Contacts of the strand formed by residues 452 - 458 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284C ARG* 4.0 35.3 - - - +
285C PHE 3.4 8.6 + - - +
286C SER* 3.2 11.9 - - - +
287C SER* 2.9 25.5 + - - -
409C ILE* 5.6 4.4 - - - +
449C SER* 5.0 1.8 - - - +
451C VAL* 1.3 78.1 - - - +
453C LEU* 1.3 60.5 + - - +
454C ASP* 4.7 0.2 - - - -
527C ASP* 3.2 43.9 + - - +
528C SER 3.7 3.4 - - - -
529C PHE 3.7 15.5 + - - +
530C GLY* 4.1 13.5 - - - +
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Residues in contact with LEU 453 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241C MET* 6.1 0.7 - - + -
287C SER* 3.5 22.9 - - - +
289C MET 3.3 24.9 - - - +
290C GLY 4.0 3.8 - - - +
291C GLY* 3.9 17.0 - - - +
304C THR* 3.7 29.6 - - + -
307C VAL* 4.3 7.9 - - + -
308C CYS* 3.8 19.1 - - - -
451C VAL* 5.6 1.6 - - + +
452C LYS* 1.3 72.6 - - - +
454C ASP* 1.3 70.7 + - - +
455C ILE* 3.7 7.1 + - + +
528C SER 3.1 17.0 + - - +
529C PHE* 3.5 13.3 - - + +
530C GLY 3.0 18.0 + - - +
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Residues in contact with ASP 454 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173C VAL* 4.0 1.7 - - - +
286C SER* 3.8 8.6 - - - -
287C SER 2.9 9.8 + - - +
288C TRP* 3.2 37.9 + - + +
291C GLY* 3.2 24.9 - - - -
292C ASP 3.8 1.4 + - - -
452C LYS 4.4 0.3 - - - +
453C LEU* 1.3 73.9 - - - +
455C ILE* 1.3 61.5 + - - +
456C ARG* 4.1 0.4 + - + -
530C GLY* 4.2 2.3 - - - -
531C PRO* 3.3 21.7 - - - +
533C ILE* 4.0 9.0 - - + +
638C PHE* 3.9 3.6 - - - -
669C ARG* 2.9 42.4 + - - -
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Residues in contact with ILE 455 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291C GLY* 3.7 13.0 - - - +
293C ARG* 4.2 15.5 - - - +
304C THR* 4.2 7.4 - - + -
453C LEU* 4.1 23.8 - - + +
454C ASP* 1.3 80.2 - - - +
456C ARG* 1.3 59.0 + - - +
517C ALA* 5.9 2.5 - - + -
521C LEU* 4.2 18.6 - - + -
529C PHE* 4.1 13.2 - - + -
531C PRO 3.0 7.9 + - - +
532C TYR* 3.4 33.9 - - + -
533C ILE* 2.6 36.9 + - - +
559C LEU* 3.9 22.4 - - + -
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Residues in contact with ARG 456 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288C TRP* 3.6 29.9 - - + -
291C GLY 3.4 7.9 + - - -
292C ASP* 2.9 46.0 + - + +
293C ARG* 3.0 33.1 + - - +
294C ASP* 3.6 16.4 + - + +
455C ILE* 1.3 78.8 - - - +
457C GLN* 1.3 64.7 + - - +
532C TYR* 5.4 0.2 - - - -
533C ILE* 3.3 31.6 - - + +
535C SER* 3.3 27.6 + - - +
564C LEU* 3.6 15.5 - - - +
566C GLU* 5.0 1.0 + - - -
598C MET* 5.0 0.8 - - - +
759C ARG* 4.6 2.0 - - - +
773C ARG* 3.8 4.4 - - - +
1001C SO4 3.2 36.6 + - - -
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Residues in contact with GLN 457 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293C ARG* 3.3 39.6 + - + +
294C ASP* 4.1 6.7 - - - +
295C GLY 4.6 0.9 + - - -
456C ARG* 1.3 76.7 - - - +
458C GLU* 1.3 86.4 + - - +
461C ARG* 3.7 45.4 + - + +
462C HIS* 3.9 12.3 - - + +
513C ASP* 5.2 3.4 + - - -
514C VAL* 4.3 11.5 - - + +
532C TYR* 3.4 25.3 - - + +
533C ILE 3.1 9.5 + - - +
534C ILE* 3.4 4.0 - - - -
535C SER* 2.9 21.6 + - - -
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Residues in contact with GLU 458 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294C ASP* 3.6 22.8 + - - +
295C GLY* 4.6 9.4 + - - -
457C GLN* 1.3 84.1 + - - +
459C SER* 1.3 66.9 + - - +
460C GLU* 4.3 7.5 + - - +
461C ARG* 3.2 46.0 + - + +
462C HIS* 3.5 8.2 + - - -
535C SER* 3.6 15.2 - - - +
536C MET* 5.1 10.2 - - + +
763C ARG* 4.6 16.9 + - - +
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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