Contacts of the strand formed by residues 396 - 404 (chain A) in PDB entry 4GFG
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 396 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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389A TYR* 3.4 40.4 - - + -
390A TYR 3.9 8.1 - - - +
391A GLN* 3.4 25.6 - - + +
392A MET 4.3 0.2 - - - +
394A LYS 5.7 0.2 - - - +
395A VAL* 1.3 80.1 - - - +
397A LYS* 1.3 63.3 + - - +
398A THR* 4.2 1.4 + - - -
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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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389A TYR* 3.3 1.9 - - - -
390A TYR* 2.8 39.0 + - + +
392A MET* 3.4 42.5 - - + +
395A VAL* 4.0 2.4 + - + -
396A VAL* 1.3 76.9 - - - +
398A THR* 1.3 73.8 + - - +
399A VAL* 3.7 5.1 - - + +
436A ILE* 4.0 21.5 - - + -
449A GLU* 4.1 24.0 + - - -
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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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387A LYS* 3.2 37.7 - - + +
388A GLY 3.5 8.5 - - - +
389A TYR* 4.2 14.7 - - + -
396A VAL 4.2 1.5 + - - -
397A LYS* 1.3 85.3 - - - +
399A VAL* 1.3 67.3 + - - +
449A GLU* 4.4 0.2 - - - -
450A MET* 3.9 20.7 + - + +
452A GLU* 3.7 15.5 + - - +
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Residues in contact with VAL 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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370A LEU* 4.1 8.3 - - + -
387A LYS* 3.7 0.2 - - - -
388A GLY 2.9 49.0 + - - +
389A TYR* 3.8 4.0 - - - +
390A TYR* 4.2 10.1 - - + -
397A LYS* 3.7 15.3 - - + +
398A THR* 1.3 82.8 - - - +
400A ALA* 1.3 61.0 + - - +
401A VAL* 3.9 12.3 - - + -
436A ILE* 4.1 13.0 - - + -
447A VAL* 3.7 27.1 - - + -
448A MET 3.2 13.9 - - - +
449A GLU* 4.9 0.2 - - - -
450A MET* 3.5 15.4 - - - +
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Residues in contact with ALA 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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385A VAL* 4.5 7.0 - - + -
386A LYS 3.7 6.7 - - - +
399A VAL* 1.3 74.3 - - - +
401A VAL* 1.3 62.9 + - - +
446A LEU 3.7 1.4 - - - +
447A VAL* 3.7 0.5 - - - -
448A MET* 2.8 37.0 + - + +
450A MET* 4.0 15.5 - - + +
701A 0XF 3.4 44.6 - - + +
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Residues in contact with VAL 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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370A LEU* 4.4 2.0 - - + -
372A LEU* 4.2 20.9 - - + -
384A THR 3.5 0.7 - - - +
385A VAL* 3.5 7.5 - - - +
386A LYS* 3.1 34.5 + - + +
388A GLY 5.2 1.3 - - - +
399A VAL* 3.9 22.0 - - + +
400A ALA* 1.3 79.2 - - - +
402A LYS* 1.3 64.8 + - - +
403A ILE* 3.6 16.5 + - + +
445A MET* 3.6 36.1 - - + -
446A LEU 3.3 6.3 - - - +
447A VAL* 4.0 16.4 - - + -
448A MET* 5.0 0.2 - - - -
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Residues in contact with LYS 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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382A PHE* 3.6 41.3 - - + -
384A THR 3.5 2.5 - - - -
385A VAL* 4.4 8.1 - - + -
400A ALA 4.2 0.6 + - - -
401A VAL* 1.3 71.2 - - - +
403A ILE* 1.3 59.7 + - - +
404A LEU* 5.6 1.1 - - + -
417A LEU* 4.8 10.0 - - + +
420A GLU* 3.5 29.5 + - - +
444A TRP 3.5 1.6 - - - +
445A MET* 3.1 8.7 - - - -
446A LEU* 2.8 52.5 + - + +
448A MET* 4.4 15.6 - - + +
512A ASP* 3.1 32.2 + - - +
514A GLY* 5.4 1.6 - - - +
701A 0XF 4.3 13.7 + - - -
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Residues in contact with ILE 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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372A LEU* 4.0 17.5 - - + -
382A PHE* 4.5 0.9 - - - -
383A GLY* 3.0 5.4 - - - -
384A THR* 2.9 40.4 + - - +
386A LYS* 3.8 42.2 - - + -
401A VAL* 3.9 17.7 - - + +
402A LYS* 1.3 77.5 - - - +
404A LEU* 1.3 67.5 + - - +
443A SER* 3.8 20.4 - - - +
444A TRP 3.7 3.8 - - - +
445A MET* 4.1 10.3 - - + -
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Residues in contact with LEU 404 (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 PHE* 3.4 26.9 - - + +
383A GLY* 4.1 0.4 - - - -
402A LYS 5.5 0.4 - - - +
403A ILE* 1.3 82.0 - - - +
405A LYS* 1.3 64.1 + - - +
406A ASN* 2.9 9.5 + - - +
407A GLU* 3.9 17.5 - - - +
413A LEU* 4.0 30.1 - - + +
414A LYS* 4.2 3.8 - - - -
417A LEU* 3.8 30.1 - - + -
443A SER* 3.7 14.5 + - - -
444A TRP* 3.2 42.4 + - + +
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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