Contacts of the helix formed by residues 75 - 87 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A ARG* 3.0 32.3 + - - +
28A PHE* 4.7 5.5 - - + -
42A GLU* 5.5 1.2 - - - +
73A GLY 3.2 5.3 + - - +
74A ARG* 1.3 77.2 - - - +
76A ILE* 1.3 64.0 + - - +
77A ARG* 3.1 21.8 + - - +
78A PHE* 3.1 19.9 + - + +
79A MET* 3.1 19.9 + - - +
127A GLN* 3.7 4.8 + - - +
34C GLN* 5.6 2.4 + - - +
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Residues in contact with ILE 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A VAL* 3.9 17.3 - - + -
74A ARG* 4.6 1.5 - - - +
75A ASP* 1.3 72.7 + - - +
77A ARG* 1.3 69.6 + - - +
79A MET* 3.5 11.3 + - - +
80A GLU* 3.0 29.2 + - - +
92A ALA* 3.9 27.8 - - + -
126A ILE* 3.7 37.7 - - + +
127A GLN* 2.9 25.1 - - - +
129A THR* 3.8 19.3 - - + +
131A ASN* 3.8 26.9 - - + +
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Residues in contact with ARG 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A ASP* 3.1 9.2 + - - +
76A ILE* 1.3 87.7 - - + +
78A PHE* 1.3 64.3 + - - +
80A GLU* 3.2 34.2 - - - +
81A LYS* 3.2 23.4 + - - +
127A GLN* 2.8 43.8 + - - +
128A GLY* 4.2 7.5 + - - -
129A THR* 3.8 14.8 - - + +
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Residues in contact with PHE 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A LEU* 4.1 15.5 - - + -
26A ARG* 3.4 63.5 - - + +
42A GLU* 3.6 20.0 - - - +
45A GLU* 3.7 28.0 - - + -
46A PHE* 3.8 29.4 - + + -
49A ALA* 4.2 4.7 - - + -
75A ASP* 3.1 17.7 + - + +
77A ARG* 1.3 75.6 - - - +
79A MET* 1.3 69.9 + - + +
81A LYS* 3.3 11.4 + - + +
82A VAL* 3.2 32.7 + - + +
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Residues in contact with MET 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A VAL* 4.0 6.5 - - + -
25A LEU* 4.1 18.8 - - + -
66A ASP* 3.9 33.2 - - + +
68A THR* 5.6 4.3 - - - +
74A ARG* 4.6 13.2 - - - -
75A ASP 3.1 19.4 + - - +
76A ILE* 3.7 23.1 - - - +
78A PHE* 1.3 80.4 - - + +
80A GLU* 1.3 58.5 + - - +
82A VAL* 3.2 4.0 + - - +
83A VAL* 3.0 29.8 + - - +
90A LEU* 3.6 26.9 - - + +
92A ALA* 3.8 24.2 - - + -
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Residues in contact with GLU 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A VAL* 3.7 16.5 - - + +
7A GLY* 4.9 9.8 - - - -
76A ILE 3.0 18.1 + - - +
77A ARG* 3.2 37.9 - - - +
79A MET* 1.3 75.5 - - - +
81A LYS* 1.4 57.4 + - - +
83A VAL* 3.7 4.5 - - - +
84A LYS* 2.9 45.3 + - + +
129A THR* 4.3 8.6 - - - +
131A ASN* 3.0 22.9 + - - +
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Residues in contact with LYS 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A GLU* 4.1 23.0 + - - +
46A PHE* 3.6 23.1 - - + -
77A ARG* 3.2 22.2 + - - +
78A PHE* 3.4 12.8 - - + +
79A MET 3.2 0.2 - - - -
80A GLU* 1.4 74.5 - - + +
82A VAL* 1.3 65.2 + - - +
84A LYS* 3.3 21.0 + - - +
85A ALA* 3.0 24.3 + - - +
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Residues in contact with VAL 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A LEU* 4.0 21.5 - - + -
46A PHE* 4.0 20.9 - - + -
49A ALA* 4.0 22.7 - - + +
50A VAL* 4.4 7.9 - - + -
53A VAL* 4.0 24.2 - - + -
78A PHE* 3.2 22.9 + - + +
79A MET 3.6 6.5 - - - +
81A LYS* 1.3 75.7 - - - +
83A VAL* 1.3 63.5 + - + +
85A ALA* 3.2 1.9 + - - -
86A THR* 2.9 38.0 + - + +
88A ILE* 5.1 2.9 - - + -
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Residues in contact with VAL 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A VAL* 3.5 29.8 - - + +
7A GLY* 4.7 6.1 - - - +
8A LYS* 4.2 15.5 - - + -
79A MET 3.0 17.6 + - - +
80A GLU* 3.7 9.2 - - - +
82A VAL* 1.3 75.5 - - - +
84A LYS* 1.3 62.3 + - + +
86A THR* 4.0 4.9 - - - -
87A GLY* 2.7 31.1 + - - -
88A ILE* 3.9 21.1 - - + +
90A LEU* 3.7 31.9 - - + -
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Residues in contact with LYS 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A GLY* 6.2 2.7 - - - +
80A GLU* 2.9 41.1 + - + +
81A LYS* 3.3 19.6 + - - +
83A VAL* 1.3 80.8 - - + +
85A ALA* 1.3 60.0 + - - +
86A THR 3.7 0.2 + - - -
87A GLY* 4.6 1.2 + - - -
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Residues in contact with ALA 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A PHE* 3.9 20.4 - - + -
50A VAL* 4.0 13.9 - - + -
54A LYS* 3.8 18.9 + - - -
81A LYS 3.0 17.1 + - - +
82A VAL 3.8 3.6 - - - +
83A VAL 3.1 0.4 - - - -
84A LYS* 1.3 78.5 - - - +
86A THR* 1.3 58.2 + - - +
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Residues in contact with THR 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A VAL* 3.8 36.3 - - + +
53A VAL* 3.6 21.5 - - + +
54A LYS* 4.1 11.4 - - + +
57A MET* 3.6 17.7 - - - +
82A VAL* 2.9 21.8 + - + +
85A ALA* 1.3 83.9 - - - +
87A GLY* 1.3 61.6 + - - +
88A ILE* 3.3 23.6 + - - +
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Residues in contact with GLY 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A LYS* 2.6 30.5 + - - -
57A MET* 4.0 7.7 - - - +
83A VAL 2.7 21.1 + - - -
84A LYS 4.6 1.4 + - - -
86A THR* 1.3 73.6 - - - +
88A ILE* 1.3 57.4 + - - +
89A 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