Contacts of the helix formed by residues 78 - 96 (chain B) in PDB entry 3KHE
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 SER 78 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B THR* 3.8 7.2 + - - +
77B VAL* 1.3 75.5 - - - +
79B ASP* 1.3 60.2 + - - +
80B LEU* 3.4 9.6 + - - +
81B ASP* 3.0 35.0 + - - +
82B SER* 2.8 30.3 + - - -
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Residues in contact with ASP 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B VAL 3.9 1.4 + - - +
78B SER* 1.3 73.9 - - - +
80B LEU* 1.3 64.7 + - + +
82B SER* 3.2 9.7 + - - -
83B SER* 3.0 24.6 + - - -
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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
----------------------------------------------------------
78B SER* 3.3 7.9 + - - +
79B ASP* 1.3 78.4 - - + +
81B ASP* 1.3 64.6 + - - +
83B SER* 3.0 22.0 + - - +
84B GLN* 3.1 11.3 + - - +
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Residues in contact with ASP 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B MET* 3.8 28.3 - - - +
77B VAL* 3.8 15.9 - - + -
78B SER* 3.0 28.3 + - - +
80B LEU* 1.3 76.2 - - - +
82B SER* 1.3 58.1 + - - +
84B GLN* 3.1 9.7 + - - +
85B ILE* 2.8 32.1 + - - +
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Residues in contact with SER 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B ARG* 3.1 26.3 + - - +
77B VAL* 3.3 13.3 + - - +
78B SER 2.8 22.5 + - - -
79B ASP* 3.4 11.8 + - - -
81B ASP* 1.3 75.7 - - - +
83B SER* 1.3 57.0 + - - +
85B ILE* 3.2 10.5 + - - +
86B GLU* 3.0 32.4 + - - +
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Residues in contact with SER 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B ASP 3.0 12.4 + - - -
80B LEU* 3.0 22.3 + - - +
82B SER* 1.3 75.2 - - - +
84B GLN* 1.3 61.8 + - - +
86B GLU* 3.3 11.7 + - - +
87B ALA* 3.0 20.3 + - - +
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Residues in contact with GLN 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B LYS* 5.0 2.6 - - - +
80B LEU 3.1 13.5 + - - +
81B ASP* 3.1 12.8 + - - +
83B SER* 1.3 78.8 + - - +
85B ILE* 1.3 56.8 + - + +
87B ALA* 3.0 17.5 + - - +
88B GLU* 2.7 59.4 + - + +
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Residues in contact with ILE 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B ILE* 4.0 29.2 - - + +
66B TYR* 3.7 43.3 - - + -
67B ARG* 4.1 16.8 - - + +
70B MET* 4.3 15.3 - - - -
77B VAL* 4.1 22.0 - - + -
81B ASP 2.8 19.3 + - - +
82B SER* 3.4 9.0 - - - +
84B GLN* 1.3 72.7 - - + +
86B GLU* 1.3 67.4 + - + +
88B GLU* 3.1 9.2 + - + +
89B VAL* 3.0 23.4 + - + +
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Residues in contact with GLU 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B ARG* 2.4 38.0 + - - +
63B ILE* 3.6 27.8 - - - +
82B SER* 3.0 20.2 + - - +
83B SER* 3.4 12.8 - - - +
84B GLN 3.3 0.2 - - - -
85B ILE* 1.3 75.9 - - + +
87B ALA* 1.3 58.6 + - - +
89B VAL* 3.2 4.7 + - - +
90B ASP* 2.9 36.5 + - - +
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Residues in contact with ALA 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 SER 3.0 13.0 + - - +
84B GLN* 3.0 28.7 + - - +
86B GLU* 1.3 77.4 - - - +
88B GLU* 1.3 58.0 + - - +
90B ASP* 3.3 12.1 + - - +
91B HIS* 2.9 27.9 + - - +
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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
----------------------------------------------------------
13B LYS* 3.4 48.8 + - - +
66B TYR* 3.9 33.9 - - + +
84B GLN* 2.7 49.6 + - + +
85B ILE* 3.5 8.7 - - - +
87B ALA* 1.3 72.4 - - - +
89B VAL* 1.3 59.5 + - - +
91B HIS* 3.3 10.7 + - - +
92B ILE* 3.0 32.5 + - + +
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Residues in contact with VAL 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B ARG* 3.9 32.8 - - + +
62B LEU* 3.9 28.9 - - + +
63B ILE* 3.9 31.4 - - + +
66B TYR* 4.2 12.8 - - + -
85B ILE 3.0 16.7 + - - +
86B GLU 3.8 3.8 - - - +
88B GLU* 1.3 74.3 - - - +
90B ASP* 1.3 66.3 + - - +
92B ILE* 3.2 7.1 + - + +
93B LEU* 2.9 30.4 + - + +
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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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59B ARG* 2.7 36.4 + - - +
86B GLU* 2.9 23.9 + - - +
87B ALA* 3.5 11.4 - - - +
89B VAL* 1.3 75.7 - - - +
91B HIS* 1.3 63.7 + - - +
93B LEU* 3.2 5.7 + - - +
94B GLN* 3.2 22.2 + - - +
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Residues in contact with HIS 91 (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 MET 3.4 19.9 + - - -
13B LYS* 3.5 18.6 + - - -
15B PHE 2.7 29.8 + - - -
16B GLN* 3.4 26.0 - - - -
87B ALA 2.9 14.1 + - - +
88B GLU* 3.5 16.2 - - - +
89B VAL 3.3 0.2 - - - -
90B ASP* 1.3 76.6 - - - +
92B ILE* 1.3 66.8 + - + +
94B GLN* 3.2 8.0 + - - +
95B SER* 3.0 29.6 + - - -
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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
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9B LEU 5.4 0.4 - - - +
12B MET* 3.9 49.8 - - + +
13B LYS* 5.1 1.1 - - - +
62B LEU* 4.1 18.2 - - + -
66B TYR* 4.4 21.1 - - + +
88B GLU* 3.0 21.9 + - + +
89B VAL* 3.2 12.8 + - + +
91B HIS* 1.3 77.8 - - + +
93B LEU* 1.3 59.9 + - - +
96B VAL* 2.9 46.6 + - + +
97B ASP 3.6 0.7 + - - -
104B ILE* 3.9 22.9 - - + -
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Residues in contact with LEU 93 (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 LEU 4.8 1.8 - - - +
59B ARG* 3.8 44.9 - - + +
62B LEU* 3.9 22.4 - - + -
89B VAL* 2.9 24.0 + - + +
90B ASP* 3.2 4.5 + - - +
92B ILE* 1.3 75.7 - - - +
94B GLN* 1.3 57.5 + - - +
97B ASP* 3.2 25.7 - - + +
100B ARG* 5.7 1.4 + - - +
102B GLY* 3.8 26.7 - - - +
103B TYR* 4.6 2.7 - - - -
104B ILE* 4.1 15.5 - - + -
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Residues in contact with GLN 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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17B SER* 3.9 8.9 + - - +
90B ASP 3.2 14.3 + - - +
91B HIS* 3.2 8.4 + - - +
92B ILE 3.1 0.4 - - - -
93B LEU* 1.3 80.5 - - - +
95B SER* 1.3 62.1 + - - +
97B ASP* 4.8 2.9 + - - +
100B ARG* 4.2 30.0 + - - +
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Residues in contact with SER 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B PHE* 3.5 22.2 + - - -
16B GLN* 3.2 8.5 + - - -
17B SER* 2.9 40.2 + - - -
91B HIS* 3.0 22.4 + - - -
94B GLN* 1.3 80.6 - - - +
96B VAL* 1.3 65.2 + - - +
97B ASP 3.4 1.6 - - - -
98B PHE* 3.5 21.1 - - - -
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Residues in contact with VAL 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B MET* 4.3 20.9 - - + +
15B PHE* 4.3 6.1 - - + -
92B ILE* 2.9 34.6 + - + +
95B SER* 1.3 73.8 - - - +
97B ASP* 1.3 60.4 + - - +
98B PHE* 2.8 22.4 + - - -
104B ILE* 3.4 29.8 - - + -
108B GLU* 3.5 15.7 - - - +
109B PHE 4.5 0.4 - - - +
112B VAL* 3.8 40.6 - - + -
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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
------------------------------------------------------------
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