Contacts of the strand formed by residues 446 - 451 (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 ILE 446 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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411P LEU* 3.9 23.3 - - + -
414P GLN* 3.8 28.5 - - + +
415P LEU* 4.3 6.3 - - + -
418P THR* 4.0 4.7 - - - +
419P ALA* 4.6 3.4 - - + -
422P LEU* 4.0 26.5 - - + -
435P PHE* 4.7 2.2 - - + -
439P TYR* 3.1 26.5 - - + +
444P GLU* 3.6 10.4 + - + +
445P GLU* 1.3 79.0 - - + +
447P ARG* 1.3 68.8 + - - +
458P GLY 3.5 2.9 - - - -
459P TRP* 3.4 35.0 - - + +
464P ALA* 3.9 15.5 - - + -
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Residues in contact with ARG 447 (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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300P TYR* 3.2 39.7 + - + +
316P GLU* 4.2 20.6 + - - +
317P TRP* 3.6 26.2 - - + +
414P GLN* 3.4 9.2 + - - -
439P TYR* 3.9 10.3 - - - +
442P GLY* 2.9 31.8 + - - +
443P HIS* 5.1 2.0 - - - +
444P GLU 3.1 15.0 + - - +
445P GLU 4.7 1.1 - - - -
446P ILE* 1.3 83.8 - - - +
448P GLN* 1.3 62.2 + - - +
457P LEU* 3.5 0.3 - - - -
458P GLY 2.7 35.1 + - - +
460P THR* 3.7 21.2 - - + +
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Residues in contact with GLN 448 (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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300P TYR* 4.0 1.7 - - - -
301P THR* 2.7 46.8 - - + +
302P PHE* 4.1 6.5 - - - -
317P TRP* 4.5 2.9 - - - -
407P SER* 2.6 49.1 + - - +
410P TYR* 3.6 13.0 - - - +
439P TYR* 3.4 23.3 + - + +
440P TRP* 4.5 0.2 - - - +
447P ARG* 1.3 79.2 - - - +
449P ILE* 1.3 63.8 + - - +
450P SER* 2.9 26.5 + - - -
456P MET 3.2 7.4 - - - -
457P LEU* 3.6 17.0 - - + -
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Residues in contact with ILE 449 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300P TYR* 3.5 22.0 - - + +
301P THR 3.4 4.9 - - - -
304P HIS* 3.7 11.9 - - + +
310P LYS* 5.3 4.9 - - + +
313P LYS* 3.9 18.8 - - + -
314P VAL* 3.8 22.9 - - + -
317P TRP* 4.0 13.0 - - + -
448P GLN* 1.3 75.2 - - - +
450P SER* 1.3 61.4 + - - +
455P ALA* 3.1 3.3 - - - +
456P MET* 2.9 49.3 + - + +
496P PHE* 3.3 28.9 - - + -
514P PHE* 4.8 3.1 - - + -
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Residues in contact with SER 450 (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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301P THR 2.7 16.9 + - - +
302P PHE* 3.8 22.2 - - - +
304P HIS* 3.3 17.8 + - - -
403P THR* 4.9 1.7 - - - +
407P SER* 4.4 4.9 + - - -
410P TYR* 4.8 2.7 - - - -
448P GLN* 2.9 28.5 + - - +
449P ILE* 1.3 77.5 - - - +
451P LYS* 1.3 65.4 + - - +
452P SER 4.7 4.8 + - - -
454P ASP 3.3 4.9 - - - -
455P ALA* 3.2 21.1 - - - -
496P PHE* 3.6 4.9 - - - -
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Residues in contact with LYS 451 (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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295P TYR* 3.1 29.8 + - + +
302P PHE 5.3 6.7 - - - +
304P HIS* 5.6 0.2 - - + -
399P ASP* 5.1 16.0 + - - -
403P THR* 4.2 8.3 - - - +
450P SER* 1.3 78.5 - - - +
452P SER* 1.3 77.9 + - - +
453P ASP* 4.2 0.7 - - - +
454P ASP* 2.8 23.9 + - + +
497P LEU* 4.1 32.3 - - + -
630P TYR* 3.1 37.9 + - + +
631P LYS 5.3 1.4 + - - -
632P TRP 5.2 5.7 + - - -
633P THR* 6.3 0.4 - - - -
666P GTP 6.2 0.2 - - - +
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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