Contacts of the helix formed by residues 65 - 80 (chain A) in PDB entry 1CM8
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 GLU 65 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64A SER* 1.3 75.8 - - - +
66A LEU* 1.3 62.4 + - - +
67A PHE 3.3 0.4 - - - -
68A ALA* 3.9 3.7 - - - +
69A LYS* 2.9 35.5 + - + +
335A ARG 3.4 20.9 + - - +
336A THR* 5.3 2.1 - - - -
337A LEU* 5.5 5.5 + - + +
340A TRP* 3.5 24.9 + - + +
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Residues in contact with LEU 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A SER* 3.3 6.9 + - - +
65A GLU* 1.3 80.3 - - - +
67A PHE* 1.3 74.8 + - + +
69A LYS* 3.9 22.7 - - - +
70A ARG* 3.2 70.6 + - - +
183A TPO 5.4 8.3 - - + +
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Residues in contact with PHE 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A TYR* 4.2 24.0 - + - -
60A ARG 3.6 14.4 - - - -
61A PRO* 3.3 16.8 - - + +
63A GLN* 3.2 28.5 - - + -
64A SER* 2.9 23.6 + - - +
66A LEU* 1.3 92.4 - - + +
68A ALA* 1.3 65.3 + - - +
70A ARG* 3.2 14.9 + - - +
71A ALA* 2.9 23.6 + - - +
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Residues in contact with ALA 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A PRO 2.9 16.6 + - - +
62A PHE* 3.8 14.4 - - + -
64A SER 3.4 18.3 + - - +
65A GLU 3.9 2.2 - - - +
66A LEU 3.4 0.4 - - - -
67A PHE* 1.3 76.7 - - - +
69A LYS* 1.3 63.0 + - - +
71A ALA* 3.1 5.0 + - - +
72A TYR* 2.9 24.3 + - - +
337A LEU* 5.2 2.2 - - - +
340A TRP* 3.4 32.8 - - + -
344A THR* 4.6 1.7 + - - -
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Residues in contact with LYS 69 (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 GLU* 2.9 23.4 + - - +
66A LEU* 3.9 23.5 - - - +
68A ALA* 1.3 76.7 - - - +
70A ARG* 1.3 58.6 + - - +
72A TYR* 3.5 2.6 + - - +
73A ARG* 2.9 70.4 + - + +
183A TPO 2.8 25.0 + - - -
340A TRP* 3.6 39.4 - - + -
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Residues in contact with ARG 70 (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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66A LEU* 3.2 55.9 + - + +
67A PHE* 3.2 13.5 + - - +
68A ALA 3.2 0.6 - - - -
69A LYS* 1.3 73.8 - - + +
71A ALA* 1.3 57.1 + - - +
73A ARG* 3.0 21.9 + - - +
74A GLU* 2.8 38.6 + - - +
173A GLY* 3.4 25.5 - - - +
174A LEU* 3.4 29.3 - - + +
183A TPO 4.8 14.3 + - - +
185A PTR 4.6 10.1 + - - -
186A VAL* 5.6 0.2 - - - +
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Residues in contact with ALA 71 (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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58A LEU* 4.4 15.7 - - + -
61A PRO* 3.8 26.5 - - + -
62A PHE* 5.1 3.6 - - + -
67A PHE 2.9 13.4 + - - +
68A ALA* 3.1 9.6 + - - +
70A ARG* 1.3 76.3 - - - +
72A TYR* 1.3 63.2 + - - +
74A GLU* 3.3 4.1 + - - +
75A LEU* 3.0 24.8 + - - +
105A PHE* 4.1 19.9 - - + -
344A THR* 5.3 0.4 - - - +
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Residues in contact with TYR 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 ALA 2.9 13.6 + - - +
69A LYS 3.9 2.2 - - - +
71A ALA* 1.3 76.4 - - - +
73A ARG* 1.3 67.0 + - + +
75A LEU* 3.4 6.1 + - + +
76A ARG* 2.9 61.2 + - + +
326A TYR* 4.6 1.3 - - - -
328A ASP* 2.7 37.3 + - - -
329A SER 4.4 7.8 + - - -
340A TRP* 3.8 27.6 - + + -
343A VAL* 4.1 19.7 - - + -
344A THR* 3.5 36.5 + - - +
347A GLU* 4.0 15.6 + - + +
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Residues in contact with ARG 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 LYS* 2.9 66.3 + - + +
70A ARG* 3.5 18.8 - - - +
72A TYR* 1.3 85.3 - - + +
74A GLU* 1.3 58.4 + - - +
76A ARG* 3.9 3.0 - - - +
77A LEU* 3.0 39.9 + - + +
152A ARG* 4.5 1.8 - - - +
172A PHE 4.9 0.4 - - - +
173A GLY 5.9 0.7 - - - +
174A LEU* 5.4 1.8 + - - +
175A ALA 3.3 25.5 + - - +
176A ARG* 3.5 36.9 - - - +
177A GLN 5.3 0.2 - - - +
183A TPO 2.9 33.0 + - - -
326A TYR* 5.4 2.2 - - - +
340A TRP* 5.8 0.4 - - + -
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Residues in contact with GLU 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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56A LYS* 2.8 35.2 + - - +
58A LEU* 3.7 22.3 - - + +
70A ARG 2.8 19.6 + - - +
71A ALA* 3.6 5.0 - - - +
73A ARG* 1.3 71.3 - - - +
75A LEU* 1.3 68.2 + - - +
77A LEU* 4.3 0.5 - - - +
78A LEU* 3.2 42.7 + - + +
107A LEU* 4.1 12.2 - - + +
171A ASP* 4.6 0.5 - - - -
172A PHE* 3.9 27.6 + - + +
173A GLY* 3.4 24.7 + - - -
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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
----------------------------------------------------------
71A ALA 3.0 16.8 + - - +
72A TYR* 3.8 4.9 - - - +
74A GLU* 1.3 79.0 - - - +
76A ARG* 1.3 53.0 + - + +
78A LEU* 3.1 3.3 + - - +
79A LYS* 2.8 59.0 + - + +
89A LEU* 4.5 3.4 - - + -
92A VAL* 4.0 12.6 - - + -
105A PHE* 4.1 11.6 - - + -
107A LEU* 3.7 28.9 - - + +
344A THR* 4.2 7.4 - - + +
347A GLU* 3.9 24.5 - - + -
348A VAL* 3.6 31.4 - - + -
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Residues in contact with ARG 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 TYR* 2.9 45.0 + - + +
73A ARG 3.9 2.5 - - - +
75A LEU* 1.3 78.5 - - - +
77A LEU* 1.3 60.1 + - - +
79A LYS* 3.4 6.4 + - - +
80A HIS* 3.1 23.9 + - - +
326A TYR* 3.0 31.1 + - - +
327A ASP 2.6 30.7 + - - -
328A ASP* 2.8 25.3 + - - +
347A GLU* 3.3 42.6 + - + +
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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 ARG* 3.0 29.6 + - + +
74A GLU 4.3 1.6 - - - +
76A ARG* 1.3 73.3 - - - +
78A LEU* 1.3 61.8 + - - +
80A HIS* 3.2 1.6 + - - +
81A MET* 2.8 48.7 + - + +
149A ILE* 3.4 35.2 - - + -
172A PHE* 4.4 9.6 - - + +
175A ALA* 3.6 44.4 - - + +
176A ARG* 3.8 8.3 - - - +
326A TYR* 3.9 28.7 - - + -
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Residues in contact with LEU 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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74A GLU* 3.2 27.2 + - + +
75A LEU 3.1 1.8 + - - +
77A LEU* 1.3 80.3 - - - +
79A LYS* 1.3 62.6 + - - +
80A HIS 3.3 0.5 + - - -
81A MET* 3.7 29.0 - - + +
87A ILE* 3.5 45.4 - - + +
88A GLY* 5.1 2.6 - - - -
89A LEU* 3.2 35.3 + - + +
107A LEU* 3.6 31.0 - - + -
109A MET* 5.4 3.4 - - - -
172A PHE* 4.0 14.1 - - + +
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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 LEU* 2.8 39.9 + - + +
76A ARG* 3.8 5.4 - - - +
78A LEU* 1.3 76.8 - - - +
80A HIS* 1.3 59.1 + - - +
81A MET 4.5 1.4 - - - +
89A LEU* 4.0 6.7 - - + -
347A GLU* 2.7 56.0 + - - +
350A SER* 3.0 20.7 + - - -
351A PHE* 3.9 36.5 - - + +
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Residues in contact with HIS 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 ARG 3.1 17.2 + - - +
77A LEU 3.2 2.4 + - - +
79A LYS* 1.3 78.1 - - - +
81A MET* 1.3 83.5 + - + +
82A ARG* 3.7 4.2 + - - +
143A TYR* 4.3 7.8 + - - -
147A ALA* 4.8 3.4 - - + +
149A ILE* 4.6 2.7 - - + -
324A GLN* 3.1 35.5 + - + +
325A LYS 4.0 4.0 - - - -
326A TYR* 3.7 44.5 + + + -
327A ASP 5.3 0.4 + - - -
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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