Contacts of the strand formed by residues 465 - 470 (chain D) 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 TYR 465 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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377D PHE* 3.8 20.0 - + - -
437D ARG* 3.9 24.2 - - + -
438D VAL 2.9 18.9 + - - +
439D ILE* 4.0 15.3 - - + -
440D LEU* 2.8 32.6 + - - +
463D LYS 4.2 3.6 - - - -
464D PRO* 1.3 74.2 - - - +
466D LEU* 1.3 61.0 + - - +
467D PHE* 3.7 17.2 - + + -
527D PHE* 2.7 54.0 + + - -
528D ASN 3.4 8.3 + - - -
529D ASP 3.3 14.9 + - - -
530D ASN* 3.5 10.7 + - + -
532D LYS 6.1 0.2 - - - -
534D ARG* 3.2 29.2 + - - -
536D ILE* 4.5 2.7 - - + -
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Residues in contact with LEU 466 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419D THR* 6.3 0.2 - - + -
422D THR* 4.1 8.1 - - + -
440D LEU* 4.0 26.9 - - + -
442D ILE* 5.7 0.7 - - + -
454D ILE* 4.2 27.6 - - + -
457D MET* 4.1 7.0 - - + -
464D PRO* 3.9 28.0 - - + +
465D TYR* 1.3 72.8 - - - +
467D PHE* 1.3 61.9 + - - +
468D VAL* 4.5 3.4 - - + -
499D LEU* 4.8 2.9 - - + -
533D ILE* 4.3 20.2 - - + -
534D ARG 2.8 19.8 + - - +
535D MET* 3.3 27.8 - - + +
536D ILE* 2.8 26.6 + - - +
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Residues in contact with PHE 467 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377D PHE* 4.2 16.4 - + - -
439D ILE* 4.0 12.8 - - + -
440D LEU* 2.8 22.2 + - - +
441D PHE* 3.5 37.4 - + + -
442D ILE* 3.0 28.4 + - - +
465D TYR* 3.8 26.0 - - + -
466D LEU* 1.3 71.2 - - - +
468D VAL* 1.3 60.4 + - - +
469D LEU* 4.0 1.0 + - - -
518D TRP* 4.0 19.3 - + - -
521D LEU* 5.5 0.2 - - + -
522D THR* 4.6 9.4 - - + -
527D PHE* 4.1 14.4 - + - -
536D ILE* 3.4 42.8 - - + +
538D VAL* 4.1 10.5 - - + -
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Residues in contact with VAL 468 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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442D ILE* 3.4 16.2 - - + +
443D GLY 4.7 0.4 - - - -
444D ASP* 4.3 10.5 - - - -
447D LEU* 4.1 27.8 - - + -
466D LEU* 4.1 4.7 - - + +
467D PHE* 1.3 74.3 - - - +
469D LEU* 1.3 64.7 + - - +
470D ASN 3.3 3.7 + - - +
495D HIS* 4.1 26.5 - - + +
535D MET* 4.1 33.2 - - + -
536D ILE 2.9 12.0 + - - +
537D GLU* 3.6 6.8 - - + +
538D VAL 2.8 28.2 + - - -
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Residues in contact with LEU 469 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367D GLN* 4.1 1.1 - - - +
370D MET* 4.1 5.8 - - + -
371D TRP* 3.8 21.1 - - + -
390D THR* 3.9 14.4 - - - +
391D SER* 3.3 26.5 - - - +
441D PHE* 4.0 20.0 - - + -
442D ILE 2.9 17.0 + - - +
443D GLY* 4.0 4.7 - - - -
444D ASP* 3.1 23.7 + - - +
467D PHE 4.8 1.1 - - - +
468D VAL* 1.3 70.7 - - - +
470D ASN* 1.3 60.6 + - - +
471D ASN* 3.3 11.2 + - - +
538D VAL* 3.7 30.5 - - + -
540D LEU* 4.0 22.4 - - + -
1564D TPP 4.9 5.2 - - - +
1565D MG 4.1 0.3 - - - -
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Residues in contact with ASN 470 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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444D ASP* 3.6 10.6 - - - +
468D VAL 3.3 1.8 + - - +
469D LEU* 1.3 69.7 - - - +
471D ASN* 1.3 58.4 + - - +
472D ASP* 3.2 19.4 + - - +
493D TRP 5.4 2.4 + - - -
495D HIS* 4.0 13.4 + - + -
537D GLU* 2.7 35.5 + - + +
538D VAL 2.8 15.0 + - - +
539D MET* 3.7 25.0 - - - +
540D LEU* 3.0 26.2 + - - +
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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