) in PDB entry 2VK8
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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361A ALA 3.3 14.6 + - - +
362A SER* 3.7 23.1 - - - +
363A THR 3.2 7.4 - - - +
364A PRO* 4.7 1.1 - - + -
365A LEU* 3.6 8.5 - - - +
513A ALA* 1.3 89.3 - - + +
515A THR* 1.3 60.8 + - - +
517A GLU* 3.0 37.7 + - - +
518A TRP* 2.9 27.9 + - - +
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Residues in contact with THR 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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359A VAL* 3.9 11.2 - - + +
360A PRO 3.2 27.4 - - - +
361A ALA* 3.6 2.7 - - - +
363A THR* 2.8 29.0 + - - +
364A PRO 4.5 2.6 + - - -
365A LEU* 3.9 5.4 - - - +
369A TRP* 3.4 44.4 + - - -
514A THR* 1.3 71.6 - - - +
516A GLY* 1.3 60.0 + - - +
518A TRP* 3.4 1.7 + - - +
519A ASP* 3.0 34.9 + - - +
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Residues in contact with GLY 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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361A ALA* 2.9 36.3 + - - -
515A THR* 1.3 78.5 - - - +
517A GLU* 1.3 56.7 + - - +
519A ASP* 4.0 4.5 - - - +
520A LYS* 3.0 31.1 + - - +
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Residues in contact with GLU 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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511A ARG 4.3 4.9 - - - +
512A VAL* 3.7 19.1 - - + +
513A ALA* 2.8 35.7 + - - +
514A THR* 3.0 31.2 + - - +
516A GLY* 1.3 76.0 - - - +
518A TRP* 1.3 63.3 + - - +
520A LYS* 3.9 5.5 - - - +
521A LEU* 3.1 26.2 + - - +
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Residues in contact with TRP 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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365A LEU* 3.9 15.5 - - + -
369A TRP* 3.7 16.8 - + + -
370A MET* 3.6 42.0 - - + -
373A GLN* 3.8 18.2 + - + +
374A LEU* 4.2 24.2 - - + +
377A PHE* 5.7 2.1 - - + +
441A PHE* 4.0 19.5 - + - -
467A PHE* 4.1 17.7 - + - -
512A VAL* 4.0 25.0 - - + +
514A THR 2.9 13.2 + - - +
515A THR 3.6 7.2 - - - +
517A GLU* 1.3 77.3 - - - +
519A ASP* 1.3 66.9 + - - +
521A LEU* 3.9 0.5 - - - -
522A THR* 2.7 62.2 + - + +
536A ILE* 6.0 0.2 - - + -
538A VAL* 4.3 11.9 - - + -
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Residues in contact with ASP 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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369A TRP* 3.8 5.3 - - - -
373A GLN* 2.9 33.1 + - - +
376A ASN* 5.2 0.2 + - - -
515A THR* 3.0 20.3 + - - +
516A GLY* 4.0 4.0 - - - +
518A TRP* 1.3 85.8 - - - +
520A LYS* 1.3 63.9 + - - +
522A THR* 3.9 4.5 + - - -
523A GLN* 3.0 53.6 + - - +
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Residues in contact with LYS 520 (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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516A GLY 3.0 18.1 + - - +
517A GLU* 3.9 5.8 - - - +
519A ASP* 1.3 77.1 - - - +
521A LEU* 1.3 64.9 + - - +
523A GLN* 4.5 2.0 - - - +
524A ASP* 3.6 17.5 + - - +
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Residues in contact with LEU 521 (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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467A PHE* 5.5 0.4 - - + -
510A HIS* 3.5 48.5 - - + +
512A VAL* 3.9 12.1 - - + -
517A GLU 3.1 18.1 + - - +
518A TRP 3.9 2.0 - - - +
520A LYS* 1.3 78.8 - - - +
522A THR* 1.3 67.2 + - + +
524A ASP* 3.3 20.4 + - + +
527A PHE* 3.4 51.7 - - + +
536A ILE* 3.9 19.7 - - + -
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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
----------------------------------------------------------
377A PHE* 3.5 30.3 - - + +
467A PHE* 4.6 11.7 - - + -
518A TRP* 2.7 57.7 + - + +
519A ASP* 3.8 4.9 + - - -
521A LEU* 1.3 82.8 - - + +
523A GLN* 1.3 62.2 + - - +
524A ASP 3.3 0.2 - - - -
527A PHE* 3.9 18.8 - - + -
528A ASN* 2.8 21.6 + - - +
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Residues in contact with GLN 523 (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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373A GLN* 5.1 2.8 - - - +
376A ASN* 5.2 13.2 - - + +
519A ASP* 3.0 48.0 + - - +
520A LYS* 4.5 2.3 - - - +
522A THR* 1.3 80.8 - - - +
524A ASP* 1.3 63.8 + - - +
525A LYS* 3.4 3.3 + - - -
528A ASN* 3.9 3.0 + - - +
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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