Contacts of the strand formed by residues 446 - 452 (chain G) in PDB entry 1H1V
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 SER 446 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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424G ARG* 3.6 3.8 - - - +
425G ILE* 3.1 31.3 + - - +
445G ASP* 1.3 74.5 + - - +
447G TYR* 1.3 65.2 + - - +
466G TRP 3.5 9.9 - - - -
467G GLN* 4.0 8.4 - - - +
468G GLY 4.4 0.2 - - - +
471G SER* 2.7 27.7 + - - -
475G GLU* 4.4 7.7 + - - +
476G VAL* 3.8 11.3 + - - -
479G SER* 3.6 27.4 - - - -
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Residues in contact with TYR 447 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422G ILE* 3.9 7.9 - - + -
423G TRP 3.2 19.1 - - - +
424G ARG* 3.5 27.5 + - + +
425G ILE* 4.3 0.2 - - - -
433G VAL* 3.9 13.2 - - + +
440G GLN 4.6 4.6 + - - -
441G PHE* 3.4 44.7 - + + -
442G TYR* 2.9 55.4 + - - +
445G ASP* 4.1 6.1 - - + -
446G SER* 1.3 80.2 - - - +
448G ILE* 1.3 68.7 + - - +
449G ILE* 5.4 1.1 - - + -
464G TYR 4.5 0.2 - - - -
465G ASN* 3.0 24.1 + - - -
466G TRP* 2.8 31.4 + + + +
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Residues in contact with ILE 448 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422G ILE* 3.5 0.5 - - - +
423G TRP* 2.7 57.0 + - + +
425G ILE* 3.4 26.9 - - + -
430G LYS* 4.6 9.0 - - + +
447G TYR* 1.3 80.7 - - - +
449G ILE* 1.3 65.1 + - - +
463G ILE* 3.7 22.4 - - + -
464G TYR 3.5 3.8 - - - -
479G SER 3.7 9.4 - - - +
482G LEU* 3.6 28.0 - - + +
483G THR* 3.7 17.5 - - - +
486G LEU* 4.3 9.6 - - + -
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Residues in contact with ILE 449 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420G LYS* 4.2 9.9 - - + -
421G GLN 3.3 4.3 - - - +
422G ILE* 3.8 32.5 - - + -
441G PHE* 5.6 5.4 - - + -
447G TYR* 5.2 3.6 - - + -
448G ILE* 1.3 80.1 - - - +
450G LEU* 1.3 68.2 - - - +
451G TYR 4.6 1.1 - - - +
462G ILE 3.6 1.7 - - - +
463G ILE* 3.2 8.5 - - - -
464G TYR* 3.0 59.1 + - + +
466G TRP* 5.2 7.4 - - + -
508G LEU* 4.2 10.3 - - + -
511G LEU* 3.4 34.8 - - + -
512G PHE* 5.4 2.0 - - + -
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Residues in contact with LEU 450 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419G GLN 4.1 0.2 - - - +
420G LYS* 3.0 4.0 - - - +
421G GLN* 2.6 43.4 + - + +
423G TRP* 3.5 26.4 - - + -
449G ILE* 1.3 72.1 - - - +
451G TYR* 1.3 68.7 + - - +
452G ASN* 3.8 11.8 - - - +
461G GLN* 3.6 28.0 - - + +
462G ILE 3.8 4.9 - - - +
463G ILE* 4.5 6.7 - - + -
486G LEU* 3.8 20.2 - - + -
490G LEU* 3.4 28.7 - - + -
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Residues in contact with TYR 451 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414G ASP* 2.6 40.1 + - - -
416G GLY* 3.1 35.1 + - - -
418G GLY* 3.3 20.5 + - - -
419G GLN 3.6 2.5 - - - -
420G LYS* 4.0 14.6 - - + -
449G ILE* 3.9 3.8 + - + -
450G LEU* 1.3 76.7 - - - +
452G ASN* 1.3 69.9 + - - +
453G TYR* 3.4 13.5 - + - -
454G ARG* 5.0 0.2 - - - +
461G GLN* 3.4 4.5 - - - +
462G ILE* 3.1 47.4 + - + +
464G TYR* 5.3 2.2 - - + -
507G HIS* 3.6 20.6 - + - -
511G LEU* 3.8 30.1 - - + -
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Residues in contact with ASN 452 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418G GLY* 3.9 10.9 - - - -
419G GLN* 2.9 26.9 + - + +
420G LYS* 5.7 0.2 - - - -
450G LEU* 3.8 11.3 - - - +
451G TYR* 1.3 81.3 - - - +
453G TYR* 1.3 73.1 + - - +
460G GLY 4.1 4.9 + - - +
461G GLN* 3.1 36.2 + - - +
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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