Contacts of the helix formed by residues 60 - 71 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55C SER* 3.7 16.2 - - - +
57C ASN* 3.1 14.6 + - + -
59C GLU* 1.3 87.1 - - + +
61C ALA* 1.3 54.4 + - - +
63C SER* 3.3 7.8 + - - -
64C SER* 2.7 38.6 + - - -
57N ASN* 3.2 28.9 - - + +
60N LEU* 3.7 25.6 - - + -
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Residues in contact with ALA 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C TYR* 3.8 13.7 - - - +
55C SER 3.2 18.3 + - - +
56C SER 4.2 2.7 - - - +
57C ASN 2.6 24.3 + - - +
58C ILE* 4.2 6.7 - - - +
59C GLU 3.4 1.4 - - - -
60C LEU* 1.3 71.4 - - - +
62C PHE* 1.3 64.4 + - - +
64C SER* 2.6 22.1 + - - -
65C VAL* 3.1 10.3 + - - +
134C CYS 3.8 6.3 - - - +
135C VAL 4.3 1.6 - - - -
136C TYR* 4.2 14.1 - - + -
176C ILE* 4.7 2.2 - - + -
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Residues in contact with PHE 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58C ILE 5.1 1.2 + - - +
59C GLU 4.8 2.3 + - - +
60C LEU 3.7 0.2 - - - -
61C ALA* 1.3 78.6 - - - +
63C SER* 1.3 60.4 + - - +
65C VAL* 3.3 7.7 + - - +
66C GLU* 3.1 41.2 + - + +
135C VAL* 3.3 25.2 + - + +
136C TYR* 3.6 25.1 - - + +
137C GLY* 4.0 2.7 - - - -
256C ASN 3.9 13.0 - - - -
257C TYR* 3.3 36.1 - + - -
258C ILE 3.8 3.6 - - - -
259C PRO* 3.7 32.5 - - + -
109D ARG* 3.8 28.9 - - - -
179D LEU* 4.0 6.5 - - + -
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Residues in contact with SER 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C GLU 3.6 14.9 + - - -
60C LEU* 3.7 7.9 - - - -
61C ALA 3.1 0.6 - - - -
62C PHE* 1.3 73.9 - - - +
64C SER* 1.3 61.7 + - - +
66C GLU* 3.1 6.9 + - - +
67C HIS* 2.7 27.7 + - - +
109D ARG* 3.5 25.9 + - - +
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Residues in contact with SER 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C HIS 3.8 11.4 - - - -
54C TYR* 3.4 8.3 - - - -
55C SER* 3.2 35.6 + - - -
60C LEU* 2.7 20.0 + - - -
61C ALA 2.6 17.8 + - - -
63C SER* 1.3 72.5 - - - +
65C VAL* 1.3 57.3 + - - +
67C HIS* 3.0 13.1 + - - +
68C ILE* 2.9 32.2 + - - +
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Residues in contact with VAL 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C TYR* 3.7 26.9 - - + -
61C ALA 3.1 15.6 + - - +
62C PHE* 3.6 8.1 - - - +
64C SER* 1.3 77.7 + - - +
66C GLU* 1.3 56.1 + - + +
68C ILE* 2.9 13.9 + - + +
69C MET* 2.8 29.9 + - - +
79C ARG* 3.8 39.0 - - + +
135C VAL* 4.4 17.0 - - + -
501C HEC 3.9 25.6 - - + +
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Residues in contact with GLU 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62C PHE* 3.1 35.1 + - + +
63C SER* 3.1 11.6 + - - +
65C VAL* 1.3 75.8 - - - +
67C HIS* 1.3 56.3 + - - +
69C MET* 3.3 18.5 + - - +
70C ARG* 2.9 76.7 + - - +
79C ARG* 4.7 3.9 + - - +
257C TYR* 3.8 14.9 - - - -
109D ARG* 4.2 12.8 - - + +
179D LEU* 3.5 25.4 - - + +
182D LYS* 4.9 1.2 + - - -
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Residues in contact with HIS 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C HIS* 3.9 29.6 + - + +
63C SER 2.7 12.1 + - - +
64C SER* 3.0 19.5 + - - +
66C GLU* 1.3 76.7 - - - +
68C ILE* 1.3 59.8 + - - +
69C MET 3.1 0.2 - - - -
71C ASP* 2.8 60.1 + - + +
72C VAL* 3.3 14.3 + - + +
85E THR* 4.0 12.8 + - + +
87E ASP* 3.6 29.9 + - - -
88E VAL* 6.1 0.4 - - + -
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Residues in contact with ILE 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50C MET* 4.0 52.9 - - + +
53C HIS* 3.7 21.5 - - + -
54C TYR* 4.4 11.7 - - + +
64C SER 2.9 20.6 + - - +
65C VAL* 2.9 17.2 + - + +
67C HIS* 1.3 77.3 - - - +
69C MET* 1.3 61.8 + - - +
70C ARG 3.5 0.7 + - - -
72C VAL* 3.5 18.9 - - + +
75C GLY* 3.2 38.0 - - - +
78C LEU* 5.3 1.3 - - + -
79C ARG* 4.9 4.0 - - + -
501C HEC 4.7 7.2 - - + -
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Residues in contact with MET 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65C VAL* 2.8 17.7 + - + +
66C GLU* 3.4 29.6 - - - +
67C HIS 3.1 0.2 - - - -
68C ILE* 1.3 79.7 - - - +
70C ARG* 1.3 61.8 + - + +
72C VAL 5.3 1.0 - - - +
76C TYR* 4.0 33.8 + - + +
79C ARG* 3.7 42.4 - - + +
80C TYR* 3.3 39.5 - - + +
257C TYR* 4.3 4.3 - - - +
182D LYS* 3.8 14.4 - - - +
261D PRO* 5.4 1.4 - - - +
262D GLU* 4.7 13.5 - - - +
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Residues in contact with ARG 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66C GLU* 2.9 45.0 + - - +
68C ILE 3.3 0.2 - - - -
69C MET* 1.3 83.5 - - + +
71C ASP* 1.3 76.0 + - - +
72C VAL 3.6 3.8 - - - +
73C HIS* 6.1 0.2 - - - -
109D ARG* 4.0 35.1 + - - +
110D VAL* 4.5 7.7 - - - +
178D SER* 3.8 5.7 + - - -
179D LEU* 3.5 21.6 - - - +
258D CYS 2.8 29.1 + - - -
259D ALA 4.0 6.1 + - - -
261D PRO* 4.2 24.3 - - + +
86E ALA* 5.1 3.1 - - - +
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Residues in contact with ASP 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67C HIS* 2.8 44.0 + - + +
70C ARG* 1.3 84.7 - - - +
72C VAL* 1.3 62.7 + - - +
73C HIS* 3.3 10.9 + - - -
113D ARG* 3.2 23.4 + - - -
154D TYR* 4.1 9.9 + - - -
85E THR* 3.7 4.1 - - - +
86E ALA* 3.3 26.6 + - - +
87E ASP* 3.5 31.3 - - - +
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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