Contacts of the strand formed by residues 452 - 458 (chain G) in PDB entry 6V3O
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 LYS 452 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171G ASP* 3.7 5.1 + - - -
284G ARG* 3.3 46.0 - - - +
285G PHE 2.6 29.4 + - - +
286G SER* 3.2 21.2 + - - +
287G SER* 3.0 23.6 + - - -
445G THR 5.2 0.8 + - - -
446G PHE* 5.6 5.2 - - - +
449G SER* 4.9 3.1 - - - +
450G LEU 5.2 2.4 + - - +
451G VAL* 1.3 79.3 - - - +
453G LEU* 1.3 60.9 + - - +
454G ASP* 4.7 0.2 - - - -
527G ASP 4.0 16.4 - - - +
528G SER 3.6 6.3 - - - +
529G PHE 3.9 20.2 - - - +
530G GLY* 4.0 5.4 - - - +
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Residues in contact with LEU 453 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241G MET* 6.3 0.2 - - + -
287G SER* 3.6 21.1 - - - +
289G MET 3.3 25.4 - - - +
290G GLY 4.1 1.8 - - - -
291G GLY* 3.9 19.3 - - - +
304G THR* 3.7 29.8 - - + -
307G VAL* 4.4 8.5 - - + -
308G CYS* 4.0 16.2 - - - -
451G VAL* 5.5 1.3 - - + +
452G LYS* 1.3 74.0 - - - +
454G ASP* 1.3 61.7 - - - +
455G ILE* 3.8 12.3 + - + -
528G SER 3.1 15.9 + - - +
529G PHE* 3.4 12.7 - - + +
530G GLY 2.7 24.3 + - - -
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Residues in contact with ASP 454 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173G VAL* 4.2 0.5 - - - +
286G SER* 3.7 10.3 - - - -
287G SER 2.9 10.1 + - - +
288G TRP* 3.2 38.2 + - + +
291G GLY* 3.2 24.1 - - - -
292G ASP* 3.8 2.1 + - - -
453G LEU* 1.3 74.1 - - - +
455G ILE* 1.3 60.7 + - - +
456G ARG* 5.4 0.2 - - - +
530G GLY* 4.1 2.4 - - - -
531G PRO* 3.2 22.2 - - + +
533G ILE* 3.9 7.1 - - + +
638G PHE* 3.8 5.2 - - - -
669G ARG* 2.8 42.6 + - - -
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Residues in contact with ILE 455 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291G GLY* 3.8 13.0 - - - +
293G ARG* 4.2 15.9 - - - +
304G THR* 4.2 7.6 - - + -
453G LEU* 3.8 24.9 - - + +
454G ASP* 1.3 80.4 - - - +
456G ARG* 1.3 59.0 + - - +
517G ALA* 5.9 2.9 - - + -
521G LEU* 3.9 24.7 - - + -
529G PHE* 4.1 12.8 - - + -
531G PRO 3.0 10.1 + - - +
532G TYR* 3.7 31.9 - - + -
533G ILE* 2.6 34.8 + - - +
559G LEU* 4.1 14.1 - - + -
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Residues in contact with ARG 456 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288G TRP* 3.5 29.2 - - + -
291G GLY 3.5 5.3 + - - -
292G ASP* 2.8 46.5 + - + +
293G ARG* 3.0 32.8 + - - +
294G ASP* 3.6 8.5 + - + +
454G ASP 4.1 0.6 + - - -
455G ILE* 1.3 80.0 - - - +
457G GLN* 1.3 65.1 + - - +
532G TYR* 5.5 0.2 - - - -
533G ILE* 3.2 33.0 - - + +
535G SER* 3.2 26.4 + - - +
564G LEU* 3.5 17.0 - - - +
566G GLU* 5.2 0.4 + - - -
598G MET* 5.0 0.6 - - - +
759G ARG* 4.3 1.6 - - - +
773G ARG* 3.6 13.1 - - - +
1002G SO4 3.1 37.2 + - - -
1003G SO4 5.5 0.6 + - - -
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Residues in contact with GLN 457 (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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293G ARG* 3.2 39.1 + - + +
294G ASP* 4.4 6.2 - - - +
295G GLY 4.8 1.6 + - - -
455G ILE* 5.8 0.2 - - + -
456G ARG* 1.3 76.1 - - - +
458G GLU* 1.3 81.3 + - - +
461G ARG* 3.5 45.5 + - + +
462G HIS* 3.7 19.9 - - + +
513G ASP* 5.2 3.8 + - - -
514G VAL* 4.2 11.7 - - + +
532G TYR* 3.5 20.6 - - + +
533G ILE 3.1 4.9 + - - +
534G ILE* 3.3 9.2 - - - -
535G SER* 2.8 23.5 + - - -
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Residues in contact with GLU 458 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294G ASP* 3.6 17.1 + - - +
295G GLY* 5.4 2.6 + - - +
457G GLN* 1.3 86.1 + - - +
459G SER* 1.3 67.7 + - - +
460G GLU* 3.3 27.7 + - + +
461G ARG* 3.3 27.2 + - + +
462G HIS* 3.3 14.7 + - - -
535G SER* 3.7 13.7 - - - +
536G MET* 4.5 13.1 - - + +
763G ARG* 4.1 29.5 + - - +
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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