Contacts of the helix formed by residues 514 - 524 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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361C ALA 3.2 15.8 + - - +
362C SER* 3.8 20.9 - - - +
363C THR 3.1 8.7 - - - +
364C PRO* 4.7 1.6 - - + -
365C LEU* 3.6 12.5 - - - +
513C ALA* 1.3 86.8 - - + +
515C THR* 1.3 65.0 + - - +
517C GLU* 3.1 36.1 + - - +
518C TRP 3.0 18.2 + - - -
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Residues in contact with THR 515 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359C VAL* 3.7 11.2 - - + +
360C PRO 3.2 27.4 - - - +
361C ALA* 3.7 1.3 - - - +
363C THR* 2.9 34.2 + - - +
364C PRO 4.4 2.4 + - - -
365C LEU* 3.8 11.3 - - - +
369C TRP* 3.5 39.2 + - - -
514C THR* 1.3 71.9 - - - +
516C GLY* 1.3 65.0 + - - +
518C TRP* 3.6 1.2 - - - +
519C ASP* 3.0 29.5 + - - +
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Residues in contact with GLY 516 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361C ALA* 2.9 35.2 + - - -
514C THR* 4.1 0.2 - - - -
515C THR* 1.3 79.8 - - - +
517C GLU* 1.3 56.3 + - - +
519C ASP* 4.1 4.8 - - - +
520C LYS* 3.0 31.8 + - - +
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Residues in contact with GLU 517 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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511C ARG 4.0 7.7 - - - +
512C VAL* 3.6 17.9 - - + +
513C ALA* 2.8 30.1 + - - +
514C THR* 3.1 32.3 + - - +
516C GLY* 1.3 75.5 - - - +
518C TRP* 1.3 64.1 + - - +
520C LYS* 3.9 5.4 - - - +
521C LEU* 3.1 26.7 + - - +
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Residues in contact with TRP 518 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365C LEU* 3.9 17.5 - - + -
369C TRP* 3.7 16.6 - + + -
370C MET* 3.6 38.8 - - + -
373C GLN* 3.8 17.0 + - + +
374C LEU* 4.1 24.4 - - + +
377C PHE* 5.6 1.4 - - + +
441C PHE* 4.0 19.7 - + - -
467C PHE* 4.1 12.1 - + - -
512C VAL* 3.9 25.2 - - + +
514C THR 3.0 13.2 + - - +
515C THR 3.6 7.4 - - - +
516C GLY 3.3 0.2 - - - -
517C GLU* 1.3 78.0 - - - +
519C ASP* 1.3 74.2 + - - +
521C LEU* 3.9 0.2 - - - -
522C THR* 2.8 57.4 + - + +
538C VAL* 4.2 16.6 - - + -
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Residues in contact with ASP 519 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369C TRP* 3.9 4.4 - - - -
373C GLN* 3.0 32.7 + - - +
376C ASN* 5.3 0.2 + - - -
515C THR* 3.0 19.8 + - - +
516C GLY* 4.1 4.5 - - - +
518C TRP* 1.3 87.6 - - - +
520C LYS* 1.3 62.8 + - - +
522C THR* 3.9 4.0 + - - -
523C GLN* 2.9 54.0 + - - +
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Residues in contact with LYS 520 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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516C GLY 3.0 19.9 + - - +
517C GLU* 3.9 5.4 - - - +
519C ASP* 1.3 76.9 - - - +
521C LEU* 1.3 64.4 + - - +
523C GLN* 4.3 2.3 - - - +
524C ASP* 3.4 19.1 + - - +
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Residues in contact with LEU 521 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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510C HIS* 3.5 49.1 - - + +
512C VAL* 3.8 19.5 - - + -
517C GLU 3.1 17.3 + - - +
518C TRP 3.9 1.8 - - - +
520C LYS* 1.3 79.1 - - - +
522C THR* 1.3 67.8 + - + +
524C ASP* 3.2 18.9 + - + +
527C PHE* 3.3 52.3 - - + +
536C ILE* 3.9 13.7 - - + -
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Residues in contact with THR 522 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376C ASN* 6.2 0.3 - - - +
377C PHE* 3.6 32.2 - - + +
467C PHE* 4.7 10.3 - - + -
518C TRP* 2.8 61.0 + - + +
519C ASP* 3.9 3.5 + - - -
521C LEU* 1.3 81.4 - - + +
523C GLN* 1.3 59.4 + - - +
524C ASP 3.3 0.2 - - - -
527C PHE* 3.8 18.8 - - + -
528C ASN* 2.8 25.1 + - - +
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Residues in contact with GLN 523 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373C GLN* 5.1 1.2 - - - +
376C ASN* 5.0 16.4 - - + +
519C ASP* 2.9 49.9 + - - +
520C LYS* 4.6 2.4 - - - +
522C THR* 1.3 80.1 - - - +
524C ASP* 1.3 65.0 + - - +
525C LYS* 3.3 3.3 + - - -
528C ASN* 3.9 3.5 + - - +
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Residues in contact with ASP 524 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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520C LYS 3.4 13.9 + - - +
521C LEU* 3.2 19.3 + - + +
523C GLN* 1.3 77.0 - - - +
525C LYS* 1.3 67.2 + - - +
526C SER* 2.5 31.2 + - - -
527C PHE* 3.0 14.0 + - + +
528C ASN* 2.9 27.6 + - - -
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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