Contacts of the helix formed by residues 86 - 100 (chain D) 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 86 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77D SER* 3.6 24.1 + - - +
84D THR 3.9 0.2 + - - -
85D PHE* 1.3 71.6 - - - +
87D HIS* 1.3 54.8 + - - +
88D ALA* 3.0 22.7 + - - +
89D SER* 2.7 48.2 + - - -
90D ILE* 3.0 12.4 + - - +
249D LYS* 3.9 10.4 + - - -
253D THR* 4.4 4.2 - - + +
147F LYS* 3.9 12.7 + - - +
46I GLY 4.0 2.8 - - - +
47I LYS* 3.7 29.4 - - + +
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Residues in contact with HIS 87 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84D THR* 5.3 0.4 - - - -
85D PHE* 3.6 16.6 + - + +
86D ASP* 1.3 70.7 - - - +
88D ALA* 1.3 60.3 + - - +
89D SER 3.2 0.2 - - - -
90D ILE* 3.5 24.1 - - + +
91D ARG* 3.0 23.9 + - - +
117D GLY 5.1 1.1 - - - -
118D VAL* 3.1 41.2 + - + +
119D SER* 4.7 1.2 - - - -
257D TRP* 6.0 1.0 - - - -
264D ASP* 2.7 27.4 + - - -
47I LYS 3.0 20.9 + - - +
48I LEU* 4.3 10.0 - - + +
49I TRP* 3.6 26.4 + - + +
52I VAL* 4.2 6.5 - - + +
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Residues in contact with ALA 88 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86D ASP* 3.0 16.7 + - - +
87D HIS* 1.3 78.4 - - - +
89D SER* 1.3 62.4 + - - +
91D ARG* 3.4 5.0 + - - +
92D ARG* 3.3 29.4 + - - +
147F LYS* 3.7 20.9 - - - +
46I GLY 4.9 0.2 - - - +
52I VAL* 3.6 29.9 - - + +
55I LYS* 4.9 8.1 - - + +
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Residues in contact with SER 89 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86D ASP* 2.7 28.3 + - - -
88D ALA* 1.3 79.6 - - - +
90D ILE* 1.3 58.7 + - - -
92D ARG* 3.3 14.8 + - - +
93D GLY* 2.8 26.2 + - - -
249D LYS* 3.7 13.1 + - - +
250D ASP* 2.6 34.3 + - - +
253D THR* 3.7 15.6 + - - -
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Residues in contact with ILE 90 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85D PHE* 3.7 16.6 - - + -
86D ASP 3.0 11.0 + - - +
87D HIS* 3.5 39.7 - - + +
88D ALA 3.3 0.2 - - - -
89D SER* 1.3 76.5 - - - +
91D ARG* 1.3 63.5 + - - +
93D GLY* 3.0 3.1 + - - -
94D TYR* 3.0 19.1 + - - +
118D VAL* 4.5 9.9 - - + -
119D SER* 3.7 20.6 - - - -
253D THR* 4.1 16.4 - - + +
254D PHE* 3.9 26.2 - - + +
257D TRP* 4.0 30.7 - - + -
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Residues in contact with ARG 91 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87D HIS 3.0 12.8 + - - +
88D ALA 3.5 10.1 - - - +
89D SER 3.2 0.2 - - - -
90D ILE* 1.3 72.9 - - - +
92D ARG* 1.3 67.4 + - + +
94D TYR* 3.0 15.9 + - - +
95D GLN* 3.4 9.2 + - - +
119D SER* 2.7 45.4 + - - +
120D HIS* 3.0 40.0 + - - +
124D GLU* 2.8 30.0 + - - -
237D GLU* 3.1 30.1 + - - +
49I TRP* 4.3 4.6 - - - -
52I VAL* 4.5 18.2 - - - -
56I ILE* 4.5 23.2 - - - +
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Residues in contact with ARG 92 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88D ALA* 3.3 13.4 + - - +
89D SER* 3.3 16.3 + - - +
91D ARG* 1.3 80.6 - - + +
93D GLY* 1.3 62.1 + - - +
95D GLN* 3.1 12.1 + - - +
96D VAL* 3.1 26.9 + - - +
236D TYR* 3.6 26.3 - - + -
237D GLU 6.1 0.7 - - - +
238D ASP* 3.1 39.5 + - - +
240D THR* 4.2 1.3 - - - +
246D GLN* 3.5 4.0 - - - +
250D ASP* 2.7 41.1 + - - +
147F LYS* 2.9 68.4 + - - +
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Residues in contact with GLY 93 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89D SER 2.8 15.0 + - - -
90D ILE 3.0 6.4 + - - -
92D ARG* 1.3 74.9 - - - +
94D TYR* 1.3 65.2 + - - +
96D VAL* 3.2 4.7 + - - +
97D TYR* 3.0 21.8 + - - +
250D ASP* 3.8 16.1 - - - +
251D VAL* 3.8 6.1 - - - +
254D PHE* 3.6 19.5 - - - -
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Residues in contact with TYR 94 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90D ILE 3.0 10.0 + - - +
91D ARG 3.0 9.5 + - - +
93D GLY* 1.3 72.8 - - - +
95D GLN* 1.3 55.2 + - - +
97D TYR* 2.9 20.6 + + - +
98D ARG* 2.8 79.4 + - + +
112D TRP* 3.2 17.0 - + - -
115D LEU* 4.2 14.6 - - + -
119D SER* 5.2 1.1 - - - +
120D HIS* 3.7 30.5 - + + -
128D MET* 3.3 26.4 - - - +
155D ILE* 4.4 14.4 - - + -
254D PHE* 3.7 31.1 - + + -
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Residues in contact with GLN 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91D ARG 3.4 4.9 + - - +
92D ARG* 3.1 14.2 + - - +
94D TYR* 1.3 83.0 - - - +
96D VAL* 1.3 62.5 + - - +
98D ARG* 3.2 6.1 + - + +
99D GLU* 3.0 49.6 + - + +
234D VAL* 3.2 23.4 - - + +
235D GLU 3.1 24.7 + - - +
236D TYR* 3.9 7.7 - - + -
237D GLU* 3.7 26.8 + - - +
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Residues in contact with VAL 96 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92D ARG 3.1 18.3 + - - +
93D GLY* 3.2 4.0 + - - +
95D GLN* 1.3 75.0 - - - +
97D TYR* 1.3 60.8 + - - +
100D VAL* 3.1 25.8 + - + +
101D CYS* 3.5 2.8 + - - -
229D LEU* 4.3 14.8 - - + -
234D VAL* 4.6 8.3 - - + -
236D TYR* 3.3 31.0 - - + +
247D MET* 4.1 21.5 - - + -
250D ASP* 4.3 4.7 - - + -
251D VAL* 3.5 31.0 - - + -
503D HEC 4.8 2.5 - - + -
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Residues in contact with TYR 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93D GLY 3.0 5.6 + - - +
94D TYR* 2.9 20.5 + + - +
96D VAL* 1.3 78.3 - - - +
98D ARG* 1.3 80.2 + - - +
101D CYS* 3.2 24.3 + - + -
102D ALA* 2.6 54.8 + - + +
105D HIS* 2.6 33.7 + - + -
106D SER* 3.8 1.9 - - - -
107D LEU* 3.8 39.8 + - + +
155D ILE* 4.4 7.3 - - + +
156D PRO 4.9 3.3 + - - -
158D PRO* 5.5 0.3 - - - +
177D LEU* 5.1 2.2 - - + -
251D VAL* 3.8 3.1 - - + +
254D PHE* 3.6 32.8 - + + -
255D LEU* 5.1 5.4 - - + -
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Residues in contact with ARG 98 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94D TYR* 2.8 55.5 + - + +
95D GLN* 3.8 7.4 - - + +
97D TYR* 1.3 83.8 - - - +
99D GLU* 1.3 63.9 + - + +
102D ALA* 3.2 37.5 - - - +
103D ALA 5.5 0.2 + - - -
112D TRP* 3.9 5.9 - - - -
132D PHE* 4.0 25.4 - - - -
155D ILE* 3.6 28.5 - - - +
156D PRO 5.2 3.0 + - - -
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Residues in contact with GLU 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95D GLN* 3.0 44.4 + - + +
98D ARG* 1.3 85.7 - - + +
100D VAL* 1.3 69.1 + - + +
103D ALA* 5.7 3.5 - - - +
233D MET 4.5 3.2 - - - +
234D VAL* 3.7 25.9 - - + +
235D GLU 4.5 1.7 + - - -
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Residues in contact with VAL 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96D VAL* 3.1 14.0 + - + +
99D GLU* 1.3 83.2 - - + +
101D CYS* 1.3 66.2 + - - +
102D ALA 3.6 0.9 - - - -
103D ALA* 3.9 10.3 + - - +
228D VAL* 3.9 42.0 - - + +
229D LEU* 4.5 4.9 - - + -
233D MET* 3.9 27.4 - - + +
234D VAL* 4.0 19.3 - - + -
503D HEC 3.5 22.9 - - + +
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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