Contacts of the helix formed by residues 86 - 101 (chain O) 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 O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77O SER* 4.1 20.4 + - - +
78O HIS* 5.1 1.8 - - - +
84O THR 3.7 1.0 + - - -
85O PHE* 1.3 69.3 - - - +
87O HIS* 1.3 58.3 + - - +
88O ALA* 3.4 18.2 + - - +
89O SER* 3.0 42.4 + - - -
90O ILE* 3.1 13.0 + - - +
92O ARG* 4.1 6.1 + - - -
249O LYS* 3.9 9.9 + - - -
253O THR* 4.4 5.8 - - + +
147Q LYS* 4.2 4.9 - - - +
46T GLY 4.0 2.9 - - - +
47T LYS* 3.7 29.1 - - + +
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Residues in contact with HIS 87 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84O THR* 5.1 0.2 - - - -
85O PHE* 3.2 17.2 - - - +
86O ASP* 1.3 71.9 - - - +
88O ALA* 1.3 55.0 + - - +
90O ILE* 3.1 21.9 + - + +
91O ARG* 2.9 28.2 + - - +
117O GLY 5.0 1.3 - - - -
118O VAL* 2.8 44.6 + - + +
119O SER* 4.7 1.2 - - - -
257O TRP* 5.9 1.5 - + - -
264O ASP* 2.7 27.6 + - - -
47T LYS 2.8 25.6 + - - +
48T LEU* 4.5 2.7 - - - -
49T TRP* 3.9 19.3 + - + +
52T VAL* 4.0 12.5 - - + +
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Residues in contact with ALA 88 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86O ASP* 3.1 13.5 + - - +
87O HIS* 1.3 75.9 - - - +
89O SER* 1.3 63.8 + - - +
91O ARG* 3.4 7.4 + - - +
92O ARG* 3.2 39.7 + - - +
147Q LYS* 5.5 4.9 - - - +
46T GLY 4.9 3.6 - - - +
52T VAL* 3.6 28.3 - - + +
55T LYS* 5.5 7.4 - - + +
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Residues in contact with SER 89 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86O ASP* 3.0 30.7 + - - -
88O ALA* 1.3 76.8 - - - +
90O ILE* 1.3 64.7 - - - +
92O ARG* 3.3 7.3 + - - +
93O GLY 2.9 18.0 + - - -
249O LYS* 3.5 16.2 + - - -
250O ASP* 2.6 35.9 + - - +
253O THR* 3.6 21.5 + - - -
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Residues in contact with ILE 90 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85O PHE* 3.7 22.2 - - + -
86O ASP 3.1 11.4 + - - +
87O HIS* 3.1 33.7 - - + +
89O SER* 1.3 76.2 - - - +
91O ARG* 1.3 64.8 + - - +
93O GLY* 2.8 13.5 + - - -
94O TYR* 2.9 12.1 + - - +
118O VAL* 4.6 2.7 - - + -
119O SER* 3.9 17.5 - - - +
253O THR* 4.3 16.2 - - + +
254O PHE* 3.7 31.7 - - + +
257O TRP* 4.3 28.5 - - + -
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Residues in contact with ARG 91 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87O HIS 2.9 12.4 + - - +
88O ALA* 3.5 11.4 - - - +
90O ILE* 1.3 75.3 - - - +
92O ARG* 1.3 65.5 + - - +
94O TYR* 3.2 17.2 + - - +
95O GLN* 3.4 6.1 + - - +
119O SER* 3.1 40.0 + - - +
120O HIS* 4.0 16.2 + - - +
124O GLU* 2.7 41.4 + - - -
237O GLU* 2.9 42.5 + - - -
238O ASP* 6.2 2.7 - - - -
49T TRP* 3.9 10.5 - - - -
52T VAL* 4.8 10.1 - - + -
56T ILE* 4.3 25.4 - - - +
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Residues in contact with ARG 92 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86O ASP* 4.1 2.6 + - - -
88O ALA* 3.2 19.5 + - - +
89O SER* 3.6 26.6 - - - +
90O ILE 3.2 0.2 - - - -
91O ARG* 1.3 78.3 - - + +
93O GLY* 1.3 64.6 + - - +
95O GLN* 3.0 19.5 + - - +
96O VAL* 3.1 14.2 + - - +
236O TYR* 3.6 30.8 - - + -
238O ASP* 3.0 43.7 + - + +
240O THR* 3.5 10.6 + - - -
246O GLN* 3.8 3.9 - - - +
250O ASP* 3.0 34.0 + - - +
147Q LYS* 3.2 47.9 + - - +
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Residues in contact with GLY 93 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89O SER 2.9 6.7 + - - -
90O ILE 2.8 7.1 + - - -
92O ARG* 1.3 74.8 - - - +
94O TYR* 1.3 65.5 + - - +
96O VAL* 3.1 3.1 + - - -
97O TYR* 2.8 20.3 + - - +
250O ASP* 3.1 34.2 - - - +
251O VAL* 3.4 11.2 - - - +
254O PHE* 3.9 6.5 - - - -
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Residues in contact with TYR 94 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90O ILE 2.9 10.9 + - - +
91O ARG* 3.2 9.8 + - - +
93O GLY* 1.3 73.4 - - - +
95O GLN* 1.3 57.3 + - + +
97O TYR* 2.8 17.4 + + - +
98O ARG* 2.8 74.0 + - + +
112O TRP* 3.5 17.5 - + - -
115O LEU* 4.5 7.6 - - + -
119O SER* 5.3 0.4 - - - +
120O HIS* 3.7 29.4 - + + -
128O MET* 3.5 25.7 - - - +
155O ILE* 4.2 20.4 - - + -
254O PHE* 3.6 35.3 - + + -
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Residues in contact with GLN 95 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91O ARG 3.4 6.1 + - - +
92O ARG* 3.0 12.5 + - - +
94O TYR* 1.3 85.4 - - + +
96O VAL* 1.3 61.9 + - - +
98O ARG* 4.5 4.3 - - - -
99O GLU* 2.9 56.6 + - + +
234O VAL* 3.6 18.6 - - + +
235O GLU 2.9 25.0 + - - +
236O TYR* 3.7 8.3 - - - -
237O GLU* 3.6 24.2 + - - +
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Residues in contact with VAL 96 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92O ARG 3.1 10.5 + - - +
93O GLY* 3.1 7.6 + - - +
95O GLN* 1.3 76.4 - - - +
97O TYR* 1.3 64.8 + - - +
100O VAL* 2.9 31.6 + - + +
101O CYS 3.6 0.3 + - - -
229O LEU* 4.3 22.4 - - + -
234O VAL* 5.0 6.1 - - + -
236O TYR* 2.9 37.0 - - + +
247O MET* 4.2 18.4 - - + +
251O VAL* 3.8 25.6 - - + -
523O HEC 4.4 4.0 - - + -
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Residues in contact with TYR 97 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93O GLY 2.8 12.8 + - - +
94O TYR* 2.8 16.5 + + - +
96O VAL* 1.3 76.1 - - - +
98O ARG* 1.3 75.8 + - - +
101O CYS* 2.9 33.6 + - + -
102O ALA* 2.7 52.3 + - + +
105O HIS* 2.6 34.6 + - + -
106O SER* 3.7 2.3 - - - -
107O LEU* 3.5 50.1 + - + +
155O ILE* 4.5 5.6 - - + +
156O PRO 4.9 3.6 + - - -
158O PRO* 5.3 0.2 - - - +
177O LEU* 4.3 9.6 - - + -
251O VAL* 3.7 6.9 - - + +
254O PHE* 3.8 18.6 - + + -
255O LEU* 5.1 1.1 - - + -
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Residues in contact with ARG 98 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94O TYR* 2.8 56.4 + - + +
95O GLN* 3.9 5.4 - - - +
97O TYR* 1.3 82.6 - - - +
99O GLU* 1.3 65.4 + - + +
102O ALA* 3.3 40.8 + - - +
103O ALA 5.2 0.2 + - - -
112O TRP* 3.9 7.9 - - - -
132O PHE* 3.9 28.4 - - - -
155O ILE* 3.5 29.7 - - - +
156O PRO 4.9 5.7 + - - -
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Residues in contact with GLU 99 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95O GLN* 2.9 52.6 + - + +
98O ARG* 1.3 80.0 - - + +
100O VAL* 1.3 61.9 + - + +
103O ALA* 6.0 2.3 - - - +
233O MET 4.7 1.9 - - - +
234O VAL* 3.7 29.5 - - + +
235O GLU 4.6 1.4 + - - -
87W PHE 5.6 0.3 - - - -
88W GLY* 4.6 17.1 + - - -
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Residues in contact with VAL 100 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96O VAL* 2.9 21.7 + - + +
97O TYR 3.3 0.4 + - - -
99O GLU* 1.3 83.6 - - - +
101O CYS* 1.3 62.5 + - - +
102O ALA 3.7 0.4 - - - -
103O ALA* 4.3 8.4 + - - +
228O VAL* 3.8 37.2 - - + +
229O LEU* 4.1 7.0 - - + -
233O MET* 3.9 22.4 - - + +
234O VAL* 3.9 24.5 - - + -
523O HEC 3.1 28.1 - - + +
88W GLY* 6.4 0.2 - - - -
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Residues in contact with CYS 101 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96O VAL 4.0 2.7 - - - -
97O TYR* 2.9 42.0 + - + -
100O VAL* 1.3 70.3 - - - +
102O ALA* 1.3 50.8 + - - +
103O ALA 2.6 18.6 + - - -
104O CYS* 2.8 17.5 + - - +
105O HIS* 3.1 11.4 + - + +
177O LEU* 4.5 3.4 - - + -
251O VAL* 4.1 5.6 - - - -
523O HEC 1.8 87.7 - - + +
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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