Contacts of the strand formed by residues 452 - 459 (chain D) in PDB entry 1HVU
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 LEU 452 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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446D ALA* 3.1 4.6 - - - +
447D ASN* 2.9 26.6 + - + +
450D THR* 4.3 14.4 - - - +
451D LYS* 1.3 78.6 - - - +
453D GLY* 1.3 58.9 + - - +
469D LEU 3.2 15.5 - - - +
470D THR* 4.7 2.9 - - - -
471D ASN 4.2 1.3 - - - +
472D THR 5.0 1.1 - - - +
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Residues in contact with GLY 453 (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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445D ALA 2.9 17.0 - - - -
446D ALA* 3.7 4.2 - - - +
452D LEU* 1.3 76.3 - - - +
454D LYS* 1.3 55.9 + - - +
468D PRO* 3.9 0.9 - - - +
469D LEU* 2.5 49.8 + - - +
472D THR* 5.8 1.8 - - - -
477D THR* 5.5 1.1 - - - -
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Residues in contact with LYS 454 (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 GLY* 3.2 2.3 - - - -
445D ALA 3.0 28.0 + - - +
453D GLY* 1.3 75.0 - - - +
455D ALA* 1.3 63.4 + - - +
466D VAL* 5.8 3.4 - - + -
467D VAL 2.9 17.9 - - - +
468D PRO* 4.9 1.6 - - + -
469D LEU* 5.0 1.3 - - - -
477D THR* 3.7 3.3 - - - -
551D LEU 5.1 2.0 - - - +
552D VAL* 3.9 31.3 + - - +
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Residues in contact with ALA 455 (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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443D ASP 3.8 7.0 - - - -
444D GLY* 4.4 0.7 - - - -
454D LYS* 1.3 78.1 - - - +
456D GLY* 1.3 57.0 + - - +
466D VAL* 3.4 1.6 - - - -
467D VAL* 2.7 41.3 + - + +
469D LEU* 5.8 3.4 - - + -
477D THR* 4.1 7.0 - - - +
480D GLN* 3.9 15.0 - - + -
481D ALA* 3.9 29.2 - - + +
552D VAL* 5.1 0.9 - - - -
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Residues in contact with GLY 456 (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 VAL* 3.8 2.1 - - - +
443D ASP 3.2 27.7 + - - +
455D ALA* 1.3 75.4 - - - +
457D TYR* 1.3 65.9 + - - +
465D LYS* 3.4 15.5 - - - -
466D VAL* 3.7 5.8 - - - -
481D ALA* 3.9 9.1 - - - +
484D LEU* 5.7 6.7 - - - -
548D VAL* 5.3 2.9 - - - -
551D LEU* 6.4 2.0 - - - -
552D VAL* 5.2 3.2 - - - +
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Residues in contact with TYR 457 (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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440D PHE* 4.9 2.2 - - + -
441D TYR 2.9 23.1 - - - +
442D VAL* 4.2 4.5 - - + -
456D GLY* 1.3 75.2 - - - +
458D VAL* 1.3 67.3 + - - +
464D GLN* 3.4 14.1 - - - +
465D LYS* 2.9 24.5 + - + +
481D ALA 5.7 0.4 - - - +
484D LEU* 6.2 0.9 - - + -
485D ALA* 4.9 15.3 - - + +
548D VAL* 4.5 8.3 - - - +
551D LEU* 5.8 4.5 - - - +
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Residues in contact with VAL 458 (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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440D PHE* 3.8 4.0 - - - +
441D TYR* 3.2 33.0 + - + +
457D TYR* 1.3 78.8 - - - +
459D THR* 1.3 64.2 + - - +
463D ARG 3.6 10.8 - - - -
464D GLN* 4.4 4.9 - - + +
544D GLY* 4.8 10.3 - - - +
547D GLN* 5.1 6.7 - - + -
548D VAL* 4.9 9.6 - - + +
286E THR* 5.8 4.9 - - - -
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Residues in contact with THR 459 (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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438D GLU* 5.1 9.4 - - - -
439D THR 3.3 15.0 - - - -
440D PHE* 4.9 2.5 - - - -
441D TYR* 4.9 0.7 - - - +
458D VAL* 1.3 77.9 - - - +
460D ASN* 1.3 67.5 + - - +
461D LYS* 3.1 11.5 + - - -
462D GLY* 3.9 10.0 + - - -
463D ARG* 3.3 25.1 + - - -
286E THR* 4.0 15.2 - - - +
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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