Contacts of the helix formed by residues 88 - 109 (chain B) in PDB entry 4K06
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 ASN 88 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B CYS* 5.4 0.3 - - - +
86B GLU* 4.3 1.9 - - - +
87B ASN* 1.3 77.5 + - - +
90B PRO* 1.3 64.0 - - - +
91B CYS* 3.1 21.0 + - - +
92B LEU* 3.1 34.6 + - + +
93B LYS* 2.8 34.3 + - - +
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Residues in contact with PRO 90 (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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87B ASN* 3.4 10.3 - - - +
88B ASN* 1.3 89.6 - - - +
91B CYS* 1.3 56.2 + - - +
93B LYS* 3.5 5.5 - - + +
94B GLU* 2.8 50.5 + - + +
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Residues in contact with CYS 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B LEU* 4.0 15.8 - - - +
59B THR 3.5 23.8 - - - +
60B GLY* 4.2 3.6 - - - -
61B CYS* 2.0 62.1 - - + +
88B ASN* 3.1 9.8 + - - +
90B PRO* 1.3 78.8 - - - +
92B LEU* 1.3 52.6 + - - +
94B GLU* 3.3 8.2 + - - +
95B LEU* 2.7 36.7 + - - +
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Residues in contact with LEU 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B CYS* 4.2 14.1 - - + -
71B ASP* 4.2 21.3 - - + +
72B ARG 4.0 21.3 - - - +
73B TYR* 4.4 8.0 - - + +
86B GLU* 3.8 34.0 - - + +
88B ASN* 3.1 27.0 + - + +
91B CYS* 1.3 76.3 - - - +
93B LYS* 1.3 61.1 + - - +
95B LEU* 3.7 8.5 - - + +
96B CYS* 2.9 30.5 + - - +
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Residues in contact with LYS 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B CYS* 4.1 17.0 + - + +
86B GLU* 3.8 28.4 - - - +
87B ASN 4.6 2.5 - - - +
88B ASN 2.8 21.2 + - - +
90B PRO* 3.5 7.0 - - + +
92B LEU* 1.3 76.6 - - - +
94B GLU* 1.3 62.2 + - + +
96B CYS* 3.3 4.9 + - - +
97B GLU* 2.7 68.2 + - + +
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Residues in contact with GLU 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B CYS* 4.6 0.2 - - - -
57B LYS* 5.0 5.4 - - - +
58B LEU* 3.6 26.2 - - + +
59B THR 5.6 0.5 + - - -
90B PRO* 2.8 39.3 + - - +
91B CYS* 3.8 2.8 - - - +
93B LYS* 1.3 74.8 - - + +
95B LEU* 1.3 55.5 + - - +
97B GLU* 3.6 7.2 - - - +
98B CYS* 2.7 39.0 + - - -
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Residues in contact with LEU 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B TYR* 3.4 34.8 - - + +
58B LEU* 3.6 21.5 - - + +
61B CYS* 4.2 11.4 - - - -
67B ASP 4.0 4.5 - - - +
68B PRO* 3.6 27.6 - - + +
71B ASP 4.0 13.0 - - - +
73B TYR* 3.9 24.0 - - + -
91B CYS 2.7 22.0 + - - +
92B LEU* 3.7 10.5 - - + +
94B GLU* 1.3 69.7 - - - +
96B CYS* 1.3 61.3 + - - +
98B CYS* 3.2 4.7 - - - +
99B ASP* 3.0 28.9 + - - +
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Residues in contact with CYS 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B MET* 3.8 8.9 - - - +
73B TYR* 3.5 39.7 - - + -
74B SER 4.7 1.1 - - - -
75B TYR* 3.9 2.7 - - - -
84B CYS* 2.0 55.0 - - + -
86B GLU* 5.2 1.8 - - + -
92B LEU 2.9 19.0 + - - +
93B LYS* 3.4 4.0 - - - +
95B LEU* 1.3 78.2 - - - +
97B GLU* 1.3 50.2 + - - +
99B ASP* 3.3 3.5 + - - +
100B LYS* 2.7 34.7 + - - +
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Residues in contact with GLU 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B CYS* 3.2 19.3 + - - +
93B LYS* 2.7 56.9 + - + +
94B GLU* 3.7 7.6 - - - +
96B CYS* 1.3 72.8 - - - +
98B CYS* 1.3 60.6 + - - +
100B LYS* 3.6 25.4 + - - +
101B ALA* 2.8 32.4 + - - +
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Residues in contact with CYS 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B HIS* 3.3 12.3 - - + +
51B CYS* 2.0 68.4 - - + -
52B TYR* 4.0 15.9 - - + -
58B LEU* 4.2 8.1 - - - -
94B GLU* 2.7 23.2 + - - -
95B LEU 3.2 11.0 - - - +
97B GLU* 1.3 77.1 - - - +
99B ASP* 1.3 61.6 + - - +
101B ALA* 3.4 4.1 + - - +
102B VAL* 3.2 17.8 + - - +
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Residues in contact with ASP 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B SER 3.8 4.0 - - - +
5B LEU* 3.7 27.9 - - + +
8B MET* 3.5 9.3 - - - +
48B HIS* 2.8 10.3 + - - -
52B TYR* 2.4 33.2 + - - -
68B PRO 5.3 0.2 - - - +
73B TYR* 2.5 39.2 + - - +
95B LEU* 3.0 14.0 + - - +
96B CYS 3.6 2.9 - - - +
98B CYS* 1.3 74.2 - - - +
100B LYS* 1.3 66.3 + - - +
102B VAL* 3.2 4.3 - - - +
103B ALA* 3.2 23.4 + - - +
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Residues in contact with LYS 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B MET* 3.4 9.4 - - - -
81B THR* 4.2 13.2 - - - +
82B ILE* 2.8 50.3 + - + +
83B VAL* 4.8 2.6 - - - +
84B CYS* 4.5 3.1 - - - +
96B CYS 2.7 21.2 + - - +
97B GLU* 3.6 31.0 + - - +
98B CYS 3.3 0.2 - - - -
99B ASP* 1.3 74.4 - - - +
101B ALA* 1.3 62.9 + - - +
103B ALA* 3.3 4.4 + - - +
104B ILE* 3.0 47.3 + - + +
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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
----------------------------------------------------------
47B VAL* 6.3 3.8 - - + -
51B CYS* 6.1 1.3 - - - -
97B GLU 2.8 17.9 + - - +
98B CYS* 3.8 5.6 - - - +
100B LYS* 1.3 79.0 - - - +
102B VAL* 1.3 56.1 + - - +
104B ILE* 3.5 7.9 + - - +
105B CYS* 2.8 30.0 + - - +
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Residues in contact with VAL 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B LEU* 3.5 17.3 - - + -
9B ILE* 5.0 3.8 - - + -
44B CYS* 3.5 31.9 - - + +
45B CYS* 4.1 7.4 - - - +
48B HIS* 3.4 41.1 - - + +
98B CYS 3.2 2.8 + - - +
99B ASP 3.2 13.2 - - - +
101B ALA* 1.3 76.0 - - - +
103B ALA* 1.3 63.5 + - - +
105B CYS* 3.5 4.9 - - - +
106B LEU* 2.8 47.4 + - + +
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Residues in contact with ALA 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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8B MET* 3.6 39.3 - - + +
9B ILE* 3.7 15.9 - - + +
12B GLU* 3.3 19.0 - - + +
13B THR* 3.9 1.6 - - - +
82B ILE* 4.3 0.7 - - + -
99B ASP 3.2 14.3 + - - +
100B LYS 3.3 4.2 + - - +
102B VAL* 1.3 80.6 - - - +
104B ILE* 1.3 63.8 + - - +
106B LEU* 3.5 4.6 + - - +
107B ARG 3.3 15.6 + - - -
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Residues in contact with ILE 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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12B GLU* 3.7 29.6 - - + +
81B THR* 6.3 0.9 - - + -
82B ILE* 5.7 0.4 - - + +
100B LYS* 3.0 47.1 + - + +
101B ALA* 3.8 7.0 - - - +
103B ALA* 1.3 74.9 - - - +
105B CYS* 1.3 59.5 - - - +
107B ARG* 3.1 18.2 + - - +
108B GLU* 2.9 52.2 + - - +
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Residues in contact with CYS 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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40B ALA 4.6 0.2 - - - -
43B ARG* 5.2 0.7 - - - -
44B CYS* 2.0 53.8 - - + -
47B VAL* 6.2 1.3 - - - -
101B ALA 2.8 19.7 + - - +
102B VAL* 3.5 4.0 - - - +
104B ILE* 1.3 77.1 - - - +
106B LEU* 1.3 61.1 + - - +
108B GLU* 3.2 13.1 + - - -
109B ASN* 2.7 39.4 + - - -
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Residues in contact with LEU 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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9B ILE* 3.8 29.2 - - + -
13B THR* 3.8 11.0 - - + -
22B TYR* 3.7 37.9 + - + -
41B THR* 3.6 40.9 + - + +
44B CYS* 3.7 10.8 - - + -
45B CYS* 4.1 9.2 - - - -
102B VAL* 2.8 34.1 + - + +
103B ALA 3.7 4.9 - - - +
105B CYS* 1.3 74.5 - - - +
107B ARG* 1.3 61.7 + - - +
109B ASN* 3.3 4.2 + - - +
110B LEU* 3.2 23.0 + - - +
204B 7PE 5.9 0.2 - - - -
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Residues in contact with ARG 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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12B GLU* 2.6 55.1 + - - +
13B THR* 3.6 7.3 - - + +
103B ALA 3.3 9.1 + - - +
104B ILE* 3.1 30.2 + - - +
106B LEU* 1.3 73.3 - - - +
108B GLU* 1.3 78.7 + - - +
109B ASN 3.0 9.5 + - - -
110B LEU* 3.2 27.7 + - + +
111B GLY 4.8 0.2 + - - -
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Residues in contact with GLU 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 ILE* 2.9 39.3 + - + +
105B CYS* 3.2 12.2 + - - +
107B ARG* 1.3 96.4 + - - +
109B ASN* 1.3 67.1 + - - +
110B LEU 3.7 0.4 - - - -
111B GLY* 5.0 2.1 + - - -
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Residues in contact with ASN 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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40B ALA* 3.1 32.6 + - + +
41B THR* 3.2 21.6 + - - +
44B CYS* 3.4 14.6 - - - -
105B CYS* 2.7 32.7 + - - +
106B LEU 3.3 3.8 + - - +
107B ARG 3.0 0.6 - - - -
108B GLU* 1.3 88.9 + - - +
110B LEU* 1.3 59.9 + - - +
111B GLY 3.0 6.5 - - - +
112B THR* 3.1 17.2 + - - +
113B TYR 3.1 7.6 + - - -
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Residues in contact with LEU 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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13B THR* 3.9 25.6 - - - +
16B LYS* 4.4 26.0 - - + +
21B SER* 6.2 0.2 - - - -
22B TYR* 3.2 22.4 - - - +
41B THR* 4.9 0.2 - - - -
106B LEU 3.2 12.0 + - - +
107B ARG* 3.2 27.0 + - + +
109B ASN* 1.3 76.9 - - - +
111B GLY* 1.3 62.2 + - - +
113B TYR* 3.1 33.0 + - + +
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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