Contacts of the strand formed by residues 446 - 451 (chain Q) 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 Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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411Q LEU* 3.9 23.3 - - + -
414Q GLN* 3.8 28.3 - - + +
415Q LEU* 4.3 7.0 - - + -
418Q THR* 4.0 4.9 - - - +
419Q ALA* 4.6 3.4 - - + -
422Q LEU* 4.0 24.9 - - + -
435Q PHE* 4.7 2.0 - - + -
439Q TYR* 3.1 25.7 - - + +
444Q GLU* 3.6 11.4 + - + +
445Q GLU* 1.3 80.0 - - + +
447Q ARG* 1.3 67.5 + - - +
458Q GLY 3.5 2.9 - - - -
459Q TRP* 3.4 34.8 - - + +
464Q ALA* 3.9 14.6 - - + -
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Residues in contact with ARG 447 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300Q TYR* 3.2 40.0 + - + +
316Q GLU* 4.2 21.0 + - - +
317Q TRP* 3.6 26.7 - - + +
414Q GLN* 3.4 9.0 + - - +
439Q TYR* 3.9 10.5 - - - -
442Q GLY* 2.9 32.5 + - - +
443Q HIS* 5.1 1.6 - - - +
444Q GLU 3.1 16.0 + - - +
445Q GLU 4.7 0.9 - - - -
446Q ILE* 1.3 82.4 - - - +
448Q GLN* 1.3 61.8 + - - +
457Q LEU* 3.5 0.3 - - - -
458Q GLY 2.7 35.7 + - - +
460Q THR* 3.7 21.1 - - + +
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Residues in contact with GLN 448 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300Q TYR* 4.0 1.7 - - - -
301Q THR* 2.7 47.2 - - + +
302Q PHE* 4.1 6.9 - - - -
317Q TRP* 4.5 2.5 - - - -
407Q SER* 2.6 49.0 + - - +
410Q TYR* 3.6 13.4 - - - +
439Q TYR* 3.4 21.9 + - + +
440Q TRP* 4.5 0.6 - - - +
447Q ARG* 1.3 78.6 - - - +
449Q ILE* 1.3 64.0 + - - +
450Q SER* 2.9 27.1 + - - -
456Q MET 3.2 7.6 - - - +
457Q LEU* 3.6 17.0 - - + -
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Residues in contact with ILE 449 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300Q TYR* 3.5 22.4 - - + +
301Q THR 3.4 4.7 - - - -
304Q HIS* 3.7 12.1 - - + +
310Q LYS* 5.3 5.4 - - + +
313Q LYS* 3.9 17.7 - - + -
314Q VAL* 3.8 21.8 - - + -
317Q TRP* 4.0 12.3 - - + -
448Q GLN* 1.3 74.8 - - - +
450Q SER* 1.3 61.9 + - - +
455Q ALA* 3.1 3.3 - - - +
456Q MET* 2.9 48.8 + - + +
496Q PHE* 3.3 28.7 - - + -
514Q PHE* 4.8 3.4 - - + -
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Residues in contact with SER 450 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301Q THR 2.7 17.0 + - - +
302Q PHE* 3.8 22.2 - - - +
304Q HIS* 3.3 17.5 + - - -
403Q THR* 4.9 2.1 - - - +
407Q SER* 4.4 4.5 + - - -
410Q TYR* 4.8 2.5 - - - -
448Q GLN* 2.9 27.6 + - - -
449Q ILE* 1.3 77.5 - - - +
451Q LYS* 1.3 66.2 + - - +
452Q SER 4.7 5.4 + - - -
454Q ASP 3.3 5.4 - - - -
455Q ALA* 3.2 20.9 - - - -
496Q PHE* 3.6 4.3 - - - -
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Residues in contact with LYS 451 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295Q TYR* 3.1 30.5 + - + +
302Q PHE 5.3 6.1 - - - +
304Q HIS* 5.6 0.7 - - + -
399Q ASP* 5.1 15.8 + - - -
403Q THR* 4.2 7.9 - - - +
450Q SER* 1.3 78.9 - - - +
452Q SER* 1.3 76.3 + - - +
453Q ASP* 4.2 0.5 - - - +
454Q ASP* 2.8 24.4 + - + +
496Q PHE* 4.9 0.2 - - + -
497Q LEU* 4.1 32.5 - - + -
630Q TYR* 3.1 37.3 + - + +
631Q LYS 5.3 1.2 - - - -
632Q TRP 5.2 6.1 + - - -
633Q THR* 6.3 0.4 - - - -
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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