Contacts of the helix formed by residues 475 - 492 (chain A) in PDB entry 5NKS
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 PRO 475 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162A ASN* 4.5 5.6 - - - +
192A GLY 3.9 8.1 - - - +
193A ALA* 5.8 0.7 - - - -
194A LEU* 6.3 2.2 - - + -
390A LYS 3.7 12.1 - - - +
391A ILE 3.3 27.1 - - - +
393A ASN* 3.5 33.7 - - + +
472A LYS 4.2 3.8 - - - +
473A THR* 3.4 4.4 - - - -
474A PHE* 1.4 86.3 - - - +
476A ASP* 1.3 61.6 + - - +
478A VAL* 3.1 14.3 + - + -
479A TYR* 2.8 30.8 + - + +
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Residues in contact with ASP 476 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393A ASN* 4.7 2.6 + - - -
474A PHE 3.2 9.8 + - - +
475A PRO* 1.3 71.7 - - - +
477A PHE* 1.3 64.1 + - - +
478A VAL 3.0 1.4 + - - -
479A TYR* 4.3 1.1 - - - +
480A LYS* 3.1 55.3 + - + +
481A ARG 4.9 0.2 + - - -
483A LYS* 4.9 5.1 + - - +
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Residues in contact with PHE 477 (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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275A PHE* 3.8 18.6 - + - -
327A GLN* 3.8 20.0 - - - -
387A ASN* 4.7 12.1 - - + -
390A LYS* 3.6 46.7 - - + +
391A ILE* 3.7 35.2 - - + -
475A PRO* 3.2 1.0 - - - +
476A ASP* 1.3 78.4 - - - +
478A VAL* 1.3 57.4 + - - +
481A ARG* 2.9 29.2 + - - -
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Residues in contact with VAL 478 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A LEU* 4.1 8.3 - - + -
249A PRO* 3.3 40.2 - - + -
273A VAL* 4.1 7.6 - - + +
275A PHE* 4.0 21.1 - - + -
391A ILE* 3.6 35.0 - - + +
475A PRO* 3.1 11.8 + - + +
476A ASP 3.0 0.4 - - - -
477A PHE* 1.3 81.6 - - + +
479A TYR* 1.3 73.9 + - + +
480A LYS 3.5 1.7 + - - -
481A ARG* 4.0 10.5 + - - +
482A ILE* 3.5 15.4 + - - +
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Residues in contact with TYR 479 (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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189A ARG* 3.3 32.1 - - - -
192A GLY* 3.4 23.3 - - - -
193A ALA 2.5 32.6 + - - -
249A PRO* 3.5 18.1 - - + +
474A PHE* 3.7 42.4 - + + +
475A PRO* 2.8 21.8 + - + +
476A ASP* 5.1 0.4 - - - -
478A VAL* 1.3 80.1 - - + +
480A LYS* 1.3 67.0 + - - +
481A ARG 3.2 2.2 - - - -
482A ILE* 3.5 31.6 - - + -
483A LYS* 2.8 36.1 + - + +
486A ASN* 5.8 0.7 - - - -
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Residues in contact with LYS 480 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476A ASP* 3.1 47.3 + - + +
478A VAL 3.5 0.2 - - - -
479A TYR* 1.3 76.4 - - - +
481A ARG* 1.3 63.5 + - + +
483A LYS* 4.0 22.3 - - - +
484A ALA* 3.1 23.7 + - - +
487A ARG* 5.0 2.3 + - - +
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Residues in contact with ARG 481 (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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268A LYS* 5.4 7.3 - - - +
271A GLY 5.7 0.6 + - - -
272A VAL 4.9 4.2 + - - -
273A VAL* 4.0 40.2 - - + +
275A PHE* 3.9 23.4 - - - -
477A PHE* 2.9 31.7 + - - -
478A VAL* 4.0 4.1 + - - +
479A TYR 3.2 0.4 - - - -
480A LYS* 1.3 79.9 - - + +
482A ILE* 1.3 62.7 + - - +
484A ALA* 3.3 7.3 + - - +
485A ARG* 3.0 48.2 + - - +
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Residues in contact with ILE 482 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A ARG* 4.1 7.2 - - + -
247A ASN* 3.0 56.0 + - - +
248A CYS 4.2 0.7 - - - -
249A PRO* 3.8 27.6 - - + -
273A VAL* 3.9 23.6 - - + -
478A VAL 3.5 15.5 - - - +
479A TYR* 3.1 36.1 + - + +
481A ARG* 1.3 74.2 - - - +
483A LYS* 1.3 57.2 + - - +
485A ARG* 3.2 2.7 + - - +
486A ASN* 2.9 28.9 + - - +
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Residues in contact with LYS 483 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474A PHE* 4.2 33.9 + - + +
476A ASP* 4.9 6.1 + - - -
479A TYR* 2.8 41.5 + - + +
480A LYS* 4.1 26.9 - - - +
482A ILE* 1.3 70.8 - - - +
484A ALA* 1.3 63.4 + - - +
486A ASN* 3.2 15.1 + - - +
487A ARG* 3.0 43.6 + - - +
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Residues in contact with ALA 484 (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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480A LYS 3.1 15.3 + - - +
481A ARG* 3.5 10.5 - - - +
483A LYS* 1.3 76.5 - - - +
485A ARG* 1.3 60.9 + - + +
487A ARG* 3.3 25.3 + - - +
488A LEU* 2.9 40.9 + - + +
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Residues in contact with ARG 485 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A ASN* 3.5 27.5 + - - +
271A GLY* 2.8 34.1 + - - -
272A VAL* 4.4 1.6 - - - +
273A VAL* 3.7 22.3 - - - +
481A ARG* 3.0 41.8 + - - +
482A ILE* 3.5 6.7 - - - +
484A ALA* 1.3 76.1 - - + +
486A ASN* 1.3 66.0 + - - +
488A LEU* 3.8 12.7 - - + +
489A ALA* 3.0 24.8 + - - +
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Residues in contact with ASN 486 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A ARG* 3.8 23.5 + - - +
247A ASN* 2.8 24.5 + - - +
474A PHE* 6.3 1.0 - - - -
479A TYR* 5.8 0.8 - - - -
482A ILE* 2.9 23.4 + - - +
483A LYS* 3.2 19.4 + - - +
485A ARG* 1.3 76.8 - - - +
487A ARG* 1.3 62.6 + - + +
489A ALA* 3.3 8.0 + - - +
490A GLU* 3.2 28.4 + - + +
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Residues in contact with ARG 487 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480A LYS* 5.0 2.6 + - - +
483A LYS* 3.0 37.6 + - - +
484A ALA* 3.5 30.5 - - - +
486A ASN* 1.3 75.8 - - + +
488A LEU* 1.3 63.1 + - - +
490A GLU* 3.2 17.6 + - - +
491A ILE* 3.0 35.2 + - + +
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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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484A ALA* 2.9 30.0 + - + +
485A ARG* 3.8 12.8 - - + +
487A ARG* 1.3 76.8 - - + +
489A ALA* 1.3 57.5 + - - +
491A ILE* 3.4 13.1 + - + -
492A HIS* 2.9 58.5 + - + +
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Residues in contact with ALA 489 (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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485A ARG 3.0 14.0 + - - +
486A ASN* 3.3 10.7 + - - +
488A LEU* 1.3 75.6 - - - +
490A GLU* 1.3 57.1 + - - +
492A HIS 3.3 1.2 + - - -
493A GLY 3.0 8.5 + - - -
494A VAL* 2.9 56.1 + - + +
495A PRO 3.8 18.4 - - - +
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Residues in contact with GLU 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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486A ASN* 3.2 17.3 + - + +
487A ARG* 3.2 18.3 + - - +
489A ALA* 1.3 74.9 - - - +
491A ILE* 1.3 67.7 + - + +
493A GLY* 3.1 13.4 + - - +
494A VAL 4.9 1.1 - - - -
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Residues in contact with ILE 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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487A ARG* 3.0 30.0 + - + +
488A LEU* 3.8 16.6 - - + +
490A GLU* 1.3 79.5 - - + +
492A HIS* 1.3 79.6 + - + +
493A GLY 3.2 3.2 + - - -
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Residues in contact with HIS 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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488A LEU* 2.9 49.3 + - + +
489A ALA 4.2 1.1 - - - +
491A ILE* 1.3 93.0 - - + +
493A GLY* 1.3 63.0 + - - +
494A VAL* 3.3 22.5 + - + +
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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