Contacts of the helix formed by residues 81 - 94 (chain A) in PDB entry 3CAN
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 81 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65A LEU* 6.0 0.2 - - + -
67A SER 3.0 23.0 + - - +
68A MSE 3.1 26.3 + - - +
70A SER* 3.1 25.1 + - - +
73A HIS* 3.7 27.6 - - + +
80A PRO* 1.3 70.8 - - - +
82A GLU* 1.3 72.1 + - - +
83A LEU 3.3 2.9 - - - -
84A ILE* 3.0 11.3 + - + +
85A LEU* 3.0 41.6 + - + +
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Residues in contact with GLU 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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70A SER* 2.8 28.6 + - - -
80A PRO* 3.1 18.4 - - + +
81A ASN* 1.3 78.0 + - - +
83A LEU* 1.3 57.3 + - - +
85A LEU* 3.4 7.8 + - + +
86A LYS* 3.1 35.8 + - - +
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Residues in contact with LEU 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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43A THR 4.8 1.1 - - - +
44A LEU* 4.0 15.0 - - + +
45A LEU 3.5 29.8 - - - +
46A ALA* 3.7 28.9 - - + +
79A VAL* 5.9 7.2 - - + -
80A PRO* 4.6 4.2 + - + +
81A ASN 3.3 0.8 - - - -
82A GLU* 1.3 75.0 - - - +
84A ILE* 1.3 72.5 + - + +
86A LYS* 3.3 18.9 + - + +
87A ASN* 2.9 33.3 + - - +
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Residues in contact with ILE 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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43A THR* 3.5 35.0 - - + +
44A LEU* 4.1 16.2 - - + -
63A ILE* 4.2 4.9 - - + +
64A ASP 3.5 22.2 - - - +
65A LEU* 4.2 11.7 - - + -
73A HIS* 3.8 22.4 - - + +
79A VAL* 4.6 2.2 - - + -
80A PRO 3.7 20.9 - - - +
81A ASN* 3.0 11.9 + - + +
83A LEU* 1.3 81.8 - - + +
85A LEU* 1.3 64.2 + - + +
87A ASN* 3.3 3.1 + - - +
88A ILE* 3.1 36.7 + - + +
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Residues in contact with LEU 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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65A LEU* 3.7 29.8 - - + -
68A MSE 3.9 27.6 - - + +
81A ASN* 3.0 38.8 + - - +
82A GLU* 3.8 7.0 - - + +
84A ILE* 1.3 75.2 - - + +
86A LYS* 1.3 65.5 + - - +
88A ILE* 3.4 1.8 + - + -
89A ARG* 3.0 21.3 + - - +
121A PHE* 3.6 38.3 - - + -
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Residues in contact with LYS 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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48A LYS* 6.4 2.7 - - + -
82A GLU* 3.1 23.5 + - - +
83A LEU* 3.5 21.2 - - + +
85A LEU* 1.3 76.1 - - - +
87A ASN* 1.3 60.8 + - - +
89A ARG* 3.3 7.9 + - - +
90A ARG* 2.9 30.7 + - + +
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Residues in contact with ASN 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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42A THR* 3.3 24.8 + - - +
43A THR 3.3 13.4 + - - +
45A LEU* 2.7 29.9 + - - +
46A ALA 4.9 1.7 - - - +
48A LYS* 5.8 1.6 - - - -
51A VAL* 4.1 18.2 - - + +
63A ILE* 4.3 7.6 - - + -
83A LEU* 2.9 26.9 + - - +
84A ILE* 3.6 5.2 - - - +
86A LYS* 1.3 76.2 - - - +
88A ILE* 1.3 66.4 + - - +
90A ARG* 3.3 8.6 + - - +
91A VAL* 3.0 32.0 + - + +
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Residues in contact with ILE 88 (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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63A ILE* 3.5 34.1 - - + -
65A LEU* 4.0 15.7 - - + -
84A ILE* 3.1 27.4 + - + +
85A LEU* 3.8 4.0 - - + +
86A LYS 3.3 0.2 - - - -
87A ASN* 1.3 76.5 - - - +
89A ARG* 1.3 63.4 + - - +
91A VAL* 3.4 2.5 + - - +
92A ALA* 3.0 21.7 + - - +
98A TYR* 4.0 19.5 - - + -
100A ILE* 3.8 16.8 - - + -
121A PHE* 3.9 20.6 - - + -
122A LEU* 4.0 3.8 - - + -
125A LEU* 3.6 24.2 - - + -
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Residues in contact with ARG 89 (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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85A LEU 3.0 14.4 + - - +
86A LYS* 3.3 10.5 + - - +
88A ILE* 1.3 77.8 - - - +
90A ARG* 1.3 56.5 + - - +
92A ALA* 3.3 1.6 + - - +
93A GLU* 2.9 61.2 + - + +
121A PHE* 4.0 19.7 - - + -
124A SER* 4.1 13.9 + - - -
125A LEU* 3.5 36.1 - - + +
126A PRO* 5.0 6.1 - - - +
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Residues in contact with ARG 90 (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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48A LYS* 3.3 55.5 + - - +
51A VAL* 4.6 11.9 - - + -
52A ASP* 3.1 39.7 + - - +
55A MSE 5.2 1.8 - - + -
86A LYS* 2.9 19.8 + - + +
87A ASN* 3.7 9.4 - - - +
88A ILE 3.2 0.2 - - - -
89A ARG* 1.3 77.9 - - - +
91A VAL* 1.3 63.5 + - + +
93A GLU* 3.4 11.3 + - + +
94A ALA* 3.0 22.7 + - + +
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Residues in contact with VAL 91 (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 THR* 4.7 0.9 - - - +
51A VAL* 4.1 13.5 - - + -
55A MSE 4.2 7.0 - - - -
61A LEU* 3.1 38.4 - - + -
63A ILE* 4.1 12.6 - - + -
87A ASN* 3.0 18.0 + - + +
88A ILE 3.9 3.1 - - - +
90A ARG* 1.3 74.9 - - - +
92A ALA* 1.3 64.0 + - - +
94A ALA* 3.2 10.9 + - - +
95A ASP 3.4 7.6 + - - -
96A PHE* 3.4 33.0 + - + +
98A TYR* 3.9 20.0 - - + -
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Residues in contact with ALA 92 (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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88A ILE 3.0 18.1 + - - +
89A ARG 3.6 4.7 - - - +
91A VAL* 1.3 77.2 - - - +
93A GLU* 1.3 56.3 + - - +
95A ASP* 3.1 15.6 + - - +
98A TYR* 4.0 14.7 - - - +
125A LEU* 3.8 21.1 - - + -
126A PRO* 3.8 11.3 - - + +
127A ARG* 3.5 37.2 - - - +
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Residues in contact with GLU 93 (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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89A ARG* 2.9 50.3 + - + +
90A ARG* 3.8 11.2 - - + +
92A ALA* 1.3 75.5 - - - +
94A ALA* 1.3 58.6 + - - +
95A ASP* 3.2 3.3 + - - +
126A PRO* 4.0 20.2 - - + -
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Residues in contact with ALA 94 (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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55A MSE 3.7 31.4 - - + -
90A ARG* 3.0 16.1 + - + +
91A VAL 3.2 7.1 + - - +
93A GLU* 1.3 75.9 - - - +
95A ASP* 1.3 68.8 + - - +
96A PHE* 3.3 3.7 + - + +
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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