Contacts of the helix formed by residues 76 - 87 (chain Q) 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 76 (chain Q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196O THR* 6.0 0.3 - - - +
231O ASP* 3.3 24.7 + - - +
243O THR* 3.7 5.5 - - - -
244O THR* 3.4 20.6 + - + +
245O SER* 2.7 39.1 + - - -
75Q THR* 1.3 74.8 + - - +
77Q GLN* 1.3 62.8 + - - +
78Q LEU* 3.3 11.5 + - - +
79Q GLU* 3.2 35.9 + - + +
80Q ASP* 3.2 21.9 + - - +
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Residues in contact with GLN 77 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241O PRO* 5.1 5.2 - - - +
243O THR* 2.5 38.5 + - - +
245O SER* 3.1 11.5 + - - -
246O GLN* 4.9 2.6 - - - +
75Q THR 4.4 4.3 - - - +
76Q ASP* 1.3 72.1 - - - +
78Q LEU* 1.3 60.0 + - - +
80Q ASP* 3.9 7.5 - - - +
81Q LEU* 3.4 27.9 + - - +
142Q LEU* 3.9 15.9 - - + -
145Q LYS* 4.0 33.7 - - + +
146Q LEU* 3.4 14.8 - - + +
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Residues in contact with LEU 78 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74O TYR* 4.3 6.3 - - + +
192O PHE* 4.4 9.9 - - + -
196O THR* 3.6 29.8 - - + +
245O SER* 3.8 11.2 + - - -
76Q ASP* 3.3 12.4 + - - +
77Q GLN* 1.3 77.5 - - - +
79Q GLU* 1.3 59.4 + - - +
81Q LEU* 3.6 1.5 + - + +
82Q ARG* 3.0 76.2 + - - +
138Q THR* 4.1 27.4 - - - +
142Q LEU* 3.9 22.4 - - + +
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Residues in contact with GLU 79 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227O ARG* 6.3 0.7 - - - +
244O THR* 6.2 0.7 - - + -
75Q THR* 5.2 4.0 - - - +
76Q ASP* 3.2 29.1 + - + +
78Q LEU* 1.3 75.4 - - - +
80Q ASP* 1.3 65.3 + - - +
81Q LEU 3.1 0.2 - - - -
82Q ARG* 3.1 30.6 + - - +
83Q GLU* 2.9 35.3 + - - +
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Residues in contact with ASP 80 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75Q THR* 3.4 31.5 + - + +
76Q ASP 3.2 11.6 + - - +
77Q GLN* 3.9 9.4 - - - +
79Q GLU* 1.3 77.4 - - - +
81Q LEU* 1.3 59.9 + - + +
83Q GLU* 3.6 6.3 + - - +
84Q HIS* 3.2 25.3 + - - +
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Residues in contact with LEU 81 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77Q GLN 3.4 19.3 + - - +
78Q LEU* 3.9 2.5 - - + +
79Q GLU 3.1 0.6 - - - -
80Q ASP* 1.3 79.0 - - + +
82Q ARG* 1.3 64.2 + - - +
83Q GLU 3.1 2.0 - - - -
84Q HIS* 4.0 8.7 - - + +
85Q PHE* 3.1 55.8 + - + +
138Q THR* 3.8 18.2 - - + -
141Q ARG* 4.3 15.0 - - + -
142Q LEU* 4.1 30.5 - - + +
145Q LYS* 4.1 28.9 - - + +
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Residues in contact with ARG 82 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74O TYR* 4.5 4.8 + - - -
193O SER* 6.1 0.4 - - - +
196O THR* 4.1 20.6 + - - -
197O GLY* 4.8 7.3 - - - -
217O TYR* 4.0 9.5 + - - -
78Q LEU* 3.0 65.8 + - + +
79Q GLU* 3.1 26.3 + - - +
81Q LEU* 1.3 76.1 - - - +
83Q GLU* 1.3 57.3 + - - +
85Q PHE* 3.8 2.6 - - - -
86Q LYS* 3.0 39.1 + - + +
131Q GLN* 3.6 31.1 - - - +
134Q LEU* 4.1 21.7 - - + +
135Q ASP* 4.2 5.7 + - - -
138Q THR* 4.5 11.8 + - + -
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Residues in contact with GLU 83 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79Q GLU* 2.9 23.9 + - - +
80Q ASP* 3.7 7.4 - - - +
82Q ARG* 1.3 75.0 - - - +
84Q HIS* 1.3 66.1 + - - +
85Q PHE 3.1 1.1 - - - -
86Q LYS* 3.1 28.5 + - - +
87Q ASN* 3.3 41.5 + - - +
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Residues in contact with HIS 84 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80Q ASP 3.2 14.2 + - - +
81Q LEU* 4.0 9.0 - - + +
83Q GLU* 1.3 79.8 - - - +
85Q PHE* 1.3 94.4 + + - +
87Q ASN* 3.5 12.0 + - - +
88Q THR* 3.4 17.6 - - + +
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Residues in contact with PHE 85 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81Q LEU* 3.1 40.9 + - + +
82Q ARG* 5.0 0.2 - - - -
84Q HIS* 1.3 99.7 - + - +
86Q LYS* 1.3 64.0 + - - +
87Q ASN 3.1 2.0 + - - -
88Q THR* 3.5 27.8 + - + -
91Q GLY* 3.6 1.7 - - - -
133Q TYR* 3.5 29.4 - - + -
134Q LEU* 3.8 15.7 - - + -
137Q ALA* 3.7 29.4 - - + -
138Q THR* 4.5 5.2 - - + -
141Q ARG* 3.5 40.6 - - - -
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Residues in contact with LYS 86 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82Q ARG* 3.0 25.2 + - + +
83Q GLU* 3.1 29.3 + - - +
85Q PHE* 1.3 78.0 - - - +
87Q ASN* 1.3 61.0 + - - +
88Q THR 3.5 0.4 - - - -
91Q GLY* 3.3 24.6 - - - +
92Q LYS* 3.4 6.8 + - - +
95Q VAL* 4.3 25.7 - - + +
130Q LEU* 5.0 9.6 - - - +
134Q LEU* 4.1 24.7 - - + -
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Residues in contact with ASN 87 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83Q GLU* 3.3 39.9 + - - +
84Q HIS* 3.5 6.6 + - - +
85Q PHE 3.1 0.6 - - - -
86Q LYS* 1.3 81.6 - - - +
88Q THR* 1.3 63.0 + - - +
92Q LYS* 3.8 29.1 + - - +
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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