Contacts of the helix formed by residues 75 - 90 (chain B) in PDB entry 4KBQ
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 GLN 75 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70B TYR* 2.6 32.0 + - + +
71B LEU* 4.1 0.6 + - - -
73B MET* 3.3 36.2 + - - +
74B GLN* 1.3 73.4 - - - +
76B HIS* 1.3 66.2 + - - +
77B GLU* 2.9 5.3 + - + -
78B GLN* 2.4 41.7 + - + +
79B ALA* 3.1 19.6 + - - +
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Residues in contact with HIS 76 (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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71B LEU* 4.9 4.9 - - - +
74B GLN* 3.0 51.5 + - + +
75B GLN* 1.3 72.0 + - - +
77B GLU* 1.3 57.2 + - - +
79B ALA* 3.9 8.2 - - - +
80B LEU* 3.1 27.9 + - - +
103B CYS* 4.2 12.8 - - - +
106B GLU* 3.1 26.5 + - + +
107B MET* 3.6 37.8 - - + +
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Residues in contact with GLU 77 (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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75B GLN* 2.9 2.6 + - + -
76B HIS* 1.3 77.3 - - - +
78B GLN* 1.3 65.7 + - + +
80B LEU* 3.3 15.5 + - - +
81B ALA* 3.3 19.8 + - - +
107B MET* 3.7 22.0 - - + +
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Residues in contact with GLN 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B TYR* 3.5 47.0 + - + -
75B GLN* 2.4 42.6 + - + +
77B GLU* 1.3 74.7 - - + +
79B ALA* 1.3 65.4 + - - +
81B ALA* 3.4 8.1 + - - +
82B ASP* 3.2 20.6 + - - +
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Residues in contact with ALA 79 (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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67B ALA* 3.6 26.1 - - + +
70B TYR* 3.7 11.7 - - + +
71B LEU* 3.9 7.9 - - + +
75B GLN 3.1 15.5 + - - +
76B HIS* 3.9 2.0 - - - +
78B GLN* 1.3 77.7 - - - +
80B LEU* 1.3 61.9 + - - +
82B ASP 3.5 0.3 + - - -
83B CYS* 3.0 30.3 + - - -
99B PHE* 6.4 0.2 - - + -
103B CYS* 3.6 24.7 - - - -
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Residues in contact with LEU 80 (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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76B HIS 3.1 16.1 + - - +
77B GLU* 3.5 15.3 - - - +
78B GLN 3.2 0.2 - - - -
79B ALA* 1.3 78.1 - - - +
81B ALA* 1.3 64.0 + - - +
83B CYS* 3.5 6.2 + - - +
84B ARG* 3.1 36.0 + - + +
100B LEU* 4.1 12.3 - - + +
103B CYS* 4.5 8.2 - - + -
104B GLN* 4.9 19.1 - - + +
107B MET* 4.3 23.6 - - + -
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Residues in contact with ALA 81 (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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77B GLU 3.3 10.8 + - - +
78B GLN* 3.7 9.9 - - - +
79B ALA 3.3 0.2 - - - -
80B LEU* 1.3 83.0 - - - +
82B ASP* 1.3 55.7 + - - +
84B ARG* 3.2 7.0 + - - +
85B ARG* 2.9 54.9 + - - +
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Residues in contact with ASP 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B TYR* 3.5 24.9 - - - +
66B ARG* 2.5 58.8 + - - +
67B ALA* 3.7 13.4 + - + -
70B TYR* 3.6 7.7 - - - -
78B GLN 3.2 12.0 + - - +
81B ALA* 1.3 74.6 - - - +
83B CYS* 1.3 60.7 + - - +
85B ARG* 2.8 24.8 + - - +
86B ALA* 2.9 28.2 + - - +
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Residues in contact with CYS 83 (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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64B THR* 5.6 1.1 - - - -
67B ALA* 4.0 10.9 - - - +
79B ALA* 3.0 26.3 + - - +
80B LEU 3.7 0.2 - - - +
82B ASP* 1.3 77.0 - - - +
84B ARG* 1.3 63.2 + - - +
86B ALA* 3.1 8.6 + - - +
87B LEU* 3.1 27.2 + - + +
96B ALA* 3.9 10.4 - - - +
99B PHE* 3.7 18.6 - - - -
100B LEU* 3.4 53.4 - - + -
103B CYS* 5.2 1.6 - - - -
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Residues in contact with ARG 84 (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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80B LEU* 3.1 30.7 + - + +
81B ALA* 3.2 8.7 + - - +
83B CYS* 1.3 77.5 - - - +
85B ARG* 1.3 64.0 + - - +
87B LEU* 3.2 12.4 + - - +
88B GLU* 3.2 34.0 + - + +
100B LEU* 4.4 18.9 - - + +
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Residues in contact with ARG 85 (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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63B TYR* 3.7 31.8 - - + -
66B ARG* 4.4 7.3 - - - +
78B GLN 4.8 0.4 + - - -
81B ALA* 2.9 48.6 + - - +
82B ASP* 2.8 41.7 + - - +
84B ARG* 1.3 78.0 - - + +
86B ALA* 1.3 62.8 + - - +
88B GLU* 3.0 26.1 + - + +
89B LEU* 3.6 8.1 + - - +
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Residues in contact with ALA 86 (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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60B ALA* 4.0 11.8 - - + +
63B TYR* 4.0 16.7 - - + +
64B THR* 3.7 28.9 - - + -
82B ASP 2.9 13.1 + - - +
83B CYS 3.1 8.5 + - - +
85B ARG* 1.3 76.5 - - - +
87B LEU* 1.3 57.7 + - - +
89B LEU* 3.2 5.5 + - - +
90B ASP* 3.0 29.0 + - - +
93B SER* 5.6 1.3 - - - +
96B ALA* 4.2 6.7 - - + -
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Residues in contact with LEU 87 (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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83B CYS 3.1 16.0 + - - +
84B ARG* 3.2 13.0 + - - +
85B ARG 3.1 0.2 - - - -
86B ALA* 1.3 74.9 - - - +
88B GLU* 1.3 64.4 + - - +
89B LEU 3.4 0.5 + - - -
90B ASP 3.5 17.7 - - - +
91B GLY* 3.5 23.1 + - - -
93B SER* 4.4 1.1 - - - -
96B ALA* 3.7 24.7 - - + +
97B HIS* 3.6 44.0 - - + +
100B LEU* 4.4 20.4 - - + -
116B ASN* 5.3 0.2 - - - +
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Residues in contact with GLU 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B ARG* 3.2 26.2 + - - +
85B ARG* 3.0 16.7 + - - +
87B LEU* 1.3 79.8 - - - +
89B LEU* 1.3 61.9 + - + +
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Residues in contact with LEU 89 (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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57B PRO 4.1 1.3 - - - +
58B LEU* 3.5 56.1 - - + +
59B VAL 3.8 1.3 - - - +
60B ALA* 3.5 31.6 - - + +
63B TYR* 3.9 17.9 - - + -
85B ARG 3.6 5.1 + - - +
86B ALA 3.2 2.3 + - - +
87B LEU 4.1 0.2 - - - -
88B GLU* 1.3 82.5 - - + +
90B ASP* 1.3 58.3 + - - +
91B GLY 3.9 1.9 + - - -
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Residues in contact with ASP 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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60B ALA* 4.1 16.7 - - + +
86B ALA 3.0 11.2 + - - +
87B LEU* 3.5 10.0 - - - +
89B LEU* 1.3 77.6 - - - +
91B GLY* 1.3 57.4 + - - +
92B GLN* 3.0 26.7 + - - +
93B SER* 3.2 32.6 + - - -
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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