Contacts of the helix formed by residues 485 - 505 (chain A) in PDB entry 3K5N
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 ASN 485 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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354A GLU* 4.4 8.3 + - - -
480A ALA* 3.1 18.7 + - + +
481A LYS* 4.6 0.6 - - - +
483A GLN* 3.0 12.8 + - - +
484A GLY* 1.3 76.2 - - - +
486A LYS* 1.3 55.5 + - - +
487A PRO* 2.3 55.4 - - - +
488A LEU* 2.8 35.9 + - + +
489A SER* 3.2 11.9 + - - -
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Residues in contact with LYS 486 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481A LYS* 5.8 2.7 - - - +
484A GLY* 3.0 24.5 + - - +
485A ASN* 1.3 73.9 - - - +
487A PRO* 1.3 68.3 - - + +
489A SER* 3.2 7.8 + - - -
490A GLN* 2.9 26.9 + - - +
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Residues in contact with PRO 487 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347A GLU* 5.8 4.0 - - - +
350A PRO* 4.8 17.0 - - + +
351A PHE* 5.0 12.5 - - + -
354A GLU* 4.1 22.1 - - + +
484A GLY 4.6 0.7 - - - +
485A ASN* 2.3 42.8 - - - +
486A LYS* 1.3 82.3 - - + +
488A LEU* 1.3 58.8 + - - +
490A GLN* 3.8 5.0 + - + +
491A ALA* 3.2 20.8 + - - +
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Residues in contact with LEU 488 (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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147A ARG* 4.6 11.0 - - - +
354A GLU* 2.5 43.3 - - - +
357A THR* 5.4 1.1 - - + -
358A VAL* 4.3 13.7 - - + -
476A GLY 5.7 0.2 - - - +
480A ALA* 4.1 12.1 - - + -
483A GLN* 6.1 0.4 - - - +
485A ASN* 2.8 35.2 + - + +
487A PRO* 1.3 71.2 - - - +
489A SER* 1.3 56.1 + - - +
491A ALA* 3.0 7.2 + - - +
492A LEU* 2.7 48.9 + - + +
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Residues in contact with SER 489 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477A ARG* 3.4 29.7 + - - +
480A ALA* 2.7 31.1 - - - +
481A LYS* 3.4 17.6 + - - -
485A ASN 3.2 3.9 + - - -
486A LYS* 3.2 10.2 + - - -
488A LEU* 1.3 74.0 - - - +
490A GLN* 1.3 69.4 + - - +
491A ALA 2.9 1.6 - - - -
492A LEU* 2.7 14.6 + - - +
493A LYS* 2.8 15.4 + - - +
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Residues in contact with GLN 490 (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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284A ALA 4.7 9.1 + - - -
285A PHE* 5.4 4.6 - - - +
351A PHE* 4.7 20.1 - - + -
477A ARG* 4.8 2.9 - - - +
486A LYS 2.9 17.1 + - - +
487A PRO* 4.1 5.2 - - + +
489A SER* 1.3 76.3 - - - +
491A ALA* 1.3 65.8 + - - +
493A LYS* 3.3 10.0 + - - +
494A ILE* 3.2 39.2 + - + +
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Residues in contact with ALA 491 (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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351A PHE* 5.2 5.1 - - + +
354A GLU 4.1 5.2 - - - +
355A ARG* 3.8 36.5 - - + +
358A VAL* 4.2 8.5 - - + +
487A PRO 3.2 12.2 + - - +
488A LEU 3.0 13.4 + - - +
489A SER 2.9 0.2 - - - -
490A GLN* 1.3 84.7 - - - +
492A LEU* 1.3 61.1 + - - +
494A ILE* 3.5 12.7 + - - +
495A ILE* 3.7 14.0 + - - +
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Residues in contact with LEU 492 (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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358A VAL* 3.7 22.0 - - + -
473A ILE* 3.5 39.1 - - + +
476A GLY* 3.9 10.1 - - - +
477A ARG* 3.6 36.8 - - + +
480A ALA* 4.5 0.9 - - + -
488A LEU* 2.7 42.6 + - + +
489A SER* 2.7 9.6 + - - +
491A ALA* 1.3 72.3 - - - +
493A LYS* 1.3 57.6 + - - +
495A ILE* 2.8 29.1 - - + +
496A MET 3.7 0.3 + - - -
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Residues in contact with LYS 493 (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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422A SER* 4.0 20.9 - - - +
477A ARG* 3.5 43.7 - - + +
489A SER 2.8 15.6 + - - +
490A GLN* 3.7 9.0 - - - +
492A LEU* 1.3 73.1 - - - +
494A ILE* 1.3 68.6 + - + +
496A MET* 3.1 14.2 - - - +
497A ASN* 2.9 38.1 + - - +
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Residues in contact with ILE 494 (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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285A PHE* 4.2 28.0 - - + -
351A PHE* 5.2 10.1 - - + -
490A GLN* 3.2 34.7 + - + +
491A ALA* 3.8 7.9 - - - +
492A LEU 3.3 0.2 - - - -
493A LYS* 1.3 83.2 - - + +
495A ILE* 1.3 64.9 + - + +
497A ASN* 3.0 8.3 + - - +
498A ALA* 2.7 30.7 + - + +
913P G 5.4 8.2 - - + +
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Residues in contact with ILE 495 (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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358A VAL* 2.7 49.1 - - + +
359A ASN* 4.5 15.9 - - + -
372A ALA* 5.4 6.3 - - + -
376A LEU* 5.5 4.0 - - + -
473A ILE* 3.7 24.2 - - + -
491A ALA 3.7 4.2 + - - +
492A LEU* 2.8 25.6 - - + +
494A ILE* 1.3 75.9 - - + +
496A MET* 1.3 61.0 + - - +
498A ALA* 2.3 37.7 + - + +
499A PHE* 3.1 23.1 + - + -
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Residues in contact with MET 496 (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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422A SER* 4.1 8.3 - - - -
425A PRO* 3.1 39.1 - - + +
428A ILE* 5.6 0.3 - - - +
470A VAL* 3.7 16.6 - - + +
473A ILE* 3.6 27.8 - - + -
474A TRP* 3.1 46.0 - - + -
477A ARG* 5.2 3.1 - - - -
492A LEU 3.8 4.5 - - - +
493A LYS* 3.1 25.8 - - - +
495A ILE* 1.3 82.9 - - - +
497A ASN* 1.3 67.4 + - - +
498A ALA 3.2 0.3 + - - -
499A PHE* 3.3 32.5 + - + +
500A TYR* 4.4 1.6 + - - +
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Residues in contact with ASN 497 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422A SER* 3.7 25.6 + - - +
424A TYR* 6.1 0.5 - - - +
425A PRO* 3.8 13.3 - - - +
493A LYS* 2.9 34.6 + - - +
494A ILE* 3.3 7.4 - - - +
495A ILE 2.8 1.2 - - - -
496A MET* 1.3 86.1 - - - +
498A ALA* 1.3 57.9 + - - +
499A PHE 3.3 1.0 + - - -
500A TYR* 4.3 9.3 + - - +
501A GLY 4.7 2.6 + - - -
913P G 4.9 19.0 + - + +
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Residues in contact with ALA 498 (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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369A SER* 4.3 23.0 - - - +
494A ILE* 2.7 14.8 + - + +
495A ILE* 2.3 32.5 + - + +
497A ASN* 1.3 70.0 - - - +
499A PHE* 1.3 62.9 + - + -
500A TYR 3.4 0.4 - - - -
501A GLY* 3.4 5.6 + - - +
502A VAL* 3.4 22.2 + - - +
913P G 4.2 17.3 - - - +
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Residues in contact with PHE 499 (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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369A SER 5.8 1.3 - - - -
372A ALA* 5.7 1.8 - - + -
373A PHE* 3.7 37.0 - + + -
376A LEU* 4.5 13.2 - - + -
425A PRO* 6.0 0.2 - - + -
428A ILE* 4.6 12.8 - - + -
466A LEU* 4.2 15.7 - - + -
469A ILE* 4.1 18.6 - - + -
470A VAL* 4.2 13.0 - - + -
473A ILE* 4.0 24.9 - - + -
495A ILE* 3.1 19.0 + - + -
496A MET* 3.3 28.8 + - - +
498A ALA* 1.3 76.0 - - + +
500A TYR* 1.3 65.0 + - - +
501A GLY 3.0 1.3 - - - -
502A VAL* 2.3 31.9 - - + +
503A LEU* 3.2 10.2 + - - +
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Residues in contact with TYR 500 (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* 3.4 47.9 - + + -
428A ILE* 5.1 2.8 - - + +
496A MET 4.4 1.8 + - - +
497A ASN 4.3 8.3 + - - +
498A ALA 3.4 0.2 - - - -
499A PHE* 1.3 80.5 - - - +
501A GLY* 1.3 71.5 + - - +
503A LEU* 3.4 5.0 + - - +
504A GLY* 3.2 19.2 + - - -
516A ALA* 4.0 21.3 - - + +
519A ILE* 3.5 32.5 - - + -
520A THR* 2.7 28.6 + - - -
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Residues in contact with GLY 501 (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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497A ASN 4.7 1.4 + - - -
498A ALA* 3.4 10.8 + - - +
499A PHE 3.0 1.0 - - - -
500A TYR* 1.3 90.7 - - - +
502A VAL* 1.3 64.0 + - - +
504A GLY* 3.3 8.9 + - - -
505A THR* 3.5 13.0 + - - +
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Residues in contact with VAL 502 (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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369A SER* 3.8 15.0 - - - +
370A VAL* 3.6 37.2 - - + -
373A PHE* 3.7 25.4 - - + -
498A ALA 3.4 8.4 + - - +
499A PHE* 2.3 45.8 - - + +
501A GLY* 1.3 72.3 - - - +
503A LEU* 1.3 67.4 + - + +
504A GLY 3.0 1.7 + - - -
505A THR* 3.0 26.2 + - - +
508A CYS* 3.5 15.7 - - - +
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Residues in contact with LEU 503 (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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373A PHE* 3.8 22.9 - - + -
428A ILE* 5.1 1.3 - - + -
433A ILE* 4.8 11.0 - - + -
435A PRO* 4.4 4.3 - - + -
466A LEU* 4.1 24.7 - - + -
499A PHE 3.2 17.4 + - - +
500A TYR* 3.8 7.9 - - - +
501A GLY 3.3 0.2 - - - -
502A VAL* 1.3 85.0 - - + +
504A GLY* 1.3 59.1 + - - +
505A THR 3.4 0.2 - - - -
508A CYS* 5.0 1.3 - - - -
510A PHE* 4.3 21.3 - - + +
511A PHE* 3.5 25.0 - - - +
512A ASP 4.1 8.0 + - - +
515A LEU* 4.3 32.3 - - + +
516A ALA* 4.6 6.5 - - - +
519A ILE* 5.1 7.6 - - + -
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Residues in contact with GLY 504 (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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500A TYR* 3.2 13.6 + - - -
501A GLY 3.3 4.2 + - - -
502A VAL 3.0 1.4 - - - -
503A LEU* 1.3 77.8 - - - +
505A THR* 1.3 59.3 + - - +
506A THR* 5.1 1.0 - - - +
511A PHE* 3.8 15.0 - - - -
516A ALA* 4.0 19.5 - - - +
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Residues in contact with THR 505 (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 VAL* 4.4 7.0 - - + -
501A GLY 3.5 8.2 + - - +
502A VAL* 3.0 21.3 - - - +
504A GLY* 1.3 79.2 - - - +
506A THR* 1.3 61.3 + - - +
507A ALA* 3.1 24.4 + - + +
508A CYS* 3.3 12.0 + - + +
511A PHE* 3.2 19.5 - - - +
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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