Contacts of the helix formed by residues 71 - 85 (chain A) in PDB entry 3CMT
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 GLY 71 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A SER 3.4 2.8 - - - -
70A SER* 1.3 80.2 - - - +
72A LYS* 1.3 61.2 + - - +
74A THR* 3.8 0.8 - - - -
75A LEU* 2.8 34.0 + - - +
225A ILE* 3.8 7.3 - - - +
262A ILE* 3.9 14.4 - - - +
502A ADP 3.1 25.1 + - - -
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Residues in contact with LYS 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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64A ILE* 4.3 12.9 - - + +
65A TYR* 3.9 2.5 - - - -
66A GLY 3.4 19.7 + - - +
67A PRO 2.7 28.9 + - - -
70A SER* 3.5 7.9 - - - +
71A GLY* 1.3 72.8 - - - +
73A THR* 1.3 61.1 + - - +
75A LEU* 3.8 2.0 - - - +
76A THR* 3.1 24.3 + - - -
192A ILE* 3.6 26.6 - - + +
193A ASN 3.4 25.4 - - - +
194A GLN* 5.0 0.2 - - - +
225A ILE* 3.6 16.4 - - + -
501A ALF 3.2 23.4 - - - -
502A ADP 2.5 44.5 + - - +
1217A PHE* 3.8 3.7 - - - -
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Residues in contact with THR 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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72A LYS* 1.3 69.7 - - - +
74A THR* 1.3 67.8 + - - +
76A THR* 3.1 4.6 + - - -
77A LEU* 2.8 39.8 + - + +
92A PHE* 4.1 15.0 - - + -
99A LEU* 4.5 8.7 - - + -
144A ASP* 2.9 17.5 + - - +
192A ILE* 3.9 7.6 - - - +
500A MG 2.1 33.6 - - - -
501A ALF 3.6 0.2 - - - -
502A ADP 2.4 22.3 + - - -
1250A LYS* 5.2 1.0 - - - -
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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
----------------------------------------------------------
71A GLY* 3.8 7.6 - - - -
73A THR* 1.3 73.3 - - - +
75A LEU* 1.3 64.6 + - - +
77A LEU* 3.1 4.7 + - - +
78A GLN* 3.0 33.6 + - + +
103A TYR* 3.9 16.5 + - - +
107A LEU* 3.9 21.2 - - + +
262A ILE* 3.8 30.7 - - + -
267A GLY* 4.8 5.6 - - - -
268A ILE* 5.1 1.6 - - + +
502A ADP 2.7 39.0 + - - -
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Residues in contact with LEU 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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42A THR* 4.6 7.0 - - + +
47A LEU* 4.0 25.8 - - + -
56A LEU* 5.7 1.3 - - + -
64A ILE* 3.7 30.7 - - + -
71A GLY 2.8 21.7 + - - +
72A LYS* 3.8 2.9 - - - +
74A THR* 1.3 74.0 - - - +
76A THR* 1.3 64.6 + - - +
78A GLN* 3.0 19.2 + - - +
79A VAL* 3.0 26.7 + - + +
223A LEU* 4.9 4.5 - - + -
225A ILE* 4.0 15.3 - - + -
244A VAL* 4.3 4.5 - - + -
260A PHE* 3.9 27.8 - - + -
262A ILE* 5.4 1.5 - - + +
268A ILE* 4.5 13.0 - - + -
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Residues in contact with THR 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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64A ILE* 4.1 3.0 - - - +
72A LYS 3.1 10.4 + - - -
73A THR 3.2 9.0 - - - +
75A LEU* 1.3 79.0 - - - +
77A LEU* 1.3 64.8 + - - +
79A VAL* 3.2 14.0 + - - +
80A ILE* 3.1 22.2 + - + +
92A PHE* 3.5 19.5 - - + -
142A VAL* 3.3 36.8 - - + +
190A ILE* 3.9 14.6 - - - +
192A ILE* 3.4 22.3 - - + +
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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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73A THR* 2.8 36.5 + - + +
74A THR* 3.6 6.5 - - - +
76A THR* 1.3 73.5 - - + +
78A GLN* 1.3 52.5 + - - +
80A ILE* 3.2 11.1 + - + +
81A ALA* 2.8 34.8 + - - +
92A PHE* 4.0 27.1 - - + -
99A LEU* 4.0 21.3 - - + -
103A TYR* 4.9 6.3 - - + -
104A ALA* 4.2 22.9 - - + +
107A LEU* 3.8 24.5 - - + -
109A VAL* 3.4 18.3 - - + +
114A LEU* 5.8 3.4 - - + -
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Residues in contact with GLN 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A THR 3.9 12.3 - - - +
43A GLY* 4.5 7.0 - - - +
74A THR* 3.0 22.8 + - + +
75A LEU 3.0 7.4 + - - +
77A LEU* 1.3 76.9 - - - +
79A VAL* 1.3 56.3 + - - +
81A ALA* 3.4 5.7 + - - +
82A ALA* 3.0 27.7 + - - +
85A ARG* 4.5 2.0 + - - +
107A LEU* 3.0 41.1 + - - +
266A GLU 4.5 1.7 + - - +
267A GLY* 3.4 8.2 - - - -
268A ILE* 2.7 53.8 + - + +
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Residues in contact with VAL 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A ILE* 4.4 8.8 - - + +
41A SER 3.8 20.0 - - - +
42A THR* 3.6 20.4 - - - +
56A LEU* 4.5 13.2 - - + -
75A LEU* 3.0 28.2 + - + +
76A THR* 3.5 11.2 - - - +
78A GLN* 1.3 70.3 - - - +
80A ILE* 1.3 65.5 + - + +
82A ALA* 3.3 3.0 + - - +
83A ALA* 2.9 28.8 + - - +
140A VAL* 4.5 12.6 - - + -
188A LEU* 4.9 2.7 - - + -
190A ILE* 3.9 23.3 - - + -
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Residues in contact with ILE 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 THR* 3.1 14.8 + - + +
77A LEU* 3.4 14.4 - - + +
79A VAL* 1.3 76.4 - - + +
81A ALA* 1.3 54.6 + - - +
83A ALA* 3.0 3.4 + - - +
84A GLN* 2.8 49.3 + - - +
90A CYS* 3.8 31.9 - - + -
91A ALA 4.7 1.3 - - - +
92A PHE* 3.9 18.8 - - + -
109A VAL* 4.0 9.0 - - + -
114A LEU* 3.9 18.2 - - + -
140A VAL* 4.3 7.2 - - + -
142A VAL* 3.4 32.1 - - + -
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Residues in contact with ALA 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 2.8 20.0 + - - +
78A GLN* 3.5 8.1 - - - +
79A VAL 3.3 0.2 - - - -
80A ILE* 1.3 71.5 - - - +
82A ALA* 1.3 57.1 + - - +
84A GLN* 3.3 9.6 + - - +
85A ARG* 2.9 44.0 + - - +
107A LEU 3.9 11.2 - - - +
108A GLY 3.4 32.2 - - - +
109A VAL* 4.0 3.1 - - + -
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Residues in contact with ALA 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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40A ILE* 5.4 1.3 - - + -
41A SER* 4.2 28.9 - - - +
43A GLY* 5.0 5.8 - - - +
78A GLN 3.0 17.0 + - - +
79A VAL* 3.6 4.7 - - - +
81A ALA* 1.3 75.6 - - - +
83A ALA* 1.3 62.3 + - - +
85A ARG* 3.2 34.4 + - - +
86A GLU* 3.5 16.4 + - - +
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Residues in contact with ALA 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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40A ILE* 4.4 13.2 - - + +
79A VAL 2.9 17.8 + - - +
80A ILE 3.5 4.0 - - - +
82A ALA* 1.3 73.4 - - - +
84A GLN* 1.3 60.7 + - - +
86A GLU* 3.1 24.5 + - - +
88A LYS* 3.1 31.7 + - + +
90A CYS* 3.9 5.6 - - - -
140A VAL* 3.8 28.5 - - + -
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Residues in contact with GLN 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 ILE* 2.8 30.7 + - - +
81A ALA* 3.7 3.9 - - - +
83A ALA* 1.3 67.4 - - - +
85A ARG* 1.3 57.6 + - - +
86A GLU 2.9 9.7 + - - -
87A GLY* 2.9 14.2 + - - -
88A LYS 3.8 18.4 + - - +
90A CYS* 3.9 11.4 - - - +
108A GLY 5.8 0.4 - - - +
109A VAL* 3.5 9.1 - - - +
110A ASP* 2.7 58.8 + - + +
113A ASN* 3.9 7.9 + - - +
114A LEU* 3.6 24.4 - - - +
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Residues in contact with ARG 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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78A GLN* 4.5 2.2 + - - +
81A ALA* 2.9 24.6 + - - +
82A ALA* 3.2 45.0 - - - +
84A GLN* 1.3 75.2 - - - +
86A GLU* 1.3 60.2 + - + +
87A GLY 3.6 0.8 + - - -
107A LEU 5.5 1.0 + - - -
108A GLY* 4.6 8.1 + - - -
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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