Contacts of the helix formed by residues 59 - 69 (chain N) in PDB entry 1NSK
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 59 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57N ASP 4.4 2.5 - - - +
58N ARG* 1.3 87.8 - - + +
60N PHE* 1.3 66.3 + - + +
62N PRO* 3.2 15.4 - - - +
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Residues in contact with PHE 60 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55N LEU* 3.7 33.2 - - + -
58N ARG* 3.7 32.1 - - + -
59N PRO* 1.3 84.3 - - + +
61N PHE* 1.3 83.3 + - - +
62N PRO 3.3 0.2 - - - -
63N GLY* 2.7 18.2 + - - +
64N LEU* 2.9 29.4 + - + +
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Residues in contact with PHE 61 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49N LYS* 3.7 37.7 - - + -
52N TYR* 3.4 39.5 - - + -
55N LEU* 3.2 30.5 - - + +
56N LYS* 3.6 27.1 - - + +
58N ARG 3.0 12.8 + - - +
60N PHE* 1.3 84.3 - - - +
62N PRO* 1.3 73.2 - - + +
64N LEU* 3.1 4.8 + - + +
65N VAL* 3.0 41.2 + - + +
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Residues in contact with PRO 62 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58N ARG 4.0 2.2 - - - +
59N PRO 3.2 18.2 - - - +
60N PHE 3.3 1.8 - - - -
61N PHE* 1.3 102.3 - - + +
63N GLY* 1.3 61.0 + - - +
65N VAL* 3.3 5.4 + - + +
66N LYS* 3.0 23.4 + - - +
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Residues in contact with GLY 63 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60N PHE* 2.7 13.2 + - - +
62N PRO* 1.3 75.9 - - - +
64N LEU* 1.3 50.2 + - - -
66N LYS* 3.1 9.6 + - - +
67N TYR* 2.7 42.8 + - - +
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Residues in contact with LEU 64 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12N LYS* 5.8 4.7 - - - +
52N TYR* 3.6 59.7 - - + +
55N LEU* 4.2 4.0 - - + -
60N PHE* 2.9 42.8 + - + +
61N PHE* 3.4 11.4 - - + +
63N GLY* 1.3 74.9 - - - +
65N VAL* 1.3 55.8 + - - +
67N TYR* 3.1 11.8 - - + +
68N MET* 3.0 40.2 + - + +
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Residues in contact with VAL 65 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45N GLU* 3.4 46.9 - - + +
48N LEU* 3.6 14.3 - - + +
49N LYS* 4.0 14.4 - - + +
52N TYR* 4.8 4.3 - - + -
61N PHE* 3.0 49.4 + - + +
62N PRO* 3.7 7.2 - - + +
64N LEU* 1.3 73.7 - - - +
66N LYS* 1.3 66.9 + - - +
67N TYR 3.3 0.3 + - - -
68N MET* 4.9 0.2 - - - -
69N ASN* 3.3 22.3 + - - +
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Residues in contact with LYS 66 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45N GLU* 4.3 18.1 + - - +
62N PRO 3.0 13.7 + - - +
63N GLY* 3.5 11.0 - - - +
65N VAL* 1.3 75.7 - - - +
67N TYR* 1.3 64.1 + - - +
69N ASN* 3.2 11.2 + - - +
70N SER* 3.2 19.9 + - - -
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Residues in contact with TYR 67 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12N LYS* 6.4 2.2 - - + -
13N PRO* 4.0 7.5 - - + +
14N ASP* 5.0 8.5 - - - -
63N GLY 2.7 21.2 + - - +
64N LEU* 3.1 13.9 - - + +
66N LYS* 1.3 73.7 - - - +
68N MET* 1.3 64.7 + - + +
69N ASN 3.0 3.8 - - - -
70N SER* 2.6 41.9 + - - -
111N GLN* 5.2 0.2 + - - -
113N GLY* 2.5 38.7 + - - -
114N ARG* 2.5 64.0 + - - -
149O TRP* 5.4 1.1 - + - -
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Residues in contact with MET 68 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10N ALA* 5.7 6.7 - - + -
12N LYS* 3.6 38.4 - - + -
13N PRO* 3.8 16.7 - - - +
43N ALA* 4.0 5.4 + - - +
48N LEU* 3.6 34.7 - - + +
51N HIS* 6.2 1.6 - - + +
52N TYR* 3.6 31.0 - - + +
64N LEU* 3.0 22.4 + - + +
65N VAL 3.6 0.2 + - - -
67N TYR* 1.3 84.1 - - + +
69N ASN* 1.3 56.6 + - - +
70N SER 3.5 0.4 - - - -
71N GLY 3.7 11.1 - - - +
73N VAL* 4.2 24.9 - - + +
118N HIS* 5.9 1.6 - - + -
133N TRP* 5.2 7.4 - - + -
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Residues in contact with ASN 69 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42N ARG* 2.9 35.3 + - - +
43N ALA 3.1 24.7 - - - +
44N SER* 3.8 9.0 - - - -
45N GLU* 3.8 27.7 + - + +
48N LEU* 3.8 3.1 - - + -
65N VAL 3.3 16.4 + - - +
66N LYS* 3.6 8.1 + - - +
67N TYR 2.9 1.4 + - - -
68N MET* 1.3 75.8 - - - +
70N SER* 1.3 59.4 + - - +
71N GLY 3.2 4.5 - - - -
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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