Contacts of the strand formed by residues 417 - 425 (chain A) in PDB entry 1GRB
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 CYS 417 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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402A SER* 3.3 5.5 + - - -
403A PHE* 2.7 75.1 + - + +
405A PRO* 4.0 12.6 - - + -
416A LYS* 1.3 76.0 - - - +
418A VAL* 1.3 61.0 + - - +
419A MET* 3.7 24.2 - - - -
436A GLN 3.2 13.9 - - - +
437A GLY* 4.2 8.5 - - - -
438A LEU 5.6 0.2 - - - -
440A CYS* 4.6 4.7 - - - -
470A SER* 4.8 5.4 - - - -
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Residues in contact with VAL 418 (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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229A MET* 3.9 27.8 - - + -
230A ILE* 4.4 2.9 - - + -
233A ASN* 3.7 44.6 - - + +
401A THR 3.4 5.8 - - - +
402A SER* 3.8 19.7 - - - +
416A LYS* 4.1 6.7 - - + +
417A CYS* 1.3 77.6 - - - +
419A MET* 1.3 61.9 + - - +
435A MET* 2.9 7.5 - - - +
436A GLN* 2.9 43.4 + - + +
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Residues in contact with MET 419 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A MET* 3.8 2.6 - - - +
400A SER* 3.0 6.6 - - - -
401A THR* 2.9 47.6 + - + +
403A PHE* 4.3 1.8 - - + -
417A CYS* 3.7 24.2 - - - -
418A VAL* 1.3 80.1 - - - +
420A LYS* 1.3 62.0 + - - +
433A ILE* 6.4 0.2 - - + -
434A HIS 3.3 6.1 - - - +
435A MET* 3.9 11.9 - - + -
440A CYS* 4.9 0.4 - - - -
443A MET* 4.0 25.8 - - + -
470A SER 3.6 22.4 - - - +
471A SER* 4.8 0.4 - - - -
473A GLU* 3.6 25.6 - - + -
474A LEU* 3.9 31.6 - - + -
477A LEU* 5.0 2.1 - - + +
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Residues in contact with LYS 420 (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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227A ASP* 2.7 41.1 + - - -
228A SER* 4.6 4.6 + - - -
229A MET* 3.3 34.4 - - + +
384A GLU* 3.0 31.6 + - - +
398A THR* 4.4 10.1 - - - +
399A TYR 3.3 7.2 - - - +
400A SER* 4.1 8.7 - - - -
419A MET* 1.3 78.8 - - - +
421A MET* 1.3 64.1 + - - +
422A VAL* 4.0 15.0 - - + -
432A GLY 4.0 0.5 - - - +
433A ILE* 3.5 7.1 - - - +
434A HIS* 2.8 37.1 + - + +
474A LEU* 5.3 1.1 - - - -
477A LEU* 5.3 0.9 - - - -
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Residues in contact with MET 421 (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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397A LYS 3.9 0.3 - - - +
398A THR* 3.1 5.7 - - - -
399A TYR* 2.7 39.4 + - + +
420A LYS* 1.3 73.8 - - - +
422A VAL* 1.3 63.0 + - - +
423A CYS* 3.8 18.6 - - - -
430A VAL* 4.0 23.1 - - + -
432A GLY 3.6 3.4 - - - -
433A ILE* 4.8 3.6 - - + +
457A LYS* 3.2 36.1 - - + -
460A PHE* 3.5 38.6 - - + -
474A LEU* 3.7 21.5 - - + +
477A LEU* 3.8 20.6 - - + +
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Residues in contact with VAL 422 (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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382A LEU 4.1 5.4 - - - +
384A GLU* 4.2 14.8 - - - +
387A ALA* 3.7 30.7 - - + -
396A VAL* 4.2 13.0 - - + -
397A LYS 3.9 2.5 - - - -
398A THR* 4.1 10.1 - - + -
420A LYS* 4.0 11.4 - - + -
421A MET* 1.3 74.6 - - - +
423A CYS* 1.3 60.3 + - - +
430A VAL* 3.8 2.9 - - - -
431A VAL* 2.9 30.9 + - + +
432A GLY 2.8 18.1 + - - +
434A HIS* 4.0 28.9 - - + +
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Residues in contact with CYS 423 (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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396A VAL* 3.5 7.6 - - - +
397A LYS* 2.7 41.9 + - + +
399A TYR* 4.0 17.5 - - - -
421A MET* 3.8 33.9 - - - -
422A VAL* 1.3 73.4 - - - +
424A ALA* 1.3 60.4 + - - +
425A ASN 5.1 0.2 - - - -
428A GLU* 3.8 33.9 - - + -
429A LYS 3.1 8.1 - - - +
430A VAL* 4.4 2.9 - - - -
431A VAL* 4.4 2.5 - - - -
457A LYS* 4.1 5.8 - - - -
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Residues in contact with ALA 424 (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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391A TYR* 3.9 46.0 - - + -
395A ASN 3.4 4.5 - - - +
396A VAL* 5.1 1.1 - - + -
423A CYS* 1.3 75.7 - - - +
425A ASN* 1.3 76.2 + - - +
427A GLU* 4.1 0.2 - - - +
428A GLU 3.3 0.3 + - - -
429A LYS* 2.9 31.1 + - + +
431A VAL* 4.0 13.7 - - + -
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Residues in contact with ASN 425 (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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391A TYR* 4.0 24.8 - - - +
395A ASN* 2.9 44.8 + - - +
397A LYS* 6.0 1.6 - - - +
423A CYS 5.1 0.3 - - - -
424A ALA* 1.3 83.9 - - - +
426A LYS* 1.3 61.1 + - - +
427A GLU* 3.4 23.2 - - + +
428A GLU* 3.1 16.8 + - - +
429A LYS* 5.8 1.8 - - + +
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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