Contacts of the helix formed by residues 73 - 84 (chain A) in PDB entry 3TIN
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 ARG 73 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69A ASP* 2.9 29.0 + - + +
71A LEU 3.5 0.2 - - - -
72A CYS* 1.3 101.0 + - - +
74A LYS* 1.3 67.0 + - - +
75A ALA* 4.4 3.8 - - + +
76A SER* 3.3 21.3 - - - +
77A LEU* 2.5 38.0 + - - +
152A SER* 2.5 48.3 + - - -
153A SER* 4.4 15.5 + - - +
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Residues in contact with LYS 74 (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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72A CYS 3.6 6.0 + - - +
73A ARG* 1.3 77.9 - - - +
75A ALA* 1.3 70.4 + - - +
77A LEU* 2.9 21.6 + - + +
78A VAL* 3.3 9.5 + - - +
94A PHE* 5.5 0.2 - - - -
150A LYS* 4.7 24.3 - - + +
151A SER 3.8 17.6 + - - +
152A SER* 3.7 21.7 + - - +
181A VAL* 4.5 19.7 - - + -
330A ILE* 5.1 4.7 - - - +
331A GLU* 3.8 40.2 + - + -
332A VAL 5.9 0.4 - - - -
702A ADP 4.0 18.2 + - - -
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Residues in contact with ALA 75 (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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73A ARG* 3.2 3.8 - - + +
74A LYS* 1.3 78.3 - - - +
76A SER* 1.3 52.9 + - - +
78A VAL* 2.7 35.9 + - - +
79A LYS* 3.4 4.2 + - - +
99A VAL* 3.8 28.4 - - + +
152A SER* 5.2 14.8 - - - +
179A VAL 5.6 3.4 - - - +
181A VAL* 3.8 8.5 - - + +
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Residues in contact with SER 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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69A ASP 4.1 3.4 - - - -
70A LYS* 3.6 24.3 - - - +
73A ARG* 3.0 26.5 + - - +
75A ALA* 1.3 79.3 - - - +
77A LEU* 1.3 61.4 + - - +
79A LYS* 4.0 9.7 - - - +
80A LEU* 3.1 26.5 + - - +
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Residues in contact with LEU 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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70A LYS 4.3 4.2 + - - -
71A LEU* 3.6 43.1 - - + +
73A ARG 2.5 17.7 + - - +
74A LYS* 2.9 19.9 + - + +
76A SER* 1.3 72.5 - - - +
78A VAL* 1.3 62.6 + - - +
80A LEU* 3.8 4.7 - - + +
81A ILE* 3.3 31.8 + - + +
94A PHE* 3.7 31.9 - - + -
294A CYS* 5.5 1.3 - - - -
329A LEU* 4.7 13.2 - - + -
330A ILE 4.3 12.6 - - - +
331A GLU* 4.8 3.8 - - - -
332A VAL* 4.8 7.6 - - + +
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Residues in contact with VAL 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A LYS 3.4 11.0 - - - +
75A ALA* 2.7 17.9 + - - +
77A LEU* 1.3 73.8 - - - +
79A LYS* 1.3 68.7 + - - +
80A LEU 2.9 0.9 - - - -
81A ILE* 2.7 16.1 + - - +
82A LYS* 2.8 49.9 + - + +
94A PHE* 4.4 15.7 - - + -
97A SER* 3.8 30.1 - - - +
98A TYR* 5.0 2.2 - - - -
99A VAL* 4.6 13.2 - - + +
127A GLU* 5.5 1.1 - - - +
181A VAL* 4.8 5.6 - - + -
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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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75A ALA 3.4 3.2 + - - +
76A SER* 4.0 14.1 - - - +
78A VAL* 1.3 80.2 - - - +
80A LEU* 1.3 56.1 + - - +
82A LYS* 4.1 7.7 - - - +
83A THR* 2.9 32.9 + - - -
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Residues in contact with LEU 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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70A LYS* 3.6 23.1 - - + +
71A LEU* 3.8 26.0 - - + -
76A SER 3.1 17.6 + - - +
77A LEU* 3.8 8.1 - - + +
78A VAL 2.8 4.4 + - - -
79A LYS* 1.3 75.4 - - - +
81A ILE* 1.3 60.6 - - + +
83A THR* 3.8 3.3 - - - -
84A SER* 3.1 30.2 + - - -
87A LEU* 6.0 0.4 - - + -
294A CYS* 4.9 4.5 - - + +
297A CYS* 3.8 31.2 - - - +
298A LEU* 4.6 15.0 - - + -
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Residues in contact with ILE 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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77A LEU* 3.3 24.2 - - + +
78A VAL 2.7 11.5 + - - +
80A LEU* 1.3 75.4 - - + +
82A LYS* 1.3 65.9 + - + +
83A THR 3.2 0.6 + - - -
84A SER 3.4 16.3 - - - +
87A LEU* 3.3 32.3 - - + +
88A THR* 3.5 10.2 + - - +
91A CYS* 3.6 22.0 - - + -
93A TRP* 4.3 16.4 - - + -
94A PHE* 3.3 43.5 - - + -
294A CYS* 5.7 2.2 - - - -
329A LEU* 5.9 0.4 - - + -
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Residues in contact with LYS 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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78A VAL* 2.8 43.0 + - + +
79A LYS* 4.1 6.3 - - - +
81A ILE* 1.3 79.4 - - + +
83A THR* 1.3 64.4 + - - +
88A THR* 3.9 17.3 + - - +
96A GLU* 5.8 1.4 - - - +
97A SER 3.2 21.2 + - - +
98A TYR* 4.0 13.9 - - - -
127A GLU* 4.2 21.7 + - - +
130A GLU* 6.4 0.4 - - - -
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Residues in contact with THR 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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79A LYS 2.9 20.3 + - - -
80A LEU* 3.8 5.4 - - - -
81A ILE 3.2 0.2 - - - -
82A LYS* 1.3 80.2 - - - +
84A SER* 1.3 67.3 + - - +
85A PRO* 3.0 13.3 - - - +
88A THR* 4.9 1.0 - - - +
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Residues in contact with SER 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 LEU* 3.1 17.2 + - - -
81A ILE 4.1 0.2 - - - -
82A LYS 3.7 0.2 - - - -
83A THR* 1.3 75.6 - - - +
85A PRO* 1.3 64.3 - - - +
86A GLU 3.5 1.1 - - - -
87A LEU* 3.5 26.2 - - - -
88A THR* 2.7 37.1 + - - -
297A CYS* 3.7 18.6 - - - -
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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
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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