Contacts of the strand formed by residues 395 - 403 (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 ASN 395 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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391A TYR* 2.6 32.3 + - + +
392A GLY 2.7 4.2 + - - +
394A GLU* 1.3 105.0 + - - +
396A VAL* 1.3 59.9 + - - +
397A LYS* 4.2 0.6 + - - -
423A CYS 3.9 0.2 - - - +
424A ALA* 3.4 5.4 - - - +
425A ASN* 2.9 51.7 + - - +
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Residues in contact with VAL 396 (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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384A GLU* 4.7 4.3 - - + +
387A ALA* 3.4 39.9 - - + +
388A ILE* 3.9 21.5 - - + +
391A TYR* 4.2 7.9 - - + -
392A GLY 4.0 8.7 - - - +
393A ILE 3.5 12.0 + - - +
394A GLU 3.5 1.4 - - - +
395A ASN* 1.3 83.4 - - - +
397A LYS* 1.3 65.8 + - - +
398A THR* 4.2 10.8 - - + -
422A VAL* 4.2 18.8 - - + -
423A CYS 3.5 9.9 - - - +
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Residues in contact with LYS 397 (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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395A ASN 4.2 0.8 + - - -
396A VAL* 1.3 75.7 - - - +
398A THR* 1.3 77.4 + - - +
399A TYR* 3.8 26.3 + - + -
421A MET 3.9 0.2 - - - +
423A CYS* 2.7 42.9 + - + +
425A ASN 6.0 1.3 - - - +
428A GLU* 3.7 25.8 - - + +
478A ARG 5.6 1.4 + - - -
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Residues in contact with THR 398 (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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384A GLU* 3.8 41.2 + - + +
396A VAL* 4.2 8.1 - - + -
397A LYS* 1.3 93.2 - - - +
399A TYR* 1.3 70.4 + - - +
400A SER* 5.6 0.9 - - - -
420A LYS* 4.4 13.3 - - + +
421A MET 3.1 9.6 - - - -
422A VAL* 4.1 17.0 - - + -
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Residues in contact with TYR 399 (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* 3.8 33.0 + - + +
398A THR* 1.3 79.2 - - - +
400A SER* 1.3 64.4 + - - +
420A LYS* 3.3 1.6 - - - +
421A MET* 2.7 34.2 + - + +
423A CYS* 4.0 17.7 - - - -
428A GLU* 2.6 33.3 + - - -
457A LYS* 3.5 38.3 + - + -
477A LEU* 3.8 23.6 - - + +
478A ARG* 3.7 34.8 - - - +
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Residues in contact with SER 400 (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* 4.6 7.7 - - - -
398A THR* 5.6 1.6 - - - -
399A TYR* 1.3 77.4 - - - +
401A THR* 1.3 65.7 + - - +
419A MET 3.0 13.9 - - - -
420A LYS* 4.0 16.8 - - - -
477A LEU* 4.0 9.3 - - - +
478A ARG* 5.1 6.9 + - - +
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Residues in contact with THR 401 (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* 5.1 1.0 - - - +
400A SER* 1.3 77.5 - - - +
402A SER* 1.3 73.7 + - - +
403A PHE* 4.0 25.0 - - + +
417A CYS 4.4 0.2 - - - -
418A VAL* 3.4 4.7 - - - +
419A MET* 2.9 46.1 + - + +
473A GLU* 4.2 15.9 + - + +
477A LEU* 3.8 21.1 - - + -
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Residues in contact with SER 402 (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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401A THR* 1.3 80.6 + - - +
403A PHE* 1.3 63.5 + - - +
416A LYS* 3.2 29.8 + - - +
417A CYS 3.3 6.3 - - - -
418A VAL* 3.8 9.3 - - - +
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Residues in contact with PHE 403 (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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401A THR* 4.0 19.3 - - + +
402A SER* 1.3 79.2 + - - +
404A THR* 1.3 70.3 + - - +
405A PRO* 3.6 8.1 - - + +
416A LYS* 3.6 5.8 - - - +
417A CYS* 2.7 73.2 + - + +
419A MET* 4.3 1.8 - - + -
469A THR 5.7 0.4 - - - -
470A SER* 3.8 26.5 - - - -
473A GLU* 3.3 41.7 - - + -
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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