Contacts of the helix formed by residues 99 - 116 (chain B) in PDB entry 1OKB
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 LYS 99 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95B ALA* 3.5 24.9 - - - +
96B GLU* 2.8 46.4 + - - +
98B GLU* 1.3 82.6 - - + +
100B PRO* 1.3 75.0 - - + +
101B TYR* 3.3 19.3 - - + -
102B PHE* 3.0 13.5 + - - +
103B LYS* 3.2 11.4 + - - +
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Residues in contact with PRO 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A VAL* 4.1 37.7 - - + -
186A HIS* 5.7 1.2 + - - -
98B GLU 3.8 3.6 - - - +
99B LYS* 1.3 87.0 - - + +
101B TYR* 1.3 62.6 + - - +
103B LYS* 3.4 11.2 + - + +
104B GLN* 3.1 23.9 + - - +
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Residues in contact with TYR 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A PRO* 3.9 22.9 - - + -
166A PRO* 5.0 7.6 - - + -
186A HIS* 5.9 3.6 - - - -
96B GLU* 2.6 34.1 + - - +
99B LYS* 3.3 27.5 - - + -
100B PRO* 1.3 78.4 - - - +
102B PHE* 1.3 77.0 + + + +
104B GLN* 3.5 6.1 + - - +
105B LEU* 2.9 29.2 + - + +
220B ARG 4.7 2.6 - - - +
221B GLY* 3.3 33.0 - - - -
224B THR* 3.6 28.0 - - + -
225B PHE* 3.3 31.6 - - + +
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Residues in contact with PHE 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B GLU 3.2 23.6 - - - +
97B PHE* 3.4 46.2 - + + +
99B LYS 3.0 5.1 + - - +
101B TYR* 1.3 96.2 - + + +
103B LYS* 1.3 60.5 + - - +
105B LEU* 3.2 10.7 + - + +
106B MET* 2.9 75.2 + - + +
126B TYR* 4.2 8.3 - - - -
222B TRP* 4.8 1.6 - + - -
225B PHE* 3.6 39.5 - + - -
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Residues in contact with LYS 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B PHE 5.1 3.3 + - - +
98B GLU 5.9 0.9 - - - +
99B LYS 3.2 9.4 + - - +
100B PRO* 3.7 12.3 - - + +
102B PHE* 1.3 80.2 - - - +
104B GLN* 1.3 58.6 + - - +
106B MET* 3.3 8.3 + - - +
107B SER* 3.0 28.2 + - - -
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Residues in contact with GLN 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A HIS* 3.5 64.0 + - + +
188A GLY* 4.9 6.7 - - - -
100B PRO 3.1 15.1 + - - +
101B TYR* 3.8 5.8 - - - +
103B LYS* 1.3 79.1 - - - +
105B LEU* 1.3 61.0 + - - +
107B SER* 3.3 14.2 + - - -
108B PHE* 2.9 35.7 + - + +
220B ARG 5.0 1.6 - - - +
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Residues in contact with LEU 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B TYR* 2.9 20.2 + - + +
102B PHE* 3.2 18.6 + - + +
104B GLN* 1.3 77.2 - - - +
106B MET* 1.3 69.5 + - + +
108B PHE* 3.2 4.8 + - + +
109B VAL* 2.9 38.8 + - + +
220B ARG* 3.6 30.5 + - + +
221B GLY* 3.8 7.0 - - - +
222B TRP* 3.5 72.2 - - + +
225B PHE* 4.8 0.7 - - + -
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Residues in contact with MET 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B PHE* 2.9 53.7 + - + +
103B LYS* 3.6 6.5 - - - +
105B LEU* 1.3 87.7 - - + +
107B SER* 1.3 63.0 + - - +
109B VAL* 3.5 6.8 + - + +
110B ALA* 3.0 26.3 + - - +
126B TYR* 3.7 22.4 - - - +
222B TRP* 3.9 18.8 - - + -
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Residues in contact with SER 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B LYS* 3.0 19.4 + - - -
104B GLN* 3.5 18.2 + - - -
105B LEU 3.2 0.2 - - - -
106B MET* 1.3 77.7 - - - +
108B PHE* 1.3 61.2 + - - +
110B ALA* 3.5 5.3 + - - +
111B ASP* 3.1 37.6 + - - +
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Residues in contact with PHE 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B GLN* 2.9 26.3 + - + +
105B LEU* 3.5 6.3 - - + +
107B SER* 1.3 77.2 - - - +
109B VAL* 1.3 68.4 + - + +
111B ASP* 3.1 11.7 + - + +
112B GLU* 2.9 57.0 + - + +
210B ARG* 5.2 1.8 - - - -
216B SER 4.5 3.4 - - - -
217B HIS* 3.5 34.3 - + + -
220B ARG* 3.4 70.7 - - + +
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Residues in contact with VAL 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B LEU* 2.9 29.0 + - + +
106B MET* 4.1 8.1 - - + +
108B PHE* 1.3 85.3 - - + +
110B ALA* 1.3 57.9 + - - +
112B GLU* 3.2 6.0 + - - +
113B ARG* 2.9 51.2 + - + +
118B VAL* 4.9 3.8 - - + -
208B THR* 4.0 21.5 - - + +
217B HIS* 5.0 1.1 - - + +
222B TRP* 4.0 31.4 - - + +
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Residues in contact with ALA 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B MET 3.0 19.3 + - - +
107B SER* 3.7 6.3 - - - +
109B VAL* 1.3 76.8 - - - +
111B ASP* 1.3 65.4 + - - +
113B ARG* 3.3 8.7 + - - +
114B SER* 3.2 21.8 + - - -
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Residues in contact with ASP 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B SER* 3.1 26.9 + - - +
108B PHE* 3.3 13.2 - - + +
110B ALA* 1.3 79.2 - - - +
112B GLU* 1.3 62.6 + - + +
114B SER* 2.8 23.1 + - - -
115B ARG* 3.2 37.3 + - - +
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Residues in contact with GLU 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B PHE* 2.9 42.4 + - + +
109B VAL 3.5 7.6 - - - +
111B ASP* 1.3 78.6 - - + +
113B ARG* 1.3 54.6 + - - +
115B ARG* 4.8 3.4 + - - +
116B HIS* 2.7 48.9 + - - +
118B VAL* 3.8 9.6 - - + -
210B ARG* 2.8 46.5 + - - +
217B HIS* 2.7 35.6 + - + +
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Residues in contact with ARG 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B VAL* 2.9 31.4 + - + +
110B ALA* 3.8 8.5 - - - +
111B ASP 3.3 0.4 - - - -
112B GLU* 1.3 75.5 - - - +
114B SER* 1.3 59.5 + - - +
115B ARG 3.4 0.2 - - - -
116B HIS 3.2 15.6 - - - +
118B VAL* 3.1 40.4 + - + +
120B PRO 2.8 21.6 + - - -
121B PRO* 4.0 1.8 - - - +
122B ALA* 3.5 28.0 - - - +
125B VAL* 3.3 24.4 - - - +
208B THR* 3.9 13.7 - - - +
1306B CL 3.5 20.6 - - + +
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Residues in contact with SER 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B ALA 3.2 11.2 + - - -
111B ASP* 2.8 24.3 + - - -
113B ARG* 1.3 77.9 - - - +
115B ARG* 1.3 65.8 + - - +
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Residues in contact with ARG 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A LYS* 4.1 23.4 - - - +
111B ASP* 3.2 35.7 + - - +
112B GLU* 5.4 3.4 + - - +
114B SER* 1.3 86.4 + - - +
116B HIS* 1.3 88.0 + - + +
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Residues in contact with HIS 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B GLU* 2.7 29.3 + - - +
113B ARG* 3.2 21.1 - - - +
115B ARG* 1.3 100.2 + - + +
117B THR* 1.3 64.6 + - - +
118B VAL* 3.8 1.1 + - + -
210B ARG* 3.8 57.8 + - + -
213B GLN* 5.6 1.1 - - - -
1306B CL 4.0 1.9 - - - +
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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