Contacts of the strand formed by residues 486 - 491 (chain A) in PDB entry 5I94
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 GLY 486 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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281A PHE* 4.3 8.6 - - - -
286A CYS* 4.0 10.8 - - - -
481A SER* 3.3 3.6 - - - -
482A GLY 2.9 28.1 + - - +
484A ALA* 3.6 3.2 - - - +
485A GLY* 1.3 80.1 - - - +
487A ILE* 1.3 63.7 + - - +
498A MET* 4.2 8.1 - - - -
499A CYS 3.3 7.4 - - - -
500A TRP* 3.7 7.9 - - - -
510A SER* 5.2 0.3 + - - -
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Residues in contact with ILE 487 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464A MET* 3.9 20.9 - - + -
479A ALA* 4.1 22.9 - - + -
480A LYS 3.4 5.4 - - - +
481A SER* 4.1 11.2 - - - -
486A GLY* 1.3 79.0 - - - +
488A LEU* 1.3 62.6 + - - +
489A LEU* 3.6 3.9 + - + +
498A MET* 3.4 4.9 - - - +
499A CYS* 2.9 41.2 + - + +
510A SER* 4.1 17.7 - - - +
513A GLY* 3.8 11.2 - - - -
514A ILE* 3.8 31.6 - - + +
517A CYS* 4.3 16.4 - - - -
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Residues in contact with LEU 488 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283A LEU* 5.8 2.5 - - + -
286A CYS* 4.3 21.8 - - + +
289A PRO* 4.7 8.5 - - + -
290A LEU* 4.5 23.6 - - + -
426A ALA* 3.5 27.8 - - + +
429A MET* 5.2 1.6 - - + -
430A ALA* 3.6 22.0 - - + +
433A LEU* 5.3 4.0 - - + -
459A MET* 3.8 12.3 - - + +
479A ALA* 3.1 5.1 - - - -
480A LYS* 2.7 40.3 + - + +
486A GLY 4.2 0.4 - - - -
487A ILE* 1.3 69.6 - - - +
489A LEU* 1.3 60.5 + - - +
490A VAL* 5.5 1.1 - - + -
497A MET 3.7 5.8 - - - +
498A MET* 3.8 23.7 - - + -
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Residues in contact with LEU 489 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430A ALA* 3.7 0.3 - - - +
471A PHE* 4.1 4.5 - - + -
475A VAL* 4.8 0.2 - - + -
477A LEU* 3.8 33.0 - - + -
478A PRO 3.8 1.3 - - - +
479A ALA* 3.7 20.9 - - + -
487A ILE* 3.6 8.7 + - + +
488A LEU* 1.3 72.1 - - - +
490A VAL* 1.3 66.5 + - - +
491A VAL* 4.3 7.1 + - + +
496A GLY* 3.5 1.4 - - - -
497A MET* 2.7 75.5 + - + +
499A CYS* 5.4 0.2 - - - -
517A CYS* 4.0 21.5 - - + -
520A LEU* 3.8 21.8 - - + -
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Residues in contact with VAL 490 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430A ALA* 3.4 26.0 - - + +
433A LEU* 4.1 15.5 - - + -
434A ALA* 3.9 25.1 - - + +
456A LEU* 3.8 30.7 - - + -
459A MET* 4.6 7.6 - - + -
477A LEU* 3.8 6.8 - - - +
478A PRO* 3.0 38.1 + - + +
488A LEU* 5.2 1.6 - - + -
489A LEU* 1.3 79.7 - - - +
491A VAL* 1.3 63.4 + - - +
492A PRO* 3.3 8.8 - - + +
495A MET 3.9 2.2 - - - -
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Residues in contact with VAL 491 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434A ALA* 4.1 0.7 - - - +
477A LEU* 4.0 24.5 - - + -
489A LEU* 4.4 9.0 - - + -
490A VAL* 1.3 75.8 - - - +
492A PRO* 1.3 71.0 - - + +
493A ASN 3.4 0.2 + - - -
494A VAL* 2.9 33.1 + - + -
495A MET* 2.7 52.9 + - + +
496A GLY* 6.1 0.2 - - - -
497A MET* 6.0 0.4 - - + -
520A LEU* 4.8 0.7 - - + -
526A PHE* 3.7 33.7 - - + +
542A ARG* 5.5 0.4 - - - +
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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