Contacts of the strand formed by residues 370 - 375 (chain A) in PDB entry 4GGA
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 VAL 370 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363A TRP* 3.5 8.4 - - - -
364A CYS* 2.9 37.3 + - + +
367A GLN* 3.0 35.3 + - + +
368A SER 3.3 0.6 - - - -
369A ASN* 1.3 83.0 - - + +
371A LEU* 1.3 62.3 + - - +
384A ILE* 3.7 27.8 - - + -
385A TRP 3.3 6.3 - - - +
386A ASN* 5.2 2.5 - - + -
393A LEU* 4.5 10.1 - - + -
407A TRP* 3.8 20.9 - - + -
430A TYR* 4.0 11.7 - - + +
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Residues in contact with LEU 371 (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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325A ALA* 3.9 22.7 - - + -
333A VAL* 4.2 6.3 - - + -
335A VAL* 4.1 19.5 - - + -
351A PHE* 4.9 0.4 - - + -
361A VAL* 4.1 2.7 - - + -
362A ALA 3.6 23.1 - - - +
363A TRP* 3.8 26.5 - - + -
369A ASN 3.8 0.4 + - - -
370A VAL* 1.3 77.4 - - - +
372A ALA* 1.3 64.3 + - - +
373A THR* 3.9 21.1 - - + -
384A ILE* 3.4 2.9 - - - +
385A TRP* 2.8 50.2 + - + -
387A VAL* 3.7 18.2 - - + -
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Residues in contact with ALA 372 (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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361A VAL* 3.5 0.9 + - - -
362A ALA* 2.8 39.3 + - - +
371A LEU* 1.3 75.0 - - - +
373A THR* 1.3 65.7 + - - +
382A ILE* 5.1 0.7 - - + -
383A ARG 3.4 3.8 - - - -
384A ILE* 3.5 23.1 - - + -
405A ILE* 4.2 12.6 - - + +
407A TRP* 3.6 19.9 - - + +
414A LEU* 3.8 11.2 - - + -
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Residues in contact with THR 373 (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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333A VAL* 4.0 16.8 - - + -
354A HIS* 2.8 28.1 + - - -
358A VAL* 3.8 7.4 - - + -
360A ALA 3.1 11.2 - - - +
361A VAL* 4.4 8.5 - - + -
371A LEU* 3.9 19.5 - - + -
372A ALA* 1.3 79.7 - - - +
374A GLY* 1.3 59.9 + - - +
382A ILE* 3.3 4.3 - - - -
383A ARG 2.8 33.8 + - - -
385A TRP* 2.9 26.3 + - - +
405A ILE* 3.6 7.8 - - - +
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Residues in contact with GLY 374 (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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354A HIS* 3.9 4.3 - - - -
357A ALA 3.7 0.3 - - - +
358A VAL* 3.5 20.9 - - - +
359A LYS 3.7 0.2 + - - -
360A ALA* 2.9 30.1 + - - +
373A THR* 1.3 76.6 - - - +
375A GLY* 1.3 61.3 + - - -
381A HIS 3.3 7.6 - - - -
382A ILE* 4.5 0.2 - - - -
402A VAL* 3.7 17.4 - - - +
405A ILE* 4.1 0.7 - - - -
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Residues in contact with GLY 375 (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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354A HIS* 3.6 9.4 + - - -
356A GLY 4.7 0.7 - - - -
357A ALA 3.3 8.5 - - - -
374A GLY* 1.3 73.0 - - - -
376A GLY* 1.3 68.0 + - - +
379A ASP* 3.4 19.3 - - - -
380A ARG 3.7 5.1 + - - -
381A HIS 3.0 12.1 + - - -
402A VAL* 3.0 27.0 + - - +
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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