Contacts of the helix formed by residues 422 - 432 (chain A) in PDB entry 3K5M
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 SER 422 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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421A LYS* 1.3 74.2 - - - +
423A LEU* 1.3 58.0 + - - +
424A TYR 3.4 2.2 - - - -
425A PRO* 3.2 12.0 - - - +
426A SER* 2.7 27.4 + - - -
474A TRP* 3.6 24.7 - - - -
477A ARG* 3.6 6.9 + - - -
493A LYS* 4.9 1.4 - - - +
496A MET* 3.4 23.0 - - - +
914A DG3 2.9 41.4 + - - -
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Residues in contact with LEU 423 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420A TYR* 3.6 34.1 - - + -
421A LYS 3.0 2.8 + - - -
422A SER* 1.3 75.3 - - - +
424A TYR* 1.3 67.5 + - + +
425A PRO* 4.0 0.2 - - - +
426A SER* 2.5 28.7 + - - +
427A ILE* 2.7 41.6 + - + +
523A GLY* 4.7 7.6 - - - +
526A ILE* 4.3 13.5 - - + -
527A MET* 5.0 2.9 - - + -
546A THR* 3.5 25.6 - - + +
547A ASP* 3.8 24.2 - - + -
590A LEU* 4.6 1.6 - - + -
914A DG3 3.1 9.9 + - + +
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Residues in contact with TYR 424 (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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401A GLY 4.1 0.2 - - - -
402A GLY* 3.6 18.9 + - - -
423A LEU* 1.3 95.5 - - + +
425A PRO* 1.3 67.6 - - + +
427A ILE* 3.1 13.2 + - + +
428A ILE* 2.8 33.1 + - - +
497A ASN* 4.1 6.0 + - - +
500A TYR* 3.5 54.3 - + + -
519A ILE* 3.7 21.1 - - + +
520A THR* 3.8 20.8 + - + +
523A GLY* 5.0 4.3 - - - -
546A THR* 3.6 25.2 - - + +
914A DG3 4.0 22.9 - - + +
913P G 5.6 2.8 + - - -
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Residues in contact with PRO 425 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422A SER* 3.2 27.4 - - - +
424A TYR* 1.3 94.2 - - + +
426A SER* 1.3 56.4 + - - +
428A ILE* 3.1 15.9 + - + +
429A ARG* 2.8 32.2 + - - +
470A VAL* 3.7 21.7 - - + +
474A TRP* 4.2 5.2 - - + -
493A LYS 5.5 0.2 - - - +
496A MET* 3.8 32.5 - - + +
497A ASN* 3.5 16.4 - - - +
914A DG3 5.1 0.2 - - - +
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Residues in contact with SER 426 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421A LYS 4.0 4.6 + - - -
422A SER 2.7 18.6 + - - -
423A LEU* 2.5 26.9 + - - +
425A PRO* 1.3 74.0 - - - +
427A ILE* 1.3 55.2 + - - +
429A ARG* 3.3 6.4 + - - +
430A THR* 2.9 34.8 + - - -
474A TRP* 3.8 14.7 - - - -
589A ALA* 3.6 25.7 - - - +
590A LEU* 3.6 16.1 - - - +
591A GLU 5.0 0.2 + - - -
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Residues in contact with ILE 427 (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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423A LEU* 2.7 34.3 + - + +
424A TYR* 3.4 15.9 - - + +
426A SER* 1.3 71.5 + - - +
428A ILE* 1.3 66.1 + - - +
430A THR* 4.6 0.7 - - - -
431A PHE* 2.9 43.6 + - + +
433A ILE* 4.1 2.9 - - + +
518A SER 4.4 1.6 - - - +
519A ILE* 3.5 42.4 - - + +
522A ARG* 4.1 7.0 - - + -
523A GLY* 3.8 22.9 - - - +
526A ILE* 3.8 20.6 - - + -
590A LEU* 4.5 1.1 - - + -
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Residues in contact with ILE 428 (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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424A TYR 2.8 20.7 + - - +
425A PRO* 3.1 15.7 + - + +
427A ILE* 1.3 75.4 - - - +
429A ARG* 1.3 63.4 + - - +
432A LEU* 3.1 19.2 + - - -
433A ILE* 3.3 31.5 + - + +
466A LEU* 3.8 28.9 - - + -
467A PRO* 4.0 11.1 - - + +
470A VAL* 4.0 16.4 - - + -
496A MET 4.9 2.7 - - - +
499A PHE* 4.9 2.9 - - + -
500A TYR* 4.5 16.8 - - + +
519A ILE* 3.5 31.0 - - + -
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Residues in contact with ARG 429 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425A PRO 2.8 12.4 + - - +
426A SER 3.5 7.4 - - - +
428A ILE* 1.3 77.9 - - - +
430A THR* 1.3 60.1 + - - +
432A LEU* 3.4 20.6 - - - +
467A PRO* 4.0 13.7 - - - +
470A VAL* 3.7 24.2 - - + -
471A THR* 3.1 39.5 + - - +
474A TRP* 3.3 50.9 - - - +
475A HIS* 4.9 6.6 + - - -
587A THR 4.8 2.5 - - - +
589A ALA* 3.6 23.7 - - + +
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Residues in contact with THR 430 (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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426A SER 2.9 18.3 + - - -
429A ARG* 1.3 74.3 - - - +
431A PHE* 1.3 78.0 + - + +
432A LEU* 3.4 3.3 + - - +
581A LEU* 3.3 35.4 - - + -
586A LEU* 3.9 24.4 - - + +
587A THR 3.7 18.7 + - - +
588A SER* 3.9 1.1 - - - +
589A ALA* 2.8 26.5 + - - -
590A LEU* 3.7 6.9 + - + +
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Residues in contact with PHE 431 (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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427A ILE* 2.9 26.4 + - + +
430A THR* 1.3 93.6 - - + +
432A LEU* 1.3 73.5 + - - +
433A ILE* 3.3 18.5 + - + +
451A THR* 3.6 18.9 - - + +
452A GLU 5.3 4.6 - - - +
459A PHE* 4.2 4.2 - - - +
518A SER 5.7 0.4 - - - +
522A ARG* 3.4 58.3 - - + +
525A GLN* 5.3 0.9 - - - -
526A ILE* 4.3 17.9 - - + -
577A TRP* 5.6 2.9 - + - -
581A LEU* 4.1 15.7 - - + -
584A GLN* 5.3 6.7 - - - -
586A LEU* 4.3 23.3 - - + -
590A LEU* 4.6 3.4 - - + -
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Residues in contact with LEU 432 (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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428A ILE 3.1 10.6 + - - -
429A ARG 3.4 17.9 - - - +
430A THR 4.3 5.4 - - - +
431A PHE* 1.3 79.8 - - - +
433A ILE* 1.3 65.0 + - - +
434A ASP* 3.2 9.1 + - - +
437A GLY* 5.3 0.5 - - - -
451A THR* 4.5 11.7 - - + -
459A PHE* 3.3 18.7 - - + +
460A SER 4.0 5.6 - - - +
461A ARG* 3.8 35.2 - - + +
464A HIS* 3.9 30.0 - - + +
467A PRO* 4.2 9.9 - - + -
586A LEU* 4.5 11.9 - - + -
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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