Contacts of the strand formed by residues 419 - 425 (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 GLN 419 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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418G GLY* 1.3 73.6 - - - -
420G LYS* 1.3 60.4 + - - +
450G LEU 4.1 0.2 - - - +
451G TYR* 3.6 0.3 - - - -
452G ASN* 2.9 44.5 + - + +
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Residues in contact with LYS 420 (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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416G GLY 4.7 5.3 + - - -
418G GLY 3.6 5.9 + - - +
419G GLN* 1.3 76.9 - - - +
421G GLN* 1.3 61.4 + - - +
422G ILE* 4.4 2.5 - - + -
438G TYR* 3.6 42.1 + - + +
449G ILE* 4.2 13.0 - - + -
450G LEU 3.0 11.2 - - - +
451G TYR* 4.0 14.6 - - + -
511G LEU* 2.2 50.4 + - + +
512G PHE* 4.1 16.2 - - - +
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Residues in contact with GLN 421 (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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420G LYS* 1.3 73.2 - - - +
422G ILE* 1.3 88.7 + - - +
423G TRP* 3.1 58.3 - - + +
432G PRO* 4.4 11.0 - - - +
438G TYR* 2.6 19.8 + - - -
449G ILE* 3.3 2.4 - - - -
450G LEU* 2.6 46.5 + - + +
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Residues in contact with ILE 422 (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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420G LYS* 4.4 7.6 - - + -
421G GLN* 1.3 94.7 + - - +
423G TRP* 1.3 74.2 + - - +
432G PRO* 3.8 0.2 - - - +
433G VAL* 3.3 31.7 + - + +
438G TYR* 3.4 55.9 + - + +
441G PHE* 4.4 14.1 - - + -
447G TYR* 3.9 17.0 - - + -
448G ILE 3.5 5.4 - - - +
449G ILE* 3.8 29.8 - - + -
512G PHE* 4.4 3.1 - - + -
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Residues in contact with TRP 423 (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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421G GLN* 3.1 62.4 - - + +
422G ILE* 1.3 73.4 - - - +
424G ARG* 1.3 62.6 + - - +
430G LYS* 3.3 55.1 - - + +
431G VAL 3.9 4.7 - - - -
432G PRO* 3.6 18.1 - - + +
433G VAL* 4.0 1.6 - - - -
447G TYR* 3.2 29.3 - - - +
448G ILE* 2.7 36.2 + - + +
450G LEU* 3.5 26.9 - - + -
486G LEU* 3.8 22.4 - - + -
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Residues in contact with ARG 424 (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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423G TRP* 1.3 80.5 - - - +
425G ILE* 1.3 72.9 + - - +
426G GLU* 2.3 64.3 + - - +
431G VAL* 3.1 15.6 + - - +
433G VAL* 3.4 20.3 - - + +
442G TYR* 3.5 14.8 - - - -
445G ASP* 3.0 27.3 + - + +
446G SER 3.6 7.0 - - - +
447G TYR* 3.5 30.4 + - + +
524G THR* 2.9 29.0 + - - +
530G GLN* 2.8 30.3 + - - +
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Residues in contact with ILE 425 (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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349A LEU* 6.0 0.2 - - + -
424G ARG* 1.3 72.4 - - - +
426G GLU* 1.3 66.4 + - - +
427G GLY 5.1 5.2 - - - +
428G SER* 6.0 0.2 - - - -
429G ASN 3.6 9.4 - - - +
430G LYS* 4.2 5.8 - - + +
445G ASP* 4.8 1.4 - - - +
446G SER* 3.1 21.2 + - - +
447G TYR 4.3 1.1 - - - -
448G ILE* 3.4 42.2 - - + +
475G GLU* 3.9 25.5 - - + +
478G ALA* 3.7 24.9 - - + -
479G SER* 3.6 26.9 - - - -
482G LEU* 3.6 20.0 - - + -
524G THR* 4.9 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