Contacts of the helix formed by residues 65 - 73 (chain W) 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 ASP 65 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41W PHE* 3.3 12.5 - - - -
63W LEU* 3.1 7.5 - - + +
64W TRP* 1.3 76.7 - - - +
66W GLU* 1.3 65.3 + - - +
67W ASN* 3.8 18.0 + - - +
68W ASN* 2.9 37.9 + - - +
69W MET* 2.9 28.6 + - - +
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Residues in contact with GLU 66 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3W PHE* 3.3 51.8 - - + +
41W PHE* 3.9 26.6 - - - -
65W ASP* 1.3 78.6 - - - +
67W ASN* 1.3 57.9 + - - +
69W MET* 4.3 0.4 - - - -
70W SER* 3.1 28.9 + - - -
100W ILE* 3.3 15.4 - - + +
104W LYS* 2.7 33.3 + - - +
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Residues in contact with ASN 67 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1W THR* 3.8 10.0 + - - -
2W GLU* 3.4 60.3 + - - +
3W PHE* 4.5 5.0 - - - +
65W ASP* 3.2 13.4 + - - +
66W GLU* 1.3 78.4 - - - +
68W ASN* 1.3 63.4 + - - +
70W SER* 4.0 4.4 - - - -
71W GLU* 3.6 21.8 + - - +
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Residues in contact with ASN 68 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62W VAL* 3.4 9.0 - - - +
63W LEU* 2.8 24.9 + - - +
64W TRP* 3.8 17.8 - - + -
65W ASP* 2.9 20.3 + - - +
67W ASN* 1.3 76.9 - - - +
69W MET* 1.3 61.0 + - - +
70W SER 3.3 0.4 - - - -
71W GLU* 3.1 5.9 + - - +
72W TYR* 2.9 31.2 + - - +
79W TYR* 3.0 24.3 + - - +
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Residues in contact with MET 69 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40W ILE* 4.5 12.3 - - + -
41W PHE* 3.8 31.6 - - + -
64W TRP* 3.8 38.5 - - + -
65W ASP 2.9 15.0 + - - +
66W GLU 3.8 0.2 - - - +
68W ASN* 1.3 77.6 - - - +
70W SER* 1.3 56.2 + - - +
72W TYR* 3.7 3.0 - - - +
73W LEU* 3.0 47.5 + - + +
100W ILE* 3.7 26.9 - - + -
103W LEU* 4.7 11.4 - - + -
526W HEC 4.0 26.9 - - + -
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Residues in contact with SER 70 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2W GLU 4.6 12.9 + - - -
3W PHE* 5.2 2.5 - - - -
66W GLU 3.1 19.1 + - - -
67W ASN* 4.3 7.0 - - - -
68W ASN 3.3 0.4 - - - -
69W MET* 1.3 75.6 - - - +
71W GLU* 1.3 60.6 + - - +
72W TYR 3.5 0.2 - - - -
73W LEU* 4.1 0.7 - - - -
74W THR* 2.9 19.6 + - - -
93W GLU* 4.9 2.6 + - - -
96W ARG* 3.1 44.6 + - - +
97W ASN* 5.2 2.9 + - - -
100W ILE* 3.3 13.6 - - - +
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Residues in contact with GLU 71 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2W GLU* 5.2 5.5 - - - +
67W ASN* 3.6 18.2 + - - +
68W ASN* 3.1 7.9 + - - +
70W SER* 1.3 79.6 - - - +
72W TYR* 1.3 63.8 + - - +
73W LEU 3.5 0.2 - - - -
74W THR* 3.3 37.6 + - - +
75W ASN* 4.1 2.8 + - - +
78W LYS* 5.9 1.9 - - - +
79W TYR* 4.0 22.9 - - + +
96W ARG* 5.3 3.7 + - - -
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Residues in contact with TYR 72 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57W ASN* 4.6 0.5 + - - -
64W TRP* 4.0 12.1 - + + -
68W ASN 2.9 15.8 + - - +
69W MET* 3.4 4.9 + - - +
71W GLU* 1.3 77.0 - - - +
73W LEU* 1.3 65.7 + - + +
74W THR 3.1 4.0 - - - -
75W ASN 3.0 5.5 - - - -
76W PRO* 2.7 62.7 - - + +
79W TYR* 3.5 30.5 - + + -
80W ILE* 3.6 17.9 - - + -
83W THR* 3.7 13.6 + - - -
85W MET* 3.5 18.5 - - + +
526W HEC 3.3 63.7 - + + +
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Residues in contact with LEU 73 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69W MET* 3.0 36.6 + - + +
70W SER* 5.1 0.2 - - - -
71W GLU 3.5 0.2 - - - -
72W TYR* 1.3 91.0 - - + +
74W THR* 1.3 59.2 + - - +
75W ASN 3.2 0.4 - - - -
76W PRO* 4.0 3.6 - - + -
85W MET* 4.4 12.3 - - + -
87W PHE* 4.8 1.1 - - + -
89W GLY* 3.2 6.9 - - - -
90W LEU* 3.0 31.1 + - + +
96W ARG* 4.3 19.7 - - + -
99W LEU* 3.5 28.7 - - + -
100W ILE* 4.2 9.0 - - + -
103W LEU* 6.3 0.7 - - + -
526W HEC 4.0 33.0 - - + -
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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