Contacts of the helix formed by residues 75 - 87 (chain B) in PDB entry 4KEU
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 ASP 75 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26B ARG* 3.3 30.4 + - - +
28B PHE* 5.0 4.9 - - + -
42B GLU* 5.6 1.4 - - - +
73B GLY 3.2 6.3 + - - +
74B ARG* 1.3 76.3 - - - +
76B ILE* 1.3 64.4 + - - +
77B ARG* 2.9 23.3 + - - +
78B PHE* 3.0 12.4 + - + +
79B MET* 3.1 28.5 + - - +
127B GLN* 3.6 5.8 + - - +
34D GLN* 5.7 2.1 + - - +
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Residues in contact with ILE 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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6B VAL* 3.8 29.8 - - + -
74B ARG* 4.6 1.9 - - + +
75B ASP* 1.3 72.5 - - - +
77B ARG* 1.3 66.5 + - - +
79B MET* 3.3 11.4 + - - +
80B GLU* 2.9 26.7 + - - +
92B ALA* 3.9 16.4 - - + -
126B ILE* 3.8 22.2 - - + +
127B GLN* 2.8 26.1 - - - +
129B THR* 3.8 28.7 - - + +
131B ASN* 3.7 29.4 - - + +
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Residues in contact with ARG 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 ASP* 2.9 10.1 + - - +
76B ILE* 1.3 86.2 - - + +
78B PHE* 1.3 65.8 + - - +
80B GLU* 3.4 21.5 + - - +
81B LYS* 3.2 27.7 + - - +
127B GLN* 2.8 43.6 + - - +
128B GLY* 4.1 7.5 + - - -
129B THR* 3.5 17.1 - - + +
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Residues in contact with PHE 78 (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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25B LEU* 4.2 14.8 - - + -
26B ARG* 3.4 68.2 - - + +
42B GLU* 4.2 16.6 - - + +
45B GLU* 4.0 8.3 - - + -
46B PHE* 3.8 45.1 - + + -
49B ALA* 4.3 2.2 - - + -
75B ASP* 3.0 17.3 + - + +
77B ARG* 1.3 76.9 - - - +
79B MET* 1.3 69.0 + - + +
81B LYS* 3.2 12.0 + - + +
82B VAL* 3.2 35.7 + - + +
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Residues in contact with MET 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B VAL* 3.9 8.1 - - + -
25B LEU* 4.2 16.2 - - + -
66B ASP* 3.7 35.4 - - + +
68B THR* 5.5 4.5 - - - +
74B ARG* 4.7 11.4 - - - -
75B ASP 3.1 20.1 + - - +
76B ILE* 3.5 25.1 - - - +
77B ARG 3.3 0.2 - - - -
78B PHE* 1.3 80.8 - - + +
80B GLU* 1.4 61.2 - - - +
82B VAL* 3.3 3.3 + - - +
83B VAL* 3.0 27.4 + - - +
90B LEU* 3.5 28.6 - - + +
92B ALA* 3.9 21.8 - - + -
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Residues in contact with GLU 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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6B VAL* 3.7 12.5 - - + +
7B GLY* 4.6 9.6 - - - +
76B ILE 2.9 16.9 + - - +
77B ARG* 3.5 27.8 - - - +
78B PHE 3.2 0.2 - - - -
79B MET* 1.4 75.5 - - - +
81B LYS* 1.3 63.2 + - + +
83B VAL* 3.2 5.6 + - - +
84B LYS* 3.0 41.1 + - - +
129B THR* 4.4 11.1 - - - +
131B ASN* 2.6 31.4 + - - +
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Residues in contact with LYS 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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42B GLU* 5.0 14.3 + - - +
43B ASP* 5.9 0.8 + - - -
46B PHE* 3.6 39.2 - - + +
77B ARG 3.2 14.2 + - - +
78B PHE* 3.2 12.8 + - + +
80B GLU* 1.3 77.9 - - + +
82B VAL* 1.3 64.1 + - - +
84B LYS* 3.2 14.3 + - + +
85B ALA* 3.0 22.9 + - - +
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Residues in contact with VAL 82 (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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25B LEU* 3.9 21.3 - - + -
46B PHE* 4.0 19.1 - - + -
49B ALA* 4.0 17.7 - - + +
50B VAL* 4.6 3.6 - - + -
53B VAL* 4.3 15.9 - - + -
78B PHE* 3.2 33.0 + - + +
79B MET 3.3 7.2 + - - +
81B LYS* 1.3 73.3 - - - +
83B VAL* 1.3 67.3 + - + +
85B ALA* 3.2 2.8 + - - -
86B THR* 2.8 43.4 + - + +
88B ILE* 4.9 4.3 - - + -
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Residues in contact with VAL 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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6B VAL* 3.4 31.2 - - + +
7B GLY* 4.7 6.1 - - - +
8B LYS* 4.3 15.3 - - + -
79B MET 3.0 19.4 + - - +
80B GLU* 3.5 8.3 - - - +
82B VAL* 1.3 76.0 - - - +
84B LYS* 1.3 60.4 + - + +
86B THR* 3.8 5.2 - - - -
87B GLY* 2.6 32.3 + - - -
88B ILE* 3.7 21.3 - - + +
90B LEU* 3.8 30.7 - - + -
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Residues in contact with LYS 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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7B GLY* 6.4 2.2 - - - -
80B GLU* 3.0 32.9 + - - +
81B LYS* 3.2 13.3 + - + +
83B VAL* 1.3 80.3 - - + +
85B ALA* 1.3 60.8 + - - +
86B THR 3.3 0.9 + - - -
87B GLY* 4.2 2.6 + - - -
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Residues in contact with ALA 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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46B PHE* 3.7 11.9 - - + -
50B VAL* 3.7 30.5 - - + -
54B LYS* 3.8 18.7 + - - -
81B LYS 3.0 15.4 + - - +
82B VAL 3.2 1.3 + - - +
84B LYS* 1.3 76.4 - - - +
86B THR* 1.3 58.9 + - - +
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Residues in contact with THR 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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50B VAL* 3.7 35.7 - - + +
53B VAL* 3.8 22.7 - - + -
54B LYS* 4.2 9.1 - - + +
57B MET* 3.3 23.1 - - - +
82B VAL* 2.8 22.5 + - + +
83B VAL 3.6 0.2 + - - -
84B LYS 4.7 0.2 - - - -
85B ALA* 1.3 83.3 - - - +
87B GLY* 1.3 60.9 + - - +
88B ILE* 3.2 22.6 - - - +
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Residues in contact with GLY 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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8B LYS* 2.6 31.9 + - - -
57B MET* 4.1 7.9 - - - +
83B VAL* 2.6 22.5 + - - -
84B LYS 4.2 2.5 + - - -
86B THR* 1.3 72.0 - - - +
88B ILE* 1.3 55.3 - - - +
89B ASN 3.7 0.3 + - - -
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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