Contacts of the helix formed by residues 60 - 71 (chain N) in PDB entry 1KYO
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 LEU 60 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57C ASN* 3.4 28.5 - - - +
60C LEU* 3.7 25.6 - - + -
55N SER* 3.9 13.2 - - - -
57N ASN* 2.8 18.0 + - + +
59N GLU* 1.3 88.7 - - + +
61N ALA* 1.3 54.2 + - - +
62N PHE 3.5 1.8 - - - -
63N SER* 3.2 9.1 + - - -
64N SER* 2.8 34.5 + - - -
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Residues in contact with ALA 61 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54N TYR* 3.7 16.3 - - - +
55N SER 3.1 16.6 + - - +
56N SER 4.2 2.9 - - - +
57N ASN 2.5 22.8 + - - +
58N ILE* 4.2 7.2 - - - +
59N GLU 3.7 1.0 - - - -
60N LEU* 1.3 69.3 - - - +
62N PHE* 1.3 63.4 + - - +
64N SER* 2.8 18.2 + - - -
65N VAL* 3.3 13.0 + - - +
134N CYS 4.1 4.9 - - - +
135N VAL 4.3 2.2 - - - -
136N TYR* 4.2 15.0 - - + -
176N ILE* 4.5 3.1 - - + -
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Residues in contact with PHE 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 ILE 5.0 2.4 + - - +
59N GLU 5.4 1.0 + - - +
60N LEU 3.5 0.4 - - - -
61N ALA* 1.3 76.8 - - - +
63N SER* 1.3 63.0 + - - +
65N VAL* 3.1 15.1 + - - +
66N GLU* 3.2 28.4 + - + +
135N VAL* 3.3 25.7 + - + +
136N TYR* 3.3 26.6 - - + +
137N GLY* 3.9 1.6 - - - -
256N ASN 3.4 21.3 - - - -
257N TYR* 3.3 31.0 - + - -
258N ILE 3.7 2.2 - - - -
259N PRO* 3.6 36.8 - - + -
109O ARG* 3.7 23.3 - - - -
179O LEU* 4.2 5.8 - - + -
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Residues in contact with SER 63 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59N GLU 4.8 5.7 + - - -
60N LEU* 3.2 11.9 + - - -
62N PHE* 1.3 77.3 - - - +
64N SER* 1.3 60.4 + - - +
66N GLU* 3.1 6.5 + - - +
67N HIS* 2.8 29.2 + - - +
109O ARG* 3.0 27.2 + - - +
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Residues in contact with SER 64 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53N HIS 3.8 10.8 - - - -
54N TYR* 3.2 8.7 - - - -
55N SER* 3.1 39.7 + - - -
60N LEU* 2.8 17.5 + - - -
61N ALA 2.8 17.8 + - - -
63N SER* 1.3 72.1 - - - +
65N VAL* 1.3 57.3 + - - +
67N HIS* 3.1 12.1 + - - +
68N ILE* 3.0 33.6 + - - +
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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
----------------------------------------------------------
54N TYR* 3.8 21.8 - - + -
61N ALA 3.4 14.1 - - - +
62N PHE 3.1 8.5 + - - +
63N SER 3.1 0.4 - - - -
64N SER* 1.3 79.3 + - - +
66N GLU* 1.3 60.2 + - + +
68N ILE* 3.1 12.6 + - + +
69N MET* 3.1 19.8 + - - +
79N ARG* 3.6 40.6 - - + +
135N VAL* 4.1 25.4 - - + -
521N HEC 4.2 19.1 - - + +
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Residues in contact with GLU 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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62N PHE* 3.2 22.9 + - + +
63N SER* 3.1 10.4 + - - +
65N VAL* 1.3 75.1 - - + +
67N HIS* 1.3 55.6 + - - +
68N ILE 3.1 0.2 - - - -
69N MET* 2.9 15.1 + - - +
70N ARG* 2.6 72.4 + - - +
79N ARG* 4.6 3.3 + - - -
257N TYR* 3.9 18.7 - - - -
109O ARG* 3.9 20.8 - - - +
179O LEU* 3.4 33.7 - - - +
182O LYS* 5.1 1.3 + - - -
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Residues in contact with HIS 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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177C GLN* 6.1 0.2 - - - -
53N HIS* 4.1 31.3 + - + -
63N SER 2.8 13.8 + - - +
64N SER* 3.1 17.2 + - - +
66N GLU* 1.3 76.0 - - - +
68N ILE* 1.3 57.9 + - - +
70N ARG* 4.9 0.7 - - - +
71N ASP* 2.7 58.0 + - + +
72N VAL* 3.2 8.8 + - + +
85P THR* 4.0 19.2 - - + +
87P ASP* 3.3 31.3 + - - -
88P VAL* 6.1 0.2 - - + -
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Residues in contact with ILE 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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50N MET* 3.8 52.9 - - + +
53N HIS* 3.9 17.5 - - + -
54N TYR* 4.3 13.0 - - + +
64N SER 3.0 16.6 + - - +
65N VAL* 3.2 16.2 - - + +
67N HIS* 1.3 81.0 - - - +
69N MET* 1.3 62.9 + - + +
72N VAL* 3.5 18.5 + - + +
75N GLY* 3.2 43.3 - - - +
78N LEU* 5.1 1.1 - - + -
79N ARG* 4.8 4.0 - - + -
521N HEC 4.8 7.4 - - + -
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Residues in contact with MET 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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65N VAL 3.1 14.4 + - - +
66N GLU* 2.9 19.4 + - - +
68N ILE* 1.3 79.6 - - - +
70N ARG* 1.3 64.0 + - + +
72N VAL 4.7 2.6 - - - +
76N TYR* 4.0 35.4 + - + +
79N ARG* 3.4 49.8 - - + +
80N TYR* 3.4 40.2 - - + +
257N TYR* 4.5 1.6 - - - +
182O LYS* 3.8 14.1 - - - +
261O PRO* 6.0 0.9 - - - +
262O GLU* 5.0 10.8 - - - +
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Residues in contact with ARG 70 (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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66N GLU* 2.6 41.9 + - - +
69N MET* 1.3 78.5 - - + +
71N ASP* 1.3 71.8 + - - +
72N VAL 5.2 0.4 - - - -
109O ARG* 3.7 42.0 + - - +
110O VAL* 4.5 7.1 - - - +
113O ARG* 5.1 1.4 + - - -
178O SER* 3.4 8.3 + - - -
179O LEU* 3.3 28.7 - - - +
258O CYS 2.9 29.2 + - - -
259O ALA 4.0 4.6 + - - -
261O PRO* 4.1 23.0 - - + +
86P ALA* 5.0 4.0 - - - +
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Residues in contact with ASP 71 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67N HIS* 2.7 48.5 + - + +
70N ARG* 1.3 85.7 - - - +
72N VAL* 1.3 63.8 + - - +
73N HIS* 3.4 6.9 + - - -
113O ARG* 3.3 23.0 + - - -
154O TYR* 4.3 10.7 + - - -
85P THR* 4.0 2.8 - - - -
86P ALA* 3.3 28.7 + - - +
87P ASP* 3.5 29.7 - - - +
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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