Contacts of the helix formed by residues 88 - 108 (chain B) in PDB entry 2OFK
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 HIS 88 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B LEU* 3.8 4.2 - - - +
86B ILE* 3.0 19.6 + - + -
87B ARG* 1.3 74.1 - - - +
89B ARG* 1.3 67.1 + - - +
90B GLY* 3.2 12.0 + - - -
91B LYS* 3.0 52.9 + - + +
92B ILE* 3.0 24.5 + - - +
156B PHE* 4.0 17.0 - + - -
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Residues in contact with ARG 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B GLU* 2.8 43.2 + - - -
76B VAL* 3.7 6.5 - - + +
77B GLU* 4.2 6.7 + - - +
80B LEU* 3.8 39.3 - - + +
88B HIS* 1.3 72.1 + - - +
90B GLY* 1.3 59.1 + - - +
92B ILE* 3.3 3.5 + - - +
93B GLN* 2.8 69.3 + - + +
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Residues in contact with GLY 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B HIS* 3.2 14.8 + - - -
89B ARG* 1.3 78.6 - - - +
91B LYS* 1.3 57.0 + - - +
93B GLN* 3.7 9.2 - - - +
94B ALA* 2.8 29.6 + - - +
156B PHE* 3.7 13.9 - - - -
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Residues in contact with LYS 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B GLY 3.8 9.6 - - - +
40B GLN* 2.8 65.2 + - - +
42B ALA 2.8 28.6 + - - +
44B LEU* 3.6 15.8 - - - +
86B ILE* 4.1 10.3 - - + +
88B HIS* 3.0 44.0 + - + +
90B GLY* 1.3 74.7 - - - +
92B ILE* 1.3 65.3 + - - +
94B ALA* 3.2 12.8 + - - +
95B ILE* 3.3 7.3 + - - +
156B PHE* 3.6 24.7 - - + -
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Residues in contact with ILE 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B GLN* 4.9 3.8 - - - +
60B PHE* 4.2 12.1 - - + -
76B VAL* 4.2 20.4 - - + -
79B LEU* 3.8 44.6 - - + +
80B LEU* 3.7 34.1 - - + +
85B ILE* 4.2 12.1 - - + -
86B ILE 4.0 17.9 - - - +
87B ARG* 4.5 0.2 - - - -
88B HIS 3.0 21.2 + - - +
89B ARG* 3.8 3.6 - - - +
91B LYS* 1.3 76.3 - - - +
93B GLN* 1.3 64.3 + - - +
95B ILE* 3.2 14.6 + - - +
96B ILE* 3.4 12.4 + - + +
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Residues in contact with GLN 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B GLU* 4.2 4.0 + - - -
76B VAL* 4.1 11.4 - - + +
89B ARG* 2.8 64.9 + - + +
90B GLY* 3.8 7.1 - - - +
92B ILE* 1.3 76.4 - - - +
94B ALA* 1.3 56.2 + - - +
96B ILE* 3.2 2.6 + - - +
97B SER* 2.8 31.2 + - - +
155B LYS* 5.8 0.2 - - - -
901B PGE 3.6 46.8 + - - +
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Residues in contact with ALA 94 (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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40B GLN* 4.7 3.1 - - - +
90B GLY 2.8 18.8 + - - +
91B LYS* 3.4 8.7 - - - +
92B ILE 3.2 0.6 - - - -
93B GLN* 1.3 73.5 - - - +
95B ILE* 1.3 60.2 + - + +
97B SER* 3.3 0.6 + - - -
98B ASN* 2.8 38.4 + - - +
155B LYS* 3.8 26.0 - - + +
156B PHE* 3.7 26.5 - - + -
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Residues in contact with ILE 95 (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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32B PHE* 4.2 1.3 - - + -
36B CYS* 4.0 33.2 - - + -
40B GLN* 3.4 36.8 - - + +
56B TYR* 4.0 9.9 - - + -
60B PHE* 3.6 50.3 - - + -
63B PHE* 4.2 6.5 - - + -
68B ILE* 4.1 16.6 - - + -
91B LYS 3.3 2.7 + - - +
92B ILE 3.2 7.8 + - - +
94B ALA* 1.3 76.9 - - + +
96B ILE* 1.3 58.5 - - - +
98B ASN* 3.3 2.7 + - - +
99B ALA* 3.0 27.5 + - - +
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Residues in contact with ILE 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B PHE* 4.8 2.9 - - + -
68B ILE* 3.6 27.1 - - + +
69B ALA* 4.6 0.2 - - - -
71B MET* 3.7 31.6 - - + +
76B VAL* 3.7 18.8 - - + -
79B LEU* 5.2 0.9 - - + -
92B ILE* 3.4 17.9 + - + +
93B GLN* 3.2 6.4 + - - +
95B ILE* 1.3 77.6 - - - +
97B SER* 1.3 61.8 + - - +
99B ALA* 3.2 3.5 + - - +
100B ARG* 3.1 56.6 + - - +
901B PGE 3.7 25.1 - - - +
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Residues in contact with SER 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B GLN 2.8 20.2 + - - -
94B ALA 3.7 0.9 - - - -
96B ILE* 1.3 75.0 - - - +
98B ASN* 1.3 59.1 + - - +
100B ARG* 3.3 11.9 + - - +
101B ALA* 2.8 28.8 + - - +
153B GLY 4.2 7.8 - - - +
155B LYS* 3.7 33.3 - - - +
901B PGE 3.5 20.1 - - - -
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Residues in contact with ASN 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B PHE* 3.5 19.6 - - + -
35B ILE* 5.0 3.6 - - + +
36B CYS* 4.0 20.4 - - - -
94B ALA* 2.8 25.7 + - - +
95B ILE* 3.6 4.2 - - - +
97B SER* 1.3 74.9 - - - +
99B ALA* 1.3 60.2 + - - +
101B ALA* 3.2 2.2 + - - +
102B TRP* 2.9 25.5 + - - +
154B PHE* 3.1 29.3 - - + +
155B LYS* 2.7 44.8 - - - +
157B VAL* 4.6 3.8 - - - +
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Residues in contact with ALA 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B PHE* 3.5 17.2 - - + -
65B PRO* 3.7 19.8 - - + +
68B ILE* 3.5 38.6 - - + -
69B ALA* 3.9 2.9 - - - +
95B ILE 3.0 6.8 + - - +
96B ILE 3.2 3.1 + - - +
98B ASN* 1.3 75.5 - - - +
100B ARG* 1.3 64.8 + - - +
102B TRP* 3.3 3.2 + - - +
103B LEU* 3.0 28.3 + - - +
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Residues in contact with ARG 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B ALA* 2.9 36.5 + - + +
71B MET 2.7 29.5 + - - -
72B GLN* 3.6 10.3 - - - +
96B ILE* 3.1 23.5 + - - +
97B SER* 3.6 9.6 - - - +
99B ALA* 1.3 75.7 - - - +
101B ALA* 1.3 57.5 + - - +
103B LEU* 3.3 6.6 + - - +
104B ALA* 3.0 28.4 + - - +
901B PGE 3.1 48.4 + - - -
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Residues in contact with ALA 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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97B SER 2.8 17.1 + - - +
98B ASN 3.2 3.8 + - - +
100B ARG* 1.3 75.9 - - - +
102B TRP* 1.3 58.1 + - - +
104B ALA* 3.3 6.9 + - - +
105B MET* 3.0 32.1 + - - +
152B ARG 3.3 25.2 - - - +
153B GLY* 4.0 8.7 - - - -
154B PHE* 3.5 25.4 - - + -
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Residues in contact with TRP 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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28B SER* 3.6 21.3 - - - -
29B ARG* 3.5 30.3 - - + -
32B PHE* 3.3 45.3 - + + -
63B PHE 4.2 0.9 - - - -
65B PRO* 3.5 41.3 - - + -
98B ASN 2.9 15.9 + - - +
99B ALA 3.3 3.3 + - - +
101B ALA* 1.3 73.9 - - - +
103B LEU* 1.3 66.3 + - + +
105B MET* 3.1 7.8 + - + +
106B GLU* 2.8 50.1 + - + +
112B PHE* 3.6 23.7 - + + +
154B PHE* 3.9 11.8 - - + -
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Residues in contact with LEU 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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65B PRO* 3.8 30.1 - - + +
66B ILE* 4.1 20.2 - - + -
69B ALA* 3.5 31.4 - - + -
99B ALA 3.0 15.9 + - - +
100B ARG* 3.3 8.3 + - - +
102B TRP* 1.3 77.9 - - + +
104B ALA* 1.3 61.8 + - - +
106B GLU* 3.3 10.4 + - + +
107B GLN* 3.0 25.6 + - - +
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Residues in contact with ALA 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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100B ARG 3.0 17.4 + - - +
101B ALA* 3.6 7.6 - - - +
102B TRP 3.2 0.2 - - - -
103B LEU* 1.3 73.5 - - - +
105B MET* 1.3 66.5 + - - +
107B GLN* 3.1 33.3 + - - +
108B ASN* 3.5 10.8 + - - -
152B ARG 5.6 2.7 - - - +
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Residues in contact with MET 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 ALA 3.0 14.6 + - - +
102B TRP* 3.1 10.3 + - - +
104B ALA* 1.3 76.6 - - - +
106B GLU* 1.3 57.3 + - + +
108B ASN* 3.0 21.7 + - - +
110B GLU* 3.0 58.8 + - + +
112B PHE* 4.1 16.8 - - + -
115B PHE* 3.6 39.0 - - + -
152B ARG* 3.9 18.8 - - + -
154B PHE* 3.7 31.2 - - - -
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Residues in contact with GLU 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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28B SER* 4.5 3.3 + - - -
102B TRP* 2.8 48.0 + - + +
103B LEU* 3.7 10.5 - - + +
104B ALA 3.3 0.2 - - - -
105B MET* 1.3 75.9 - - - +
107B GLN* 1.4 57.4 + - - +
108B ASN 3.0 0.2 - - - -
109B GLY* 2.9 21.1 + - - +
110B GLU 3.5 14.0 + - - +
111B SER* 3.5 10.0 + - - -
112B PHE 3.3 15.8 + - - -
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Residues in contact with GLN 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 LEU 3.0 15.7 + - - +
104B ALA* 3.1 26.8 + - - +
106B GLU* 1.4 75.2 - - - +
108B ASN* 1.3 66.2 + - - +
109B GLY 3.3 0.4 + - - -
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Residues in contact with ASN 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B ALA 3.5 8.9 + - - +
105B MET* 3.0 12.8 + - - +
107B GLN* 1.3 85.8 - - - +
109B GLY* 1.3 61.0 + - - +
110B GLU* 3.6 5.8 + - + +
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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