Contacts of the strand formed by residues 392 - 397 (chain A) in PDB entry 3F6K
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 ILE 392 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361A LEU* 3.8 19.3 - - + -
370A ASP* 5.1 0.2 - - - +
384A SER* 3.5 30.3 - - - -
385A VAL 3.4 8.1 - - - +
386A LEU* 4.8 6.1 - - + -
390A ASN 4.5 6.3 - - - +
391A SER* 1.3 77.3 - - - +
393A GLN* 1.3 63.8 + - - +
433A TYR* 3.7 32.8 - - + +
464A ALA* 3.3 4.5 - - - +
465A ILE* 2.8 56.5 + - + +
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Residues in contact with GLN 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A SER* 3.2 4.2 - - - -
385A VAL* 2.8 47.5 + - + +
387A SER* 3.0 30.1 + - - -
391A SER* 3.0 27.7 + - - -
392A ILE* 1.3 75.5 - - - +
394A THR* 1.3 66.0 + - - +
406A HIS* 4.3 18.6 - - + -
428A HIS* 3.5 13.2 - - + -
463A ASP* 3.0 29.4 + - - +
464A ALA* 3.9 4.4 - - - +
465A ILE* 5.1 0.4 - - - -
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Residues in contact with THR 394 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382A ILE* 3.4 31.6 - - + -
383A THR 3.3 7.8 + - - +
384A SER* 4.4 3.3 + - - +
393A GLN* 1.3 73.6 - - - +
395A MET* 1.3 77.2 + - - +
406A HIS* 3.8 7.8 + - - -
407A LEU* 3.7 19.3 + - + +
427A LEU 4.1 2.9 - - - +
428A HIS* 3.0 22.6 + - - +
429A ILE* 2.9 43.6 + - + +
465A ILE* 4.3 4.7 - - - +
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Residues in contact with MET 395 (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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357A LEU* 4.6 6.5 - - + -
382A ILE* 3.3 6.4 - - - +
383A THR 2.9 31.6 + - - +
385A VAL* 3.7 37.0 - - + -
393A GLN* 4.4 4.3 - - + +
394A THR* 1.3 88.9 - - - +
396A ILE* 1.3 63.3 + - - +
404A TRP* 3.9 28.9 - - + +
405A THR* 3.2 17.7 - - - +
406A HIS* 2.8 49.1 - - + +
407A LEU* 3.9 2.2 - - - -
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Residues in contact with ILE 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380A VAL* 3.7 11.4 - - + -
381A TYR 3.4 11.4 - - - +
382A ILE* 3.6 24.5 - - + -
395A MET* 1.3 76.5 - - - +
397A THR* 1.3 69.3 + - - +
398A PHE* 3.7 40.6 - - + -
404A TRP* 3.3 5.3 - - - -
405A THR* 2.7 50.4 + - + +
406A HIS 4.2 3.6 - - - +
407A LEU* 3.7 24.2 - - + -
479A GLY* 3.9 16.6 - - - +
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Residues in contact with THR 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A PHE* 5.3 0.4 - - + -
379A GLY 4.1 0.7 - - - +
380A VAL* 3.0 8.8 - - - +
381A TYR* 2.9 55.6 + - + +
396A ILE* 1.3 73.6 - - - +
398A PHE* 1.4 61.7 + - - +
399A ASP* 3.0 7.3 + - - -
401A GLY 3.0 30.1 + - - +
403A ARG 2.6 26.1 + - - -
404A TRP* 3.6 28.7 - - + -
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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