Contacts of the helix formed by residues 77 - 88 (chain A) in PDB entry 2DLL
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 THR 77 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74A ASP* 3.0 22.4 + - - +
76A PRO* 1.3 77.5 - - - +
78A TRP* 1.3 67.2 + - + +
80A THR* 4.6 2.2 - - - -
81A ARG* 2.8 49.5 + - + +
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Residues in contact with TRP 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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53A ALA* 3.9 20.4 - - + -
56A PHE* 3.9 23.1 - - + +
57A LYS* 3.5 44.6 - - + +
59A TRP* 4.5 2.8 - - - -
60A ALA* 3.5 31.5 - - + +
66A PHE* 3.9 23.2 - + - +
73A PRO* 3.3 33.4 - - + -
74A ASP 3.7 11.8 + - - -
75A PRO* 3.0 31.5 + - + +
77A THR* 1.3 83.0 - - + +
79A LYS* 1.3 66.7 + - - +
81A ARG* 3.2 5.6 + - + +
82A LEU* 2.9 25.6 + - - +
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Residues in contact with LYS 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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39A TRP* 4.7 26.0 - - + +
40A LYS 4.6 10.8 + - - -
41A HIS* 4.5 20.0 + - - +
56A PHE* 3.6 32.3 - - + -
75A PRO* 2.7 21.5 + - + +
76A PRO* 4.0 4.0 - - + +
78A TRP* 1.3 72.7 - - - +
80A THR* 1.3 54.7 + - - +
82A LEU* 3.8 0.2 - - - -
83A ARG* 2.7 56.3 + - + +
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Residues in contact with THR 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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76A PRO* 2.6 33.9 + - - +
77A THR* 4.1 3.1 - - - -
79A LYS* 1.3 72.2 - - - +
81A ARG* 1.3 64.2 + - + +
83A ARG* 4.4 7.9 - - - +
84A CYS* 2.8 35.4 + - + +
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Residues in contact with ARG 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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59A TRP* 4.0 14.7 + - + +
60A ALA* 6.0 4.5 - - + -
77A THR* 2.8 43.7 + - + +
78A TRP* 3.4 5.6 - - + +
80A THR* 1.3 75.4 - - + +
82A LEU* 1.3 62.3 + - - +
84A CYS* 3.6 9.7 - - - +
85A ALA* 3.1 23.7 + - - +
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Residues in contact with LEU 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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9A LEU* 3.2 36.6 - - + -
12A TRP* 4.1 6.3 - - + -
13A LEU* 5.2 5.4 - - + -
37A ILE* 5.6 6.3 - - + -
55A LEU* 4.6 15.9 - - + -
56A PHE* 3.6 33.2 - - + -
59A TRP* 3.4 34.9 - - + +
78A TRP 2.9 13.0 + - - +
79A LYS 3.9 1.3 - - - +
81A ARG* 1.3 72.9 - - - +
83A ARG* 1.3 69.3 + - - +
84A CYS 2.9 1.8 - - - -
85A ALA* 2.6 15.8 + - + +
86A LEU* 2.8 19.0 + - + +
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Residues in contact with ARG 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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39A TRP* 3.6 46.2 - - + +
56A PHE* 4.9 3.2 - - + -
79A LYS* 2.7 44.6 + - + +
80A THR* 4.0 6.5 - - - +
82A LEU* 1.3 73.7 - - - +
84A CYS* 1.3 61.5 + - - +
86A LEU* 3.6 9.1 - - - +
87A ASN* 3.6 16.8 + - - +
108A LYS* 5.7 4.0 - - - +
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Residues in contact with CYS 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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80A THR* 2.8 26.5 + - + +
81A ARG* 3.6 10.5 - - - +
82A LEU 2.7 3.2 + - - -
83A ARG* 1.3 73.8 - - - +
85A ALA* 1.3 54.6 + - - +
87A ASN* 3.2 6.3 + - - +
88A LYS* 2.8 51.6 + - - +
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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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9A LEU* 4.0 18.6 - - + +
59A TRP* 4.4 14.8 - - + -
81A ARG* 3.1 16.0 + - - +
82A LEU* 2.6 16.2 + - - +
84A CYS* 1.3 71.9 - - - +
86A LEU* 1.3 63.4 + - - +
88A LYS* 3.6 8.9 - - - +
89A SER* 2.8 28.1 + - - -
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Residues in contact with LEU 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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9A LEU* 4.2 9.9 - - + +
13A LEU* 4.0 15.9 - - + -
35A PHE* 5.3 4.0 - - + -
37A ILE* 5.0 12.1 - - + -
39A TRP* 4.4 24.7 - - + -
82A LEU* 2.8 19.7 + - + +
83A ARG* 3.6 13.2 - - - +
85A ALA* 1.3 74.7 - - - +
87A ASN* 1.3 60.5 + - - +
89A SER* 3.8 11.0 - - - -
92A PHE* 3.8 42.0 - - + +
110A TYR* 4.0 40.0 - - + +
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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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83A ARG 3.6 7.0 + - - +
84A CYS* 3.2 7.3 + - - +
85A ALA 3.1 0.4 - - - -
86A LEU* 1.3 75.2 - - - +
88A LYS* 1.3 69.3 + - - +
89A SER 3.1 11.0 + - - +
90A ASN* 5.1 0.3 - - - -
94A GLU* 5.7 2.9 - - - +
110A TYR* 4.3 18.0 + - - +
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Residues in contact with LYS 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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84A CYS* 2.8 40.1 + - - +
85A ALA* 3.6 9.9 - - - +
87A ASN* 1.3 75.0 - - - +
89A SER* 1.3 65.1 + - - +
90A ASN* 2.8 8.5 + - - +
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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