Contacts of the helix formed by residues 88 - 109 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84F HIS* 3.9 26.5 - - + +
85F PHE* 3.0 14.9 + - + -
86F LYS 3.4 0.2 + - - -
87F ASN* 1.3 81.9 - - - +
89F GLU* 1.3 57.2 + - - +
90F GLU* 3.7 9.6 + - - -
91F GLY 3.0 4.0 + - - -
92F LYS* 2.7 40.0 + - - +
133F TYR* 2.9 24.9 + - - +
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Residues in contact with GLU 89 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88F THR* 1.3 73.1 - - - +
90F GLU* 1.3 64.9 + - + +
92F LYS* 3.6 24.3 + - - +
93F ALA* 2.9 37.4 + - - +
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Residues in contact with GLU 90 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88F THR* 3.7 7.8 - - - -
89F GLU* 1.3 85.8 + - + +
91F GLY* 1.3 67.1 + - - +
93F ALA* 3.4 5.6 + - - +
94F LEU* 3.0 33.5 + - + +
133F TYR* 3.6 34.3 + - + -
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Residues in contact with GLY 91 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85F PHE 3.3 22.7 - - - -
86F LYS* 3.4 9.9 - - - -
88F THR* 3.0 9.1 + - - -
90F GLU* 1.3 79.0 - - - +
92F LYS* 1.3 50.3 + - - +
94F LEU* 3.0 7.4 + - - +
95F VAL* 2.8 37.1 + - - +
130F LEU* 5.3 1.6 - - - -
133F TYR* 3.7 12.0 - - - -
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Residues in contact with LYS 92 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86F LYS 3.3 13.9 + - - +
87F ASN* 4.2 11.9 - - - +
88F THR* 2.7 39.5 + - - +
89F GLU* 3.6 26.1 + - - +
91F GLY* 1.3 69.2 - - - -
93F ALA* 1.3 59.5 + - - +
95F VAL* 3.4 14.0 - - + +
96F HIS* 3.1 27.5 + - - +
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Residues in contact with ALA 93 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89F GLU* 2.9 27.3 + - - +
90F GLU* 3.6 6.7 - - - +
92F LYS* 1.3 77.3 - - - +
94F LEU* 1.3 64.3 + - + +
96F HIS* 3.2 20.9 - - - +
97F HIS* 3.2 24.8 + - + +
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Residues in contact with LEU 94 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90F GLU* 3.0 19.1 + - + +
91F GLY 3.0 8.8 + - - +
93F ALA* 1.3 81.6 - - + +
95F VAL* 1.3 64.3 + - - +
96F HIS 3.0 1.7 + - - -
97F HIS* 3.3 15.9 + - + +
98F TYR* 3.1 21.3 + - - +
126F GLU 5.1 1.7 - - - +
129F HIS* 4.2 14.6 - - + +
130F LEU* 4.3 24.4 - - + +
133F TYR* 3.5 41.1 - - + -
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Residues in contact with VAL 95 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86F LYS* 4.3 20.2 - - + +
91F GLY 2.8 27.8 + - - +
92F LYS* 3.4 17.9 - - + +
94F LEU* 1.3 73.2 - - - +
96F HIS* 1.3 61.3 + - - +
98F TYR* 3.4 10.1 + - + +
99F GLU* 2.9 43.9 + - - +
130F LEU* 4.3 22.9 - - + -
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Residues in contact with HIS 96 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92F LYS 3.1 14.9 + - - +
93F ALA* 3.2 14.1 - - - +
94F LEU 3.0 0.2 - - - -
95F VAL* 1.3 75.8 - - - +
97F HIS* 1.3 77.7 + + - +
99F GLU* 3.0 8.6 + - + +
100F GLU* 2.7 60.2 + - + +
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Residues in contact with HIS 97 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93F ALA* 3.4 22.7 + - + +
94F LEU* 3.3 16.6 + - + +
96F HIS* 1.3 95.8 + + - +
98F TYR* 1.3 62.0 + - - +
100F GLU* 3.7 9.8 + - - +
101F CYS* 3.1 24.1 + - - +
126F GLU* 4.1 14.5 - - + +
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Residues in contact with TYR 98 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201D GLU 5.4 0.5 + - - -
202D PRO 4.2 2.9 + - - -
203D PRO* 3.3 14.6 - - + +
204D ALA* 3.2 24.3 + - - +
94F LEU 3.1 13.4 + - - +
95F VAL* 3.7 11.2 - - - +
97F HIS* 1.3 77.0 - - - +
99F GLU* 1.3 74.6 + - - +
101F CYS* 3.5 0.7 + - - +
102F ALA* 2.8 33.2 + - + +
123F CYS* 3.8 37.2 - - + -
126F GLU* 4.0 16.3 - - + +
127F PHE* 4.1 24.6 - + + -
130F LEU* 4.9 14.6 - - + -
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Residues in contact with GLU 99 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95F VAL* 2.9 32.8 + - - +
96F HIS* 3.4 7.4 - - + +
98F TYR* 1.3 90.3 - - - +
100F GLU* 1.3 57.3 + - - +
101F CYS 3.1 2.0 - - - -
102F ALA* 3.5 8.1 - - + +
103F GLU* 2.7 36.8 + - - +
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Residues in contact with GLU 100 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96F HIS* 2.7 44.8 + - + +
97F HIS* 3.7 11.9 + - - +
99F GLU* 1.3 71.1 - - - +
101F CYS* 1.3 61.2 + - - +
103F GLU* 3.6 8.1 + - - +
104F ARG* 3.2 42.6 + - - +
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Residues in contact with CYS 101 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97F HIS 3.1 14.4 + - - +
98F TYR 3.6 3.4 - - - +
99F GLU 3.1 0.4 - - - -
100F GLU* 1.3 77.5 - - - +
102F ALA* 1.3 63.8 + - - +
103F GLU 3.1 0.2 - - - -
104F ARG* 3.1 25.3 + - - +
105F VAL* 3.1 26.7 + - - +
121F GLU* 3.8 4.9 - - - -
123F CYS* 2.0 47.1 - - + -
126F GLU* 3.4 9.2 - - + -
83H LYS* 3.3 25.8 - - - -
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Residues in contact with ALA 102 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204D ALA* 3.6 26.0 - - + +
98F TYR* 2.8 34.5 + - + +
99F GLU* 3.5 14.4 - - + +
101F CYS* 1.3 71.3 - - - +
103F GLU* 1.3 64.0 + - - +
105F VAL* 3.3 10.6 + - - +
106F LYS* 3.4 13.9 + - - +
123F CYS* 3.6 0.6 - - - -
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Residues in contact with GLU 103 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99F GLU* 2.7 20.7 + - + +
100F GLU* 3.6 8.0 - - - +
102F ALA* 1.3 71.2 - - - +
104F ARG* 1.3 62.5 + - - +
105F VAL 2.9 5.5 + - - -
106F LYS* 3.2 35.9 + - - +
107F ILE* 3.3 31.2 + - + +
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Residues in contact with ARG 104 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100F GLU* 3.2 31.4 + - - +
101F CYS* 3.1 30.0 + - - +
103F GLU* 1.3 79.3 - - - +
105F VAL* 1.3 61.6 + - - +
107F ILE* 3.7 12.9 - - - +
108F GLN* 3.6 24.9 + - + +
121F GLU* 3.5 35.3 + - - +
126F GLU* 4.9 2.4 + - - -
83H LYS* 4.8 1.4 - - - +
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Residues in contact with VAL 105 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204D ALA* 4.0 7.6 - - + -
205D GLY* 3.8 28.3 - - - +
101F CYS* 3.1 16.8 - - - +
102F ALA 3.6 7.0 - - - +
103F GLU 2.9 2.8 + - - -
104F ARG* 1.3 75.2 - - - +
106F LYS* 1.3 56.7 + - - +
107F ILE 2.9 4.3 - - - -
108F GLN* 2.8 27.9 + - + +
109F GLN* 3.2 25.9 + - + +
114F TYR* 4.5 4.5 - - + +
121F GLU* 4.0 25.1 - - + +
123F CYS* 3.6 20.9 - - - -
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Residues in contact with LYS 106 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102F ALA 3.4 7.5 + - - +
103F GLU* 3.2 38.1 + - - +
105F VAL* 1.3 77.1 - - - +
107F ILE* 1.3 65.0 + - + +
108F GLN 3.4 0.2 - - - -
109F GLN* 3.4 24.3 + - - +
110F GLN* 3.1 39.2 + - - +
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Residues in contact with ILE 107 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103F GLU* 3.3 34.8 - - + +
104F ARG* 3.7 12.8 - - - +
105F VAL 2.9 0.8 + - - -
106F LYS* 1.3 88.5 - - + +
108F GLN* 1.3 60.4 + - + +
110F GLN* 3.8 13.3 + - - +
111F GLN* 3.1 29.5 + - + +
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Residues in contact with GLN 108 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104F ARG* 3.6 16.5 + - + +
105F VAL* 2.8 14.3 + - - +
107F ILE* 1.3 80.7 - - + +
109F GLN* 1.3 58.4 + - - +
110F GLN 3.2 0.7 - - - -
111F GLN* 3.1 32.6 + - + +
114F TYR* 3.4 37.2 + - + +
117F LEU* 4.5 11.1 - - + +
119F HIS 5.3 0.7 + - - +
121F GLU* 3.7 39.1 + - - +
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Residues in contact with GLN 109 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205D GLY* 4.8 7.6 + - - -
105F VAL* 3.2 23.8 + - - +
106F LYS* 3.4 28.5 + - - +
107F ILE 3.4 0.2 - - - -
108F GLN* 1.3 77.4 - - - +
110F GLN* 1.3 60.8 + - + +
111F GLN 4.3 1.9 - - - +
114F TYR* 3.7 48.1 + - + +
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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
------------------------------------------------------------
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