Contacts of the helix formed by residues 421 - 438 (chain F) in PDB entry 5KRA
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 MET 421 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343F MET* 3.8 25.4 - - + -
416F LYS* 4.2 18.3 - - + +
417F CYS* 3.7 20.8 - - - +
420F GLY* 1.3 73.6 - - - +
422F VAL* 1.3 61.0 + - - +
423F GLU 3.2 0.7 - - - -
424F ILE* 3.5 14.4 + - + -
425F PHE* 3.1 20.6 + - - +
521F GLY* 5.3 0.4 - - - -
524F HIS* 3.3 53.3 + - + +
528F MET* 5.3 0.2 - - - -
601F 6WT 3.3 52.0 - - + +
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Residues in contact with VAL 422 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412F ARG* 4.7 27.4 - - + +
416F LYS* 3.4 30.5 - - + +
417F CYS* 3.7 13.2 - - + -
420F GLY 4.3 8.7 - - - +
421F MET* 1.3 79.3 - - - +
423F GLU* 1.3 70.9 + - + +
425F PHE* 3.3 9.8 - - - +
426F ASP* 3.0 33.9 + - - +
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Residues in contact with GLU 423 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420F GLY* 3.5 18.4 + - - +
421F MET 3.2 0.6 - - - -
422F VAL* 1.3 86.0 - - + +
424F ILE* 1.3 62.3 + - - +
425F PHE 3.2 0.4 - - - -
426F ASP* 3.5 11.5 + - - +
427F MET* 3.1 36.4 + - + +
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Residues in contact with ILE 424 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388F MET* 4.3 13.2 - - + -
420F GLY 3.5 14.1 + - - +
421F MET* 3.8 27.1 - - + +
422F VAL 3.4 0.2 - - - -
423F GLU* 1.3 77.1 - - + +
425F PHE* 1.3 59.0 + - - +
427F MET* 3.3 20.5 + - + +
428F LEU* 3.0 33.4 + - + +
517F MET* 4.4 6.5 - - + +
520F LYS* 3.8 12.8 - - + +
521F GLY* 3.6 31.6 - - - +
524F HIS* 4.6 2.9 - - + -
601F 6WT 3.5 24.2 - - + -
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Residues in contact with PHE 425 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346F LEU* 6.4 0.2 - - + -
402F LEU* 3.5 27.6 - - + -
404F PHE* 3.8 17.0 - + - -
410F LEU* 3.4 30.5 - - + -
411F ASP* 3.5 11.7 - - - -
412F ARG* 3.4 37.2 - - + -
414F GLN 5.8 1.3 - - - -
416F LYS* 5.8 8.1 - - + -
421F MET 3.1 13.5 + - - +
422F VAL* 3.3 15.3 - - - +
424F ILE* 1.3 77.3 - - - +
426F ASP* 1.3 55.5 - - - +
428F LEU* 3.3 8.3 + - - +
429F LEU* 3.0 35.0 + - + +
601F 6WT 3.7 19.7 - - + +
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Residues in contact with ASP 426 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412F ARG* 2.7 53.4 + - - +
422F VAL* 3.0 22.2 + - - +
423F GLU* 3.8 13.3 - - + +
424F ILE 3.3 0.2 - - - -
425F PHE* 1.3 72.8 - - - +
427F MET* 1.3 61.3 + - + +
429F LEU* 3.2 12.0 + - - +
430F ALA* 2.9 29.2 + - - +
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Residues in contact with MET 427 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459E TYR 5.0 0.9 - - - -
460E THR* 3.9 21.3 - - + -
423F GLU* 3.1 16.5 + - + +
424F ILE* 3.6 31.0 - - + +
425F PHE 3.3 0.2 - - - -
426F ASP* 1.3 75.6 - - + +
428F LEU* 1.3 54.0 + - - +
430F ALA* 3.3 4.7 + - - +
431F THR* 2.7 36.6 + - - -
513F HIS* 3.4 20.9 - - - +
516F HIS* 3.8 28.7 - - + -
517F MET* 3.5 34.3 - - + -
520F LYS* 4.5 9.4 - - + -
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Residues in contact with LEU 428 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388F MET* 4.0 28.0 - - + +
391F LEU* 3.9 14.6 - - + -
392F VAL* 3.6 26.2 - - + +
402F LEU* 3.7 29.1 - - + +
424F ILE* 3.0 22.1 + - + +
425F PHE 3.5 6.5 - - - +
427F MET* 1.3 76.6 - - - +
429F LEU* 1.3 57.8 + - - +
431F THR* 3.3 4.4 + - - -
432F SER* 3.0 25.5 + - - -
517F MET* 3.8 17.3 - - - -
601F 6WT 3.9 32.1 - - + -
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Residues in contact with LEU 429 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400F GLY* 3.6 20.4 - - - +
401F LYS* 3.4 43.1 - - - +
402F LEU* 3.8 10.8 - - + -
412F ARG* 4.4 10.3 - - + -
425F PHE* 3.0 37.4 + - + +
426F ASP* 3.2 20.4 + - - +
428F LEU* 1.3 74.3 - - - +
430F ALA* 1.3 53.9 + - - +
432F SER* 3.1 6.9 + - - -
433F SER* 2.8 36.0 + - - -
436F ARG* 5.2 0.9 + - - -
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Residues in contact with ALA 430 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459E TYR* 3.4 33.9 - - + +
426F ASP 2.9 16.8 + - - +
427F MET 3.7 4.3 - - - +
429F LEU* 1.3 76.7 - - - +
431F THR* 1.3 57.7 + - - +
433F SER* 3.4 8.8 + - - -
434F ARG* 3.0 27.7 + - - +
513F HIS* 5.5 0.4 - - - -
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Residues in contact with THR 431 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459E TYR* 5.8 2.9 - - - -
392F VAL* 3.7 23.1 - - + -
427F MET 2.7 20.3 + - - -
428F LEU 3.5 7.9 - - - -
429F LEU 3.2 0.2 - - - -
430F ALA* 1.3 74.1 - - - +
432F SER* 1.3 64.0 + - - +
434F ARG* 3.1 7.6 + - - +
435F PHE* 3.0 29.4 + - + -
510F ILE* 4.0 25.8 - - + -
513F HIS* 3.1 20.7 + - - +
514F ILE* 4.4 6.3 - - + -
517F MET* 3.4 12.7 - - + +
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Residues in contact with SER 432 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392F VAL* 3.3 22.5 + - - +
395F SER* 3.2 37.0 + - - -
396F MET* 3.3 7.3 - - - +
401F LYS 5.5 1.3 - - - -
402F LEU* 5.1 1.6 - - - -
428F LEU 3.0 13.8 + - - -
429F LEU* 3.5 11.4 - - - -
431F THR* 1.3 77.4 - - - +
433F SER* 1.3 56.5 + - - +
435F PHE* 3.5 4.6 + - - +
436F ARG* 3.1 31.7 + - - +
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Residues in contact with SER 433 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429F LEU 2.8 17.4 + - - -
430F ALA* 3.6 10.3 - - - -
432F SER* 1.3 76.6 - - - +
434F ARG* 1.3 56.6 + - - +
436F ARG* 3.4 26.8 + - - +
437F MET* 3.1 31.1 + - - +
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Residues in contact with ARG 434 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459E TYR* 4.4 16.6 + - + -
476E HIS* 3.3 50.5 + - - +
430F ALA 3.0 14.6 + - - +
431F THR* 3.1 12.5 + - + +
433F SER* 1.3 75.4 - - - +
435F PHE* 1.3 63.7 + - - +
437F MET* 3.3 34.1 + - - +
438F MET* 3.0 45.9 + - - +
506F GLN* 3.9 34.2 + - - +
510F ILE* 3.6 28.5 - - + +
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Residues in contact with PHE 435 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389F ILE* 4.1 27.1 - - + -
392F VAL* 3.4 36.8 - - + -
393F TRP* 4.8 3.1 - - + -
396F MET* 3.6 20.7 - - + +
431F THR* 3.0 10.5 + - + -
432F SER 3.8 6.3 - - - +
433F SER 3.4 0.2 - - - -
434F ARG* 1.3 76.6 - - - +
436F ARG* 1.3 57.6 + - - +
438F MET* 3.3 5.4 + - - -
439F ASN 3.0 8.5 + - - -
440F LEU* 3.0 61.6 + - + -
448F LEU* 4.4 15.3 - - + -
507F LEU* 4.8 0.9 - - + -
510F ILE* 3.5 45.3 - - + -
511F LEU* 6.0 0.2 - - + -
514F ILE* 4.7 1.3 - - + -
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Residues in contact with ARG 436 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395F SER 4.2 2.0 + - - -
396F MET* 2.4 58.9 + - + +
397F GLU* 5.3 1.3 - - - +
399F PRO* 3.9 36.9 - - - +
400F GLY 4.7 3.2 - - - +
429F LEU 5.2 0.8 + - - -
432F SER* 3.1 20.7 + - - +
433F SER* 3.5 31.5 + - - +
434F ARG 3.2 0.2 - - - -
435F PHE* 1.3 76.2 - - - +
437F MET* 1.3 62.5 + - - +
439F ASN* 3.1 20.1 + - - +
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Residues in contact with MET 437 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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476E HIS* 4.9 5.6 - - + +
433F SER* 3.1 17.0 + - - +
434F ARG* 3.3 48.0 - - + +
435F PHE 3.3 0.2 - - - -
436F ARG* 1.3 77.7 - - - +
438F MET* 1.3 60.2 + - + +
439F ASN* 3.2 7.4 + - - +
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Residues in contact with MET 438 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434F ARG* 3.0 52.9 + - - +
435F PHE* 3.3 7.2 + - - +
436F ARG 3.3 0.2 - - - -
437F MET* 1.3 77.6 - - + +
439F ASN* 1.3 71.2 + - - +
440F LEU* 4.5 3.8 - - + +
503F ARG* 3.0 36.9 + - + +
506F GLN* 3.3 33.4 - - + +
507F LEU* 3.5 28.5 - - + -
510F ILE* 3.8 21.1 - - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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