Contacts of the strand formed by residues 487 - 493 (chain B) in PDB entry 5CHG
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 487 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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382B ASP 4.0 7.9 + - - -
385B GLU* 3.5 26.9 + - - +
386B ARG 4.8 0.8 + - - -
387B MET* 3.6 34.9 - - - +
388B PRO* 4.5 2.6 - - - +
391B GLU* 2.7 43.3 + - - +
395B ILE* 3.8 28.0 - - + -
426B GLY 5.7 3.6 - - - +
427B ASP* 5.7 0.2 - - - -
476B VAL* 3.4 4.2 - - - -
477B CYS* 2.8 41.4 + - - +
478B ARG* 5.8 0.7 - - - -
479B LEU 6.2 0.2 - - - +
485B ARG* 3.5 45.4 - - - +
486B HIS* 1.3 79.2 - - - +
488B ARG* 1.3 66.8 + - - +
489B LEU 3.7 0.2 + - - -
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Residues in contact with ARG 488 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342B TRP* 3.4 52.9 - - + +
383B PHE* 3.5 55.7 + - + +
385B GLU 5.9 0.8 + - - -
426B GLY* 3.5 35.3 + - - +
427B ASP* 3.1 24.1 + - + +
428B VAL* 3.0 25.1 + - - +
474B LEU* 5.2 1.3 - - + -
475B GLY 3.5 7.9 - - - +
476B VAL* 4.5 1.1 - - - +
477B CYS* 5.4 0.3 - - - -
487B ARG* 1.3 75.2 - - - +
489B LEU* 1.3 59.7 + - - +
603B DGT 4.9 4.8 + - - -
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Residues in contact with LEU 489 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395B ILE* 3.8 23.3 - - + -
399B VAL* 4.2 2.2 - - + -
428B VAL* 3.5 23.6 - - + +
430B VAL* 4.0 13.5 - - + -
451B LEU* 5.4 0.2 - - + -
456B PHE* 4.0 17.9 - - + -
457B LEU* 3.9 23.3 - - + -
473B TYR* 3.8 4.2 - - + +
474B LEU* 3.5 2.9 - - - +
475B GLY 2.8 40.3 + - - +
476B VAL 5.0 0.2 - - - +
477B CYS* 4.4 11.7 - - + -
487B ARG 4.5 0.4 - - - +
488B ARG* 1.3 76.4 - - - +
490B ASP* 1.3 66.1 + - - +
491B ILE* 3.7 28.5 - - + -
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Residues in contact with ASP 490 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427B ASP* 3.4 11.3 + - - +
428B VAL 2.8 11.9 + - - +
429B ASP* 2.7 30.7 - - + +
430B VAL* 2.7 32.5 + - - +
472B LYS* 4.2 18.5 + - - -
473B TYR 3.5 3.4 - - - +
474B LEU* 3.0 36.5 - - - +
489B LEU* 1.3 72.0 - - - +
491B ILE* 1.3 60.6 + - - +
492B ILE* 4.3 11.4 - - + -
603B DGT 4.5 3.5 + - - +
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Residues in contact with ILE 491 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399B VAL* 3.9 22.4 - - + -
430B VAL* 3.3 8.5 - - + +
432B ILE* 3.8 26.5 - - + -
444B PHE* 4.0 17.2 - - + -
447B LEU* 5.2 3.8 - - + -
448B LEU* 4.6 5.8 - - + -
451B LEU* 4.3 13.9 - - + -
471B GLN 3.8 0.3 - - - +
472B LYS* 3.3 4.3 - - - +
473B TYR* 2.7 57.5 + - + +
489B LEU* 3.7 31.6 - - + -
490B ASP* 1.3 79.0 - - - +
492B ILE* 1.3 66.8 + - - +
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Residues in contact with ILE 492 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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429B ASP* 5.1 3.1 - - + +
430B VAL 2.8 22.2 + - - +
431B ALA* 3.3 5.3 - - + +
432B ILE* 2.6 34.5 + - - +
470B GLN* 4.0 8.3 - - + +
471B GLN 3.3 9.6 - - - +
472B LYS* 3.9 23.8 - - + -
490B ASP* 4.3 9.2 - - + +
491B ILE* 1.3 86.1 - - - +
493B VAL* 1.3 59.2 + - - +
494B VAL* 3.6 24.4 + - + +
506B PHE* 3.7 50.5 - - + -
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Residues in contact with VAL 493 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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432B ILE* 3.2 30.3 - - + +
440B HIS* 3.5 40.2 - - + +
443B ILE* 4.6 6.7 - - + -
444B PHE* 3.4 35.4 - - + -
469B GLN 3.7 3.3 - - - +
470B GLN* 3.3 6.6 - - - +
471B GLN* 2.8 47.0 + - + +
492B ILE* 1.3 75.5 - - - +
494B VAL* 1.3 61.5 + - - +
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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