Contacts of the strand formed by residues 454 - 459 (chain P) in PDB entry 1HI0
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 ASP 454 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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323P THR 5.2 0.2 - - - -
450P SER* 3.3 1.4 - - - -
451P LYS 2.8 38.4 + - - +
453P ASP* 1.3 85.0 + - - +
455P ALA* 1.3 66.2 + - - +
495P ALA 3.2 0.5 - - - +
496P PHE* 3.1 12.3 - - + -
497P LEU* 2.6 42.1 + - + +
665P MN 1.9 39.8 + - - -
666P GTP 6.1 0.7 - - - +
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Residues in contact with ALA 455 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322P ALA* 3.9 1.7 - - - +
323P THR* 3.4 29.8 + - - +
410P TYR* 3.5 27.6 - - + -
449P ILE 3.1 7.0 - - - +
450P SER* 3.2 20.2 - - - -
453P ASP 3.7 2.8 + - - -
454P ASP* 1.3 83.1 + - - +
456P MET* 1.3 73.9 + - - +
457P LEU* 4.8 3.1 - - + -
491P GLU* 5.3 0.2 - - - +
495P ALA 5.1 0.5 - - - +
496P PHE* 3.8 4.0 - - - -
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Residues in contact with MET 456 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314P VAL* 4.7 0.4 - - - -
317P TRP* 3.4 13.1 - - + -
320P CYS* 3.8 15.7 - - - -
321P VAL 3.4 6.3 - - - +
322P ALA* 3.5 28.5 - - + -
448P GLN* 3.2 4.3 - - - -
449P ILE* 2.9 45.9 + - + +
455P ALA* 1.3 78.1 - - - +
457P LEU* 1.3 64.4 + - - +
494P GLY* 4.2 4.0 - - - -
495P ALA 4.0 23.1 - - - +
496P PHE* 3.7 22.4 - - + -
501P LEU* 4.1 17.3 - - + -
514P PHE* 3.8 19.5 - - - -
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Residues in contact with LEU 457 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317P TRP* 3.7 1.8 - - - -
320P CYS* 3.4 3.1 - - - -
321P VAL* 2.7 42.9 + - + +
323P THR* 3.4 31.6 - - + +
410P TYR* 3.5 43.3 - - + +
413P MET* 4.0 13.9 - - + -
414P GLN* 3.9 20.9 - - + +
447P ARG 3.5 2.0 - - - +
448P GLN* 3.6 22.2 - - + -
455P ALA* 4.8 1.3 - - + -
456P MET* 1.3 75.3 - - - +
458P GLY* 1.3 59.7 + - - +
459P TRP* 3.5 17.0 - - + -
471P LEU* 5.5 1.8 - - + -
475P LEU* 6.4 0.4 - - + -
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Residues in contact with GLY 458 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317P TRP* 3.3 24.7 - - - -
319P LEU 3.3 8.3 - - - -
414P GLN* 3.3 10.0 + - - -
446P ILE* 3.5 1.4 - - - -
447P ARG* 2.7 39.1 + - - -
457P LEU* 1.3 74.1 - - - +
459P TRP* 1.3 67.2 + - - -
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Residues in contact with TRP 459 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317P TRP* 3.7 3.3 - - - +
318P SER* 2.7 34.5 + - - -
319P LEU* 3.0 36.2 + - + -
321P VAL* 3.4 28.9 - - + -
414P GLN* 3.5 31.2 - - + -
418P THR* 3.1 28.6 + - + -
445P GLU 3.5 2.9 - - - -
446P ILE* 3.4 21.1 - - + +
457P LEU* 3.5 24.2 - - + -
458P GLY* 1.3 84.3 - - - -
460P THR* 1.3 61.3 + - - +
464P ALA* 3.8 22.7 - - + -
465P LEU* 4.1 8.7 - - + -
468P GLY* 3.6 20.6 - - - -
471P LEU* 4.0 18.4 - - + -
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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