Contacts of the helix formed by residues 452 - 460 (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 GLN 452 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49C ALA* 3.7 15.4 - - + +
50C ASN* 3.6 12.8 + - - +
53C ASN* 3.3 14.8 + - - +
450C THR* 3.3 11.4 - - - -
451C VAL* 1.3 80.2 - - - +
453C GLU* 1.3 57.6 + - - +
454C ILE 3.1 1.1 - - - -
455C SER* 3.0 30.4 + - - -
502C PHE* 4.0 10.5 - - - -
448D GLN 3.0 29.7 + - - +
449D LEU 3.1 14.1 + - - -
450D THR 3.8 0.6 - - - +
451D VAL* 4.0 8.2 - - + +
452D GLN* 2.9 43.2 + - - +
493D TRP* 3.8 15.9 - - + -
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Residues in contact with GLU 453 (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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48C ASN* 2.8 23.0 + - - +
49C ALA* 3.0 23.0 + - - +
50C ASN 3.6 0.3 + - - -
53C ASN* 2.9 43.6 + - + +
419C THR* 4.2 14.4 - - + +
420C GLY* 4.5 7.9 - - - -
423C LEU* 3.8 17.4 - - + +
450C THR 3.1 9.7 + - - +
451C VAL 3.1 0.8 + - - -
452C GLN* 1.3 76.2 - - - +
454C ILE* 1.3 64.0 + - - +
455C SER 3.1 0.2 - - - -
456C THR* 2.7 32.9 + - - -
457C MET* 3.4 16.7 + - - +
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Residues in contact with ILE 454 (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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419C THR* 4.1 13.6 - - + +
447C LEU* 4.1 19.1 - - + -
451C VAL* 3.2 23.1 + - + +
452C GLN 3.1 0.2 - - - -
453C GLU* 1.3 77.2 - - - +
455C SER* 1.3 63.8 + - - +
457C MET* 3.1 13.2 + - + +
458C ILE* 3.1 25.1 + - + +
466C LEU* 4.2 17.9 - - + -
498C LEU* 4.7 3.1 - - + -
499C LEU* 3.5 32.5 - - + -
502C PHE* 4.0 11.7 - - + -
533C ILE* 4.7 2.0 - - + -
535C MET* 3.9 26.2 - - + -
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Residues in contact with SER 455 (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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49C ALA* 4.9 3.7 - - - +
452C GLN 3.0 17.9 + - - -
454C ILE* 1.3 78.3 - - - +
456C THR* 1.3 57.8 + - - +
458C ILE* 3.2 7.0 + - - +
459C ARG* 3.0 27.5 + - - +
502C PHE* 4.0 15.6 - - - -
448D GLN* 4.6 2.4 + - - -
491D GLN* 3.2 20.5 - - - +
493D TRP* 2.8 39.0 + - - -
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Residues in contact with THR 456 (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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46C ALA* 3.5 27.1 - - + +
47C GLY 3.7 15.7 + - - +
48C ASN* 4.1 3.8 - - - +
49C ALA* 3.7 8.0 + - - +
423C LEU* 3.7 23.7 - - + +
427C PHE* 4.7 0.2 - - + -
453C GLU* 2.7 33.6 + - - +
455C SER* 1.3 74.7 + - - +
457C MET* 1.3 65.6 + - - +
459C ARG* 3.3 21.7 - - - +
460C TRP* 3.4 14.8 + - + +
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Residues in contact with MET 457 (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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419C THR* 3.2 43.3 - - + +
422C THR* 4.0 11.0 - - + -
423C LEU* 3.6 30.3 - - + +
426C ALA* 6.1 0.4 - - + -
453C GLU 3.6 12.6 - - - +
454C ILE* 3.1 16.8 + - + +
456C THR* 1.3 79.4 - - - +
458C ILE* 1.3 60.6 + - - +
460C TRP 3.4 0.2 + - - -
461C GLY 3.2 2.6 + - - -
462C LEU* 3.0 41.2 + - + +
464C PRO* 3.8 24.2 - - + -
466C LEU* 4.1 13.9 - - + -
533C ILE* 3.7 16.2 - - + -
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Residues in contact with ILE 458 (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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454C ILE* 3.1 18.1 + - + +
455C SER* 3.2 5.6 + - - +
457C MET* 1.3 77.0 - - - +
459C ARG* 1.3 62.6 + - - +
461C GLY* 3.1 14.5 + - - -
462C LEU 5.4 0.7 - - - -
499C LEU* 3.8 35.7 - - + +
502C PHE* 3.7 30.5 - - + +
503C GLY 4.1 1.1 - - - +
504C ALA* 3.7 25.8 - - + -
505C LYS 5.1 0.7 - - - +
533C ILE* 4.4 10.8 - - + -
491D GLN* 3.4 22.2 - - - +
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Residues in contact with ARG 459 (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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46C ALA 3.8 14.1 + - - -
47C GLY* 2.9 36.8 + - - -
455C SER* 3.0 9.8 + - - +
456C THR* 3.3 19.7 - - - +
458C ILE* 1.3 77.9 - - - +
460C TRP* 1.3 74.5 + - + +
461C GLY 3.8 0.3 + - - -
486D GLN 4.4 6.7 + - - -
489D GLU* 3.2 36.0 + - - +
490D ILE* 3.8 8.1 - - - +
491D GLN* 3.2 39.6 - - - +
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Residues in contact with TRP 460 (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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44C ARG* 3.7 49.1 + - + +
45C TRP 3.3 20.0 - - - -
46C ALA* 2.8 24.2 + - - +
427C PHE* 3.5 34.5 - + + -
430C GLU* 4.5 6.8 - - - +
456C THR* 3.4 11.0 + - + +
458C ILE 3.1 0.8 - - - -
459C ARG* 1.3 104.6 - - + +
461C GLY* 1.3 63.7 + - - +
462C LEU* 3.2 14.2 + - + +
486D GLN* 5.5 8.7 - - - -
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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