Contacts of the helix formed by residues 94 - 114 (chain O) in PDB entry 5KZ5
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 ALA 94 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92O THR 4.0 2.4 + - - -
93O HIS* 1.3 72.0 + - - +
95O TYR* 1.4 71.1 + - + +
97O TRP* 3.3 8.2 + - - +
98O GLU* 3.3 25.6 + - - +
454S TRP* 4.0 20.0 - - + +
456S GLN 5.4 6.1 - - - +
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Residues in contact with TYR 95 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83O ASN* 4.4 18.8 - - + +
84O TYR* 3.7 30.8 - - - +
85O TYR 5.5 4.0 - - - +
86O GLY 5.4 1.8 - - - +
93O HIS* 3.3 32.9 - + + +
94O ALA* 1.4 84.0 - - + +
96O GLY* 1.3 59.9 + - - +
97O TRP 3.4 0.2 - - - -
98O GLU* 3.7 0.5 + - - +
99O SER* 3.2 21.7 + - - -
454S TRP* 3.4 50.4 - + + +
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Residues in contact with GLY 96 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93O HIS* 3.4 22.7 + - - -
94O ALA 3.3 0.8 - - - -
95O TYR* 1.3 76.4 - - - +
97O TRP* 1.4 57.7 + - - +
99O SER* 3.2 8.5 + - - -
100O GLU* 3.1 33.3 + - - +
295O THR* 5.2 12.0 - - - +
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Residues in contact with TRP 97 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93O HIS 3.2 12.4 + - - +
94O ALA* 3.3 9.6 + - - +
96O GLY* 1.4 70.8 - - - +
98O GLU* 1.4 76.6 + - + +
100O GLU* 3.3 12.7 + - + +
101O ALA* 3.0 39.7 + - + +
105O ARG* 5.8 5.2 - - - -
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Residues in contact with GLU 98 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84O TYR* 3.3 18.6 + - - +
94O ALA 3.3 12.2 + - - +
95O TYR 4.0 6.7 - - - +
96O GLY 3.4 0.2 - - - -
97O TRP* 1.4 95.9 - - + +
99O SER* 1.4 55.7 + - - +
101O ALA* 3.2 6.8 + - - +
102O ALA* 2.9 24.8 + - - +
451S SER 4.4 8.2 - - - +
452S ILE* 3.5 11.0 - - - +
453S LYS 3.1 22.8 - - - +
454S TRP* 3.0 37.2 + - + -
455S THR 3.3 15.6 - - - +
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Residues in contact with SER 99 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84O TYR* 3.7 18.8 - - - -
95O TYR 3.2 15.2 + - - -
96O GLY* 3.2 13.2 + - - -
98O GLU* 1.4 72.7 - - - +
100O GLU* 1.4 63.3 + - - +
102O ALA* 3.4 4.4 + - - +
103O MET* 2.9 27.4 + - - +
295O THR* 4.0 22.0 + - - -
299O PRO* 4.2 5.0 - - - +
300O LEU* 3.8 24.9 + - - +
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Residues in contact with GLU 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 GLY 3.1 20.6 + - - +
97O TRP* 3.5 12.3 - - + +
98O GLU 3.3 0.2 - - - -
99O SER* 1.4 79.2 + - - +
101O ALA* 1.4 62.6 + - - +
103O MET* 3.2 32.6 + - + +
104O GLU* 3.1 32.2 + - + +
295O THR* 5.3 10.2 - - - +
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Residues in contact with ALA 101 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97O TRP* 3.0 32.5 + - + +
98O GLU* 3.2 12.5 + - - +
100O GLU* 1.4 74.2 - - - +
102O ALA* 1.4 55.5 + - - +
104O GLU* 3.4 15.2 + - - +
105O ARG* 3.1 54.4 + - - +
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Residues in contact with ALA 102 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84O TYR* 3.6 14.6 - - - +
98O GLU 2.9 16.8 + - - +
99O SER 3.5 6.3 - - - +
101O ALA* 1.4 74.9 - - - +
103O MET* 1.4 55.3 + - - +
105O ARG* 3.4 6.4 + - - +
106O ALA* 2.9 32.1 + - - +
299O PRO 3.6 18.2 - - - +
300O LEU* 4.1 8.1 - - - +
302O VAL* 4.6 8.9 - - + +
451S SER* 6.2 4.7 - - - -
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Residues in contact with MET 103 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99O SER 2.9 10.2 + - - +
100O GLU* 3.2 38.6 + - + +
102O ALA* 1.4 73.9 - - - +
104O GLU* 1.4 69.4 - - + +
106O ALA* 3.9 2.0 - - - +
107O ARG* 3.2 33.2 + - + +
292O ARG* 6.1 4.3 - - - +
295O THR 5.9 0.7 - - - +
299O PRO* 3.5 36.1 - - + +
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Residues in contact with GLU 104 (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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100O GLU* 3.1 19.2 + - + +
101O ALA* 3.7 15.3 - - - +
103O MET* 1.4 84.2 - - + +
105O ARG* 1.4 62.5 + - + +
107O ARG* 4.3 3.9 - - - +
108O GLN* 3.6 25.2 + - - +
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Residues in contact with ARG 105 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97O TRP* 5.8 5.1 - - - -
101O ALA* 3.1 36.1 + - - +
102O ALA* 4.0 5.4 - - - +
104O GLU* 1.4 76.0 - - + +
106O ALA* 1.4 63.4 + - - +
108O GLN* 3.5 15.3 + - - +
109O GLN* 3.1 29.6 + - - +
309O GLU* 6.0 1.8 - - - +
450S LYS* 3.4 68.3 + - - +
451S SER* 3.6 14.4 + - - +
452S ILE* 6.0 0.8 - - - +
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Residues in contact with ALA 106 (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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102O ALA 2.9 19.1 + - - +
103O MET* 3.9 5.4 - - - +
105O ARG* 1.4 77.4 - - - +
107O ARG* 1.3 61.5 + - - +
108O GLN 3.4 0.5 + - - -
109O GLN* 3.6 12.8 + - - -
110O VAL* 4.0 5.9 - - - +
299O PRO* 4.5 5.8 - - + +
302O VAL* 3.6 38.4 - - + +
305O GLY* 3.5 19.4 + - - +
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Residues in contact with ARG 107 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103O MET* 3.2 24.0 + - + +
104O GLU* 4.3 4.5 - - - +
106O ALA* 1.3 79.4 - - - +
108O GLN* 1.3 56.9 + - - +
110O VAL* 3.1 9.4 - - + +
111O ALA* 3.0 35.6 + - + +
119O ARG* 3.5 43.1 - - - +
122O ILE* 6.2 1.4 - - - +
123O PHE* 3.7 32.5 - - - -
267O ALA* 4.8 3.8 - - - +
268O ILE 5.4 1.4 + - - -
269O TYR* 3.8 35.3 + - - +
289O ARG* 4.0 9.6 - - - +
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Residues in contact with GLN 108 (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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104O GLU 3.6 15.4 + - - +
105O ARG* 3.5 16.7 + - - +
107O ARG* 1.3 77.2 - - - +
109O GLN* 1.4 68.6 + - - +
111O ALA* 4.5 4.5 - - - -
112O SER* 3.2 29.7 + - - -
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Residues in contact with GLN 109 (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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105O ARG* 3.1 29.6 + - - +
106O ALA* 3.6 4.9 + - - +
107O ARG 3.5 1.2 - - - -
108O GLN* 1.4 89.1 + - - +
110O VAL* 1.4 61.6 + - - +
112O SER* 4.2 2.8 - - - -
113O LEU* 3.5 20.8 + - - +
302O VAL* 5.1 1.2 - - - +
305O GLY* 3.4 36.4 - - - +
306O ALA 4.3 0.2 + - - -
308O CYS* 4.0 13.6 - - + +
309O GLU* 3.4 36.2 + - + +
312O GLN* 5.8 3.8 - - + -
448S ASP 5.7 0.2 + - - -
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Residues in contact with VAL 110 (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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106O ALA 4.0 4.7 + - - +
107O ARG* 3.1 25.4 - - + +
109O GLN* 1.4 71.5 - - - +
111O ALA* 1.4 62.4 + - - +
113O LEU* 3.5 6.1 + - - +
114O ILE* 3.3 29.2 + - + +
267O ALA* 4.3 14.4 - - + +
269O TYR* 3.4 21.8 - - + +
304O LEU* 4.1 28.5 - - + +
305O GLY* 4.3 2.7 - - - +
308O CYS* 3.9 23.3 - - - -
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Residues in contact with ALA 111 (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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107O ARG* 3.0 24.1 + - + +
108O GLN* 4.2 5.2 - - - +
110O VAL* 1.4 77.0 - - - +
112O SER* 1.4 50.8 + - - +
114O ILE* 3.5 4.3 + - - +
115O GLY* 2.9 29.8 + - - -
116O ALA* 3.7 13.1 + - - +
117O ASP 6.0 0.4 - - - +
269O TYR* 4.3 22.0 - - + +
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Residues in contact with SER 112 (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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108O GLN* 3.2 22.7 + - - -
109O GLN* 4.2 3.1 - - - -
111O ALA* 1.4 73.5 - - - +
113O LEU* 1.4 65.1 + - - +
115O GLY* 3.2 15.5 + - - +
116O ALA 5.2 0.9 - - - +
245O ASN* 4.9 2.1 - - - +
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Residues in contact with LEU 113 (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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109O GLN 3.5 15.5 + - - +
110O VAL* 3.8 7.0 - - - +
111O ALA 3.4 0.6 - - - -
112O SER* 1.4 75.9 - - - +
114O ILE* 1.3 65.5 + - + +
241O PRO* 5.1 9.9 - - + -
242O LEU* 3.4 40.4 - - + +
243O ASP* 3.3 27.7 - - - +
245O ASN* 3.4 5.4 + - - -
308O CYS* 5.1 15.7 - - + -
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Residues in contact with ILE 114 (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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110O VAL* 3.3 14.8 + - + +
111O ALA 3.6 7.4 - - - +
113O LEU* 1.3 78.2 - - + +
115O GLY* 1.4 63.0 - - - +
116O ALA 4.2 2.5 - - - +
117O ASP* 3.4 26.2 - - - +
242O LEU* 4.9 9.4 - - + -
243O ASP* 4.7 0.4 - - - +
244O VAL* 3.1 39.9 + - + +
245O ASN* 3.1 5.7 + - - -
252O MET* 4.1 26.9 - - + -
254O ILE* 5.1 16.2 - - + -
267O ALA 5.6 0.7 - - - +
269O TYR* 4.1 31.2 - - + +
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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