Contacts of the strand formed by residues 492 - 497 (chain C) in PDB entry 3V81
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 GLU 492 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434C ILE* 3.9 19.0 - - + +
435C VAL 4.6 2.9 - - - +
436C GLY 4.8 2.1 - - - -
437C ALA* 3.4 28.0 + - + +
438C GLU* 4.3 3.3 + - - +
490C GLY* 3.1 10.8 + - - +
491C LEU* 1.3 84.0 - - + +
493C VAL* 1.3 62.8 + - - +
529C GLU* 4.8 11.0 - - + +
530C LYS* 3.3 41.0 + - + +
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Residues in contact with VAL 493 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434C ILE* 3.6 2.3 - - - +
437C ALA* 3.9 3.3 - - - +
438C GLU* 3.3 6.7 - - + +
440C PHE* 3.2 41.5 - - + -
486C LEU* 4.5 4.9 - - + -
489C SER* 3.6 19.5 - - - +
490C GLY 4.4 0.6 + - - +
491C LEU 4.3 0.2 - - - -
492C GLU* 1.3 74.4 - - - +
494C ASN* 1.3 70.9 + - - +
495C ILE* 3.6 29.8 - - + -
528C LYS* 5.2 3.7 - - + +
530C LYS 2.9 11.0 + - - +
531C VAL* 4.3 11.0 - - + -
532C TYR 3.0 23.7 + - - -
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Residues in contact with ASN 494 (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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433C PRO* 3.7 0.7 - - - +
434C ILE* 2.8 56.1 + - - +
437C ALA* 3.4 19.6 + - - +
438C GLU 3.0 9.4 + - - +
439C THR* 3.4 13.6 + - - +
440C PHE 2.9 26.3 + - - -
493C VAL* 1.3 76.9 - - - +
495C ILE* 1.3 61.5 + - - +
496C VAL 4.2 0.2 - - - -
532C TYR* 3.3 14.2 - - + +
289D LEU* 4.0 29.9 - - + +
290D THR* 5.5 0.2 + - - -
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Residues in contact with ILE 495 (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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440C PHE* 3.5 3.4 - - + -
442C VAL* 4.0 31.6 - - + -
482C ILE* 4.3 13.7 - - + +
485C ALA* 4.2 17.0 - - + -
486C LEU* 3.3 39.3 - - + +
493C VAL* 3.6 19.3 - - + -
494C ASN* 1.3 77.9 - - - +
496C VAL* 1.3 63.8 + - - +
531C VAL* 4.4 7.2 - - + -
532C TYR 2.8 10.4 + - - +
533C LEU* 3.3 25.5 - - + +
534C ALA* 2.9 26.2 + - - +
289D LEU* 5.9 0.2 - - - -
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Residues in contact with VAL 496 (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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439C THR* 4.2 10.3 - - + -
440C PHE 2.9 9.4 + - - +
441C TYR* 3.7 38.8 - - + +
442C VAL* 3.0 27.4 + - - +
495C ILE* 1.3 74.8 - - - +
497C THR* 1.3 62.2 + - - +
534C ALA* 3.6 9.4 - - + +
536C VAL* 4.1 35.0 - - + -
545C ASN* 5.5 2.9 - - + +
258D GLN* 4.1 4.7 - - - +
289D LEU* 3.9 27.8 - - + -
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Residues in contact with THR 497 (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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442C VAL* 4.1 19.1 + - - +
478C GLU 5.6 0.2 + - - -
482C ILE* 4.2 14.2 - - + +
496C VAL* 1.3 77.0 - - - +
498C ASN* 1.3 57.7 + - - +
499C SER* 2.8 33.9 + - - +
503C LEU* 4.4 11.0 - - + -
533C LEU* 3.5 25.6 - - + -
534C ALA 2.9 20.9 + - - +
535C TRP* 3.1 27.4 - - + -
536C VAL* 3.2 5.1 + - - +
545C ASN* 4.9 0.7 - - - -
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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