Contacts of the helix formed by residues 71 - 81 (chain A) in PDB entry 3C6Q
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 VAL 71 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43A ILE* 3.9 8.7 - - + -
47A LEU* 3.7 22.4 - - + -
50A LEU* 4.7 2.7 - - + -
63A ILE* 4.2 14.6 - - + -
65A PRO* 3.6 22.0 - - + -
67A ASP 3.3 13.0 - - - +
68A PRO 3.3 21.3 - - - +
70A ALA* 1.3 76.5 - - - +
72A ILE* 1.3 68.1 + - - +
74A THR* 3.0 7.7 + - - -
75A ILE* 3.0 41.9 + - + +
92A SER* 3.7 11.4 - - - +
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Residues in contact with ILE 72 (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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68A PRO 3.5 16.6 - - - +
69A THR* 3.1 28.7 - - + +
71A VAL* 1.3 78.3 - - - +
73A PRO* 1.3 69.5 - - + +
75A ILE* 3.3 1.9 + - - +
76A LYS* 2.9 27.6 + - + +
92A SER* 3.9 6.7 - - - +
94A ASP* 3.5 39.0 - - + +
95A SER* 4.0 14.8 - - - +
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Residues in contact with PRO 73 (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 THR 3.9 2.7 - - - +
70A ALA* 3.2 20.4 - - - +
71A VAL 3.4 0.9 - - - -
72A ILE* 1.3 96.5 - - + +
74A THR* 1.3 62.6 + - - +
76A LYS* 3.2 11.7 + - + +
77A LYS* 3.0 22.1 + - - +
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Residues in contact with THR 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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47A LEU* 3.8 25.5 - - - +
50A LEU* 3.6 36.8 - - + -
51A GLU* 4.2 17.1 + - + +
54A ILE* 3.9 17.6 - - + +
70A ALA 4.3 3.3 + - - -
71A VAL 3.0 8.8 + - - -
73A PRO* 1.3 78.2 - - - +
75A ILE* 1.3 63.6 + - - +
77A LYS* 3.0 19.0 + - + +
78A ALA 3.1 9.5 + - - -
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Residues in contact with ILE 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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50A LEU* 4.3 15.9 - - + -
63A ILE* 4.2 18.4 - - + -
71A VAL* 3.0 28.9 + - + +
72A ILE 3.6 6.5 - - - +
74A THR* 1.3 76.1 - - - +
76A LYS* 1.3 63.0 + - - +
78A ALA* 3.1 16.8 + - - +
79A LEU* 3.1 25.1 + - + +
85A VAL* 4.1 24.9 - - + -
87A THR* 4.9 4.7 - - + -
95A SER* 3.2 45.3 - - - +
97A ARG 4.2 3.8 - - - +
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Residues in contact with LYS 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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72A ILE* 2.9 18.8 + - + +
73A PRO* 3.2 14.3 + - + +
75A ILE* 1.3 77.3 - - - +
77A LYS* 1.3 61.3 + - - +
79A LEU* 3.4 13.8 + - + +
80A GLU* 3.3 35.2 + - + +
95A SER 4.6 4.5 - - - +
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Residues in contact with LYS 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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51A GLU* 4.4 21.5 + - - +
54A ILE* 4.6 10.5 - - + -
73A PRO 3.0 10.7 + - - +
74A THR* 3.0 15.1 + - - +
76A LYS* 1.3 78.1 - - - +
78A ALA* 1.3 61.1 + - - +
80A GLU* 3.2 18.4 + - + +
81A MET* 3.3 35.4 + - + +
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Residues in contact with ALA 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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50A LEU* 6.3 0.9 - - + -
54A ILE* 3.8 29.6 - - + +
61A ILE* 4.5 6.7 - - + -
74A THR 3.1 5.2 + - - +
75A ILE* 3.1 10.6 + - - +
77A LYS* 1.3 73.3 - - - +
79A LEU* 1.3 64.4 + - - +
81A MET* 3.1 10.9 + - - +
83A ILE* 2.9 39.1 + - + +
85A VAL* 4.2 16.4 - - + -
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Residues in contact with LEU 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 ILE* 3.1 25.1 + - + +
76A LYS* 3.5 11.7 - - + +
78A ALA* 1.3 77.8 - - - +
80A GLU* 1.3 57.5 + - + +
82A GLY* 3.0 19.2 + - - -
83A ILE 3.4 16.8 - - - +
85A VAL* 3.8 14.4 - - + +
96A GLY* 3.6 35.7 - - - +
98A TYR* 3.7 37.9 + - + +
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Residues in contact with GLU 80 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76A LYS* 3.3 23.8 + - + +
77A LYS* 3.2 15.0 + - + +
78A ALA 3.2 0.6 - - - -
79A LEU* 1.3 78.6 - - + +
81A MET* 1.3 67.1 + - + +
82A GLY 3.2 1.1 + - - -
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Residues in contact with MET 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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54A ILE* 4.4 18.6 - - + -
77A LYS* 3.3 30.7 + - + +
78A ALA* 3.1 9.4 + - - +
80A GLU* 1.3 84.8 - - + +
82A GLY* 1.3 61.6 + - - +
83A ILE* 3.3 16.3 + - + +
294B LYS* 5.5 6.8 + - - -
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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