Contacts of the helix formed by residues 88 - 111 (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 THR 88 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84Q HIS* 3.4 27.4 - - + +
85Q PHE* 3.5 27.7 + - + +
86Q LYS 3.5 1.4 - - - -
87Q ASN* 1.3 78.1 - - - +
89Q GLU* 1.3 56.6 + - - +
90Q GLU* 3.7 4.9 + - - -
91Q GLY 3.0 10.4 + - - -
92Q LYS* 2.7 36.6 + - - +
133Q TYR* 3.0 20.3 + - - -
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Residues in contact with GLU 89 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88Q THR* 1.3 74.1 - - - +
90Q GLU* 1.3 72.7 + - - +
92Q LYS* 3.9 12.7 + - - +
93Q ALA* 3.0 30.2 + - - +
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Residues in contact with GLU 90 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88Q THR* 3.4 2.8 + - - -
89Q GLU* 1.3 88.0 + - + +
91Q GLY* 1.3 59.1 + - - +
93Q ALA* 3.7 6.1 - - - +
94Q LEU* 2.9 41.2 + - + +
133Q TYR* 3.6 38.4 + - + -
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Residues in contact with GLY 91 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85Q PHE 3.6 15.7 - - - -
86Q LYS* 3.3 16.8 - - - -
88Q THR* 3.0 13.7 + - - -
90Q GLU* 1.3 78.0 - - - +
92Q LYS* 1.3 56.0 + - - +
94Q LEU* 3.7 2.1 - - - +
95Q VAL* 3.0 34.8 + - - +
130Q LEU* 5.9 0.4 - - - -
133Q TYR* 3.8 10.5 - - - -
134Q LEU* 5.5 0.7 - - - -
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Residues in contact with LYS 92 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86Q LYS 3.4 8.7 + - - +
87Q ASN* 3.8 31.9 + - - +
88Q THR 2.7 26.5 + - - +
89Q GLU* 4.1 12.0 + - - +
91Q GLY* 1.3 69.6 - - - +
93Q ALA* 1.3 60.2 + - - +
95Q VAL* 3.3 12.3 - - + +
96Q HIS* 3.0 28.1 + - - +
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Residues in contact with ALA 93 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89Q GLU* 3.0 23.3 + - - +
90Q GLU* 3.7 7.0 - - - +
92Q LYS* 1.3 74.8 - - - +
94Q LEU* 1.3 62.8 + - + +
96Q HIS* 3.1 9.6 + - - +
97Q HIS* 3.0 43.8 + - + +
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Residues in contact with LEU 94 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90Q GLU* 2.9 25.7 + - + +
91Q GLY* 3.7 3.8 - - - +
93Q ALA* 1.3 80.4 - - + +
95Q VAL* 1.3 64.3 + - - +
97Q HIS* 3.5 15.3 + - + +
98Q TYR* 3.1 22.3 + - - +
126Q GLU* 4.9 2.1 - - - +
129Q HIS* 3.9 20.9 - - + +
130Q LEU* 4.2 18.9 - - + +
133Q TYR* 3.4 42.6 - - + -
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Residues in contact with VAL 95 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86Q LYS* 4.3 24.2 - - + +
91Q GLY 3.0 18.2 + - - +
92Q LYS* 3.3 23.1 - - + +
94Q LEU* 1.3 73.0 - - - +
96Q HIS* 1.3 59.4 + - - +
98Q TYR* 3.2 9.4 + - + +
99Q GLU* 2.7 54.1 + - - +
130Q LEU* 4.0 28.3 - - + -
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Residues in contact with HIS 96 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92Q LYS 3.0 16.5 + - - +
93Q ALA* 3.1 10.9 + - - +
95Q VAL* 1.3 78.8 - - - +
97Q HIS* 1.3 66.8 + + - +
99Q GLU* 3.0 11.4 + - + -
100Q GLU* 2.7 63.0 + - + +
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Residues in contact with HIS 97 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93Q ALA* 3.0 34.2 + - + +
94Q LEU* 3.9 17.0 - - + +
96Q HIS* 1.3 90.1 + + - +
98Q TYR* 1.3 61.6 + - - +
100Q GLU* 3.5 15.0 + - - +
101Q CYS* 3.3 20.8 + - - +
104Q ARG* 5.3 0.9 + - - -
126Q GLU* 4.3 12.5 - - + +
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Residues in contact with TYR 98 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202O PRO 4.7 0.9 + - - -
203O PRO* 3.4 8.2 - - + +
204O ALA* 3.1 25.0 + - - +
94Q LEU 3.1 14.6 + - - +
95Q VAL* 3.4 11.9 - - + +
96Q HIS 3.1 0.4 - - - -
97Q HIS* 1.3 78.2 - - - +
99Q GLU* 1.3 68.0 + - + +
101Q CYS* 3.0 18.5 + - - +
102Q ALA* 3.0 21.7 + - + +
123Q CYS* 3.7 38.1 - - + -
126Q GLU* 4.0 16.3 - - + +
127Q PHE* 3.9 27.5 - + + -
130Q LEU* 4.6 15.9 - - + -
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Residues in contact with GLU 99 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95Q VAL* 2.7 37.9 + - - +
96Q HIS* 3.7 11.1 - - + +
98Q TYR* 1.3 80.1 - - + +
100Q GLU* 1.3 64.5 + - - +
101Q CYS 3.1 2.0 - - - -
102Q ALA* 3.9 8.2 - - + +
103Q GLU* 3.2 26.3 + - - +
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Residues in contact with GLU 100 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96Q HIS* 2.7 46.5 + - - +
97Q HIS* 3.9 15.6 + - - +
99Q GLU* 1.3 73.0 - - - +
101Q CYS* 1.3 61.5 + - - +
103Q GLU* 3.9 16.7 - - - +
104Q ARG* 3.4 34.6 + - - +
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Residues in contact with CYS 101 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97Q HIS 3.3 11.7 + - - +
98Q TYR* 3.0 10.6 + - - +
100Q GLU* 1.3 76.1 - - - +
102Q ALA* 1.3 59.2 + - - +
103Q GLU 3.1 1.6 - - - -
104Q ARG* 2.8 36.0 + - - +
105Q VAL* 3.0 15.7 + - - +
121Q GLU* 3.6 23.1 - - - -
123Q CYS* 2.0 48.2 - - + -
126Q GLU* 3.5 18.8 - - - -
83S LYS* 3.7 0.7 - - - -
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Residues in contact with ALA 102 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204O ALA* 3.5 30.4 - - + +
98Q TYR* 3.0 25.3 + - + +
99Q GLU* 4.0 9.6 - - + +
101Q CYS* 1.3 74.6 - - - +
103Q GLU* 1.3 56.1 + - - +
105Q VAL* 3.2 3.1 + - - +
106Q LYS* 2.9 30.8 + - - +
123Q CYS* 3.3 0.8 - - - -
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Residues in contact with GLU 103 (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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99Q GLU 3.2 18.1 + - - +
100Q GLU* 3.9 16.7 - - - +
102Q ALA* 1.3 79.0 - - - +
104Q ARG* 1.3 60.6 + - - +
105Q VAL 3.6 0.2 + - - -
106Q LYS* 3.8 12.2 + - + +
107Q ILE* 3.3 28.2 + - + +
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Residues in contact with ARG 104 (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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97Q HIS 5.3 1.0 + - - -
100Q GLU* 3.4 32.8 + - - +
101Q CYS* 2.8 30.7 + - - +
103Q GLU* 1.3 81.2 - - - +
105Q VAL* 1.3 58.4 + - - +
107Q ILE* 3.6 13.1 - - + +
108Q GLN* 3.6 30.5 + - + +
121Q GLU* 3.4 33.2 + - - +
126Q GLU* 4.4 6.5 + - - -
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Residues in contact with VAL 105 (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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204O ALA* 4.4 7.2 - - + +
205O GLY* 4.1 11.0 - - - +
101Q CYS* 3.0 17.4 + - - +
102Q ALA 3.6 4.7 - - - +
104Q ARG* 1.3 75.6 - - + +
106Q LYS* 1.3 66.5 + - - +
107Q ILE 3.0 2.0 - - - -
108Q GLN* 2.9 26.5 + - - +
109Q GLN* 3.1 34.8 + - - +
114Q TYR* 4.0 11.2 - - + +
121Q GLU* 3.6 30.1 - - + +
123Q CYS* 3.4 21.3 - - - -
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Residues in contact with LYS 106 (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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102Q ALA 2.9 16.9 + - - +
103Q GLU* 3.9 12.7 - - + +
104Q ARG 3.5 0.2 - - - -
105Q VAL* 1.3 76.1 - - - +
107Q ILE* 1.3 66.2 + - + +
109Q GLN* 3.4 27.3 + - - +
110Q GLN* 3.7 30.2 - - - +
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Residues in contact with ILE 107 (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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103Q GLU* 3.3 22.2 + - + +
104Q ARG* 3.6 13.7 - - - +
105Q VAL 3.0 0.4 - - - -
106Q LYS* 1.3 80.5 - - + +
108Q GLN* 1.3 65.9 + - + +
110Q GLN* 3.0 26.1 + - - +
111Q GLN* 3.0 36.0 + - - +
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Residues in contact with GLN 108 (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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104Q ARG* 3.6 23.2 + - + +
105Q VAL* 2.9 17.3 + - - +
107Q ILE* 1.3 81.0 - - + +
109Q GLN* 1.3 60.0 + - - +
110Q GLN 3.3 0.7 + - - -
111Q GLN* 3.4 27.2 + - - +
114Q TYR* 3.3 41.5 - - + +
117Q LEU* 4.7 8.8 - - + +
119Q HIS 5.4 0.3 - - - +
120Q LYS* 4.4 2.6 - - - -
121Q GLU* 3.7 41.0 + - - +
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Residues in contact with GLN 109 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205O GLY* 4.4 11.8 + - - -
105Q VAL* 3.1 28.0 + - - +
106Q LYS* 3.6 21.4 + - - +
107Q ILE 3.1 0.2 - - - -
108Q GLN* 1.3 76.8 - - - +
110Q GLN* 1.3 61.4 + - + +
111Q GLN 4.4 0.2 - - - +
114Q TYR* 3.5 43.9 + - + +
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Residues in contact with GLN 110 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106Q LYS* 3.7 41.7 + - - +
107Q ILE* 3.0 13.9 + - - +
109Q GLN* 1.3 76.5 - - + +
111Q GLN* 1.3 72.6 + - - +
112Q PRO* 4.6 0.2 - - - +
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Residues in contact with GLN 111 (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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107Q ILE* 3.0 38.8 - - + +
108Q GLN* 3.4 19.6 + - - +
109Q GLN 4.4 0.2 - - - +
110Q GLN* 1.3 87.8 - - + +
112Q PRO* 1.3 81.6 - - + +
113Q GLY 3.1 4.2 + - - -
114Q TYR* 3.7 10.8 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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