Contacts of the strand formed by residues 448 - 455 (chain G) in PDB entry 1P8J
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 ARG 448 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245F ASN* 5.2 9.9 - - - +
276F ARG* 3.9 0.9 - - - -
445G ALA* 5.7 1.0 - - - +
446G PRO* 3.6 38.9 + - - +
447G GLN* 1.3 81.2 + - - +
449G LYS* 1.3 60.7 + - - +
478G PRO* 3.2 29.1 + - - +
479G ASN* 3.6 23.8 - - - +
480G HIS 3.9 13.5 - - - +
481G ILE* 3.7 6.1 - - + -
571G TYR* 3.4 5.7 - - - -
572G GLY 2.7 38.7 + - - +
573G THR* 4.2 6.5 - - - -
574G ALA* 4.5 18.9 + - - +
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Residues in contact with LYS 449 (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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269F LEU* 4.3 7.6 + - - +
272F GLU* 2.7 45.0 + - - +
273F ALA* 4.9 1.6 - - - +
276F ARG* 3.7 37.3 - - - +
448G ARG* 1.3 74.3 - - - +
450G CYS* 1.3 61.0 + - - +
451G ILE* 3.9 23.7 + - + +
479G ASN* 3.0 28.6 + - - +
569G VAL* 4.0 17.7 - - + -
570G LEU 3.4 2.9 - - - -
571G TYR* 3.3 34.8 + - + -
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Residues in contact with CYS 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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449G LYS* 1.3 73.0 - - - +
451G ILE* 1.3 62.8 + - - +
452G VAL* 3.9 10.8 + - - +
473G ALA* 3.5 9.6 - - - -
474G CYS* 2.1 58.8 - - + -
479G ASN* 3.8 12.6 - - - +
481G ILE* 4.0 8.2 - - + +
568G LEU 3.6 1.7 - - - +
569G VAL* 3.4 2.9 - - - -
570G LEU* 2.7 49.4 + - + +
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Residues in contact with ILE 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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234F ALA* 3.9 20.0 - - + -
237F ALA* 3.6 33.0 - - + +
238F ARG* 3.6 38.7 + - + +
269F LEU* 4.0 11.4 - - + -
449G LYS* 3.9 32.2 + - + +
450G CYS* 1.3 79.9 - - - +
452G VAL* 1.3 65.8 + - - +
453G GLU 5.0 0.2 - - - +
474G CYS* 4.4 2.6 - - - -
567G THR* 3.8 22.4 - - + -
568G LEU 3.8 2.7 - - - -
569G VAL* 4.5 9.4 - - + +
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Residues in contact with VAL 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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178F GLN* 6.3 0.4 - - - +
450G CYS* 4.3 14.6 - - - +
451G ILE* 1.3 78.0 - - - +
453G GLU* 1.3 66.8 + - - +
454G ILE* 3.4 22.6 + - + -
469G LYS* 5.4 4.7 - - + -
471G VAL* 4.4 23.6 - - + -
567G THR* 3.6 3.3 - - - -
568G LEU* 2.8 65.2 + - + +
570G LEU* 4.7 3.4 - - + -
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Residues in contact with GLU 453 (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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175F VAL* 5.1 4.2 - - - +
178F GLN* 6.1 0.5 - - - +
232F THR* 3.0 29.1 + - - +
234F ALA* 3.5 30.1 - - + +
235F VAL* 3.8 16.0 + - - +
238F ARG* 4.8 13.5 + - - -
451G ILE* 5.2 0.7 - - + -
452G VAL* 1.3 74.9 - - - +
454G ILE* 1.3 63.7 + - - +
455G LEU 3.6 4.0 - - - +
456G VAL* 4.9 19.3 - - + +
469G LYS* 4.7 7.4 + - - -
566G PHE 4.1 4.0 - - - -
567G THR* 4.5 7.4 - - - +
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Residues in contact with ILE 454 (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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452G VAL* 3.5 31.4 - - + +
453G GLU* 1.3 74.6 - - - +
455G LEU* 1.3 60.8 + - - +
456G VAL* 6.0 0.2 - - - -
467G VAL* 3.7 19.4 - - + +
469G LYS* 3.7 45.1 + - + +
471G VAL* 4.4 7.2 - - + -
547G TRP* 5.9 1.8 - - + -
566G PHE* 2.9 60.3 + - + +
568G LEU* 4.0 14.1 - - + -
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Residues in contact with LEU 455 (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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453G GLU* 5.3 2.7 - - - +
454G ILE* 1.3 84.2 + - + +
456G VAL* 1.3 60.3 - - - +
457G GLU 4.0 12.8 - - - +
459G LYS* 4.0 38.8 - - + +
467G VAL* 4.1 17.5 - - + -
563G LEU* 4.0 19.7 - - + +
564G THR 3.8 9.6 - - - +
565G LYS* 3.7 32.5 - - - +
566G PHE* 3.6 22.6 + - + +
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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