Contacts of the helix formed by residues 391 - 404 (chain A) in PDB entry 5KFU
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 ASP 391 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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349A GLU* 3.7 3.8 - - - +
389A ARG* 2.9 20.4 + - + +
390A TYR* 1.3 75.6 - - - +
392A ALA* 1.3 59.8 + - - +
393A HIS* 3.2 13.7 + - - +
394A LYS* 2.8 39.4 + - + +
395A MET* 2.8 36.0 + - - +
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Residues in contact with ALA 392 (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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342A LEU* 4.2 3.4 - - + -
345A ALA* 3.3 32.8 - - + +
346A GLN* 3.6 27.4 - - + -
349A GLU* 2.7 23.0 + - - +
391A ASP* 1.3 73.1 - - - +
393A HIS* 1.3 62.4 + - + +
395A MET* 4.1 2.0 - - - +
396A SER* 2.8 30.2 + - - -
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Residues in contact with HIS 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A LEU* 3.7 32.5 - - + +
346A GLN* 4.4 10.2 + - - -
391A ASP* 3.2 11.5 + - - +
392A ALA* 1.3 77.0 - - + +
394A LYS* 1.3 58.9 + - - +
396A SER* 3.2 6.2 + - - -
397A HIS* 3.0 30.5 + - - +
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Residues in contact with LYS 394 (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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386A ALA 5.4 2.4 + - - -
388A THR* 3.3 28.3 - - - +
389A ARG* 4.3 29.4 - - + +
391A ASP* 2.8 25.3 + - + +
393A HIS* 1.3 76.2 - - - +
395A MET* 1.3 59.4 + - + +
397A HIS* 3.3 5.7 + - - +
398A ASP* 2.9 60.9 + - - +
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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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345A ALA* 3.9 26.5 - - + +
348A LEU* 4.2 16.4 - - + -
349A GLU* 3.9 20.2 - - + +
352A LEU* 4.3 9.0 - - + -
366A LEU* 3.8 16.5 - - + +
387A LEU* 3.9 36.1 - - + -
389A ARG 4.1 9.2 - - - +
390A TYR 4.5 1.3 - - - -
391A ASP 2.8 38.0 + - - +
392A ALA 3.9 2.5 - - - +
394A LYS* 1.3 75.1 - - + +
396A SER* 1.3 57.7 + - - +
398A ASP* 3.3 8.7 + - - +
399A ALA* 2.9 29.2 + - - +
424A LEU* 5.4 2.5 - - + -
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Residues in contact with SER 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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338A GLN 5.1 1.3 + - - -
341A LEU* 3.6 32.8 - - - +
342A LEU* 3.7 20.1 - - - +
345A ALA* 3.8 3.3 - - - +
392A ALA 2.8 20.0 + - - -
393A HIS* 3.2 11.4 + - - -
395A MET* 1.3 73.9 - - - +
397A HIS* 1.3 66.8 + - - +
399A ALA* 3.5 7.1 + - - +
400A PHE* 3.1 23.0 + - - +
424A LEU* 5.3 0.9 - - - -
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Residues in contact with HIS 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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393A HIS 3.0 19.3 + - - +
394A LYS* 3.7 5.4 - - - +
396A SER* 1.3 78.6 + - - +
398A ASP* 1.3 71.2 + - - +
400A PHE* 3.2 13.7 + + - +
401A THR* 3.1 40.1 + - - -
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Residues in contact with ASP 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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366A LEU* 4.7 1.5 - - + +
385A CYS* 4.0 20.2 - - - -
386A ALA 4.2 11.1 - - - +
394A LYS* 2.9 54.5 + - - +
395A MET* 3.7 7.1 - - - +
397A HIS* 1.3 83.6 + - - +
399A ALA* 1.3 64.5 + - - +
401A THR* 3.2 8.6 + - - -
402A VAL* 3.2 28.4 + - - +
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Residues in contact with ALA 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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341A LEU* 4.1 12.1 - - + -
366A LEU* 4.6 1.1 - - + +
368A VAL* 3.7 22.9 - - + -
395A MET 2.9 17.8 + - - +
396A SER* 3.8 6.3 - - - +
397A HIS 3.3 0.2 - - - -
398A ASP* 1.3 75.3 - - - +
400A PHE* 1.3 64.8 + - - +
402A VAL* 3.2 14.6 + - - +
403A ILE* 3.3 17.3 + - - +
424A LEU* 3.7 28.5 - - + -
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Residues in contact with PHE 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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334A ARG* 4.1 16.6 - - + -
337A VAL* 4.2 7.2 - - + -
338A GLN* 3.3 45.5 - - + -
341A LEU* 3.8 18.1 - - + +
396A SER 3.1 14.3 + - - +
397A HIS* 3.5 16.4 - + - +
398A ASP 3.2 0.2 - - - -
399A ALA* 1.3 76.2 - - - +
401A THR* 1.3 61.1 + - - +
403A ILE* 3.3 2.7 + - + +
404A LYS* 2.9 53.8 + - + +
415A TRP* 3.5 31.4 - + - -
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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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397A HIS* 3.1 30.8 + - - -
398A ASP* 3.4 12.5 - - - -
399A ALA 3.2 0.2 - - - -
400A PHE* 1.3 79.3 - - - +
402A VAL* 1.3 64.7 + - + +
404A LYS* 3.3 42.4 + - - +
405A ASN* 4.2 5.4 + - - -
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Residues in contact with VAL 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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368A VAL* 3.8 21.8 - - + -
381A LEU* 4.9 1.6 - - - +
383A ARG* 4.1 33.0 + - + +
384A CYS 4.9 3.8 - - - +
385A CYS* 4.0 27.4 - - + -
398A ASP* 3.2 14.3 + - + +
399A ALA 3.3 13.5 - - - +
401A THR* 1.3 81.3 - - + +
403A ILE* 1.3 68.7 + - + +
405A ASN* 5.0 6.6 + - - +
406A CYS* 5.3 1.6 - - - -
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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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337A VAL* 4.0 18.4 - - + -
341A LEU* 4.1 15.3 - - + -
368A VAL* 3.5 24.0 - - + +
370A ILE* 4.2 33.4 - - + -
381A LEU* 4.6 8.7 - - + -
399A ALA 3.4 17.5 - - - +
400A PHE* 3.4 7.2 - - + +
402A VAL* 1.3 83.7 - - + +
404A LYS* 1.3 57.6 + - - +
405A ASN 3.0 5.4 - - - -
406A CYS* 2.9 35.7 + - - +
415A TRP* 3.9 25.5 - - + -
419A LEU* 4.4 2.2 - - + -
422A LEU* 4.8 2.0 - - + -
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Residues in contact with LYS 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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400A PHE* 2.9 34.9 + - + +
401A THR* 3.3 42.3 + - - +
402A VAL 3.7 0.2 - - - -
403A ILE* 1.3 75.8 - - - +
405A ASN* 1.3 74.5 + - - +
406A CYS 3.2 1.9 + - - -
407A ASN* 3.5 20.1 + - - +
415A TRP* 3.8 12.7 - - + -
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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