Contacts of the helix formed by residues 68 - 84 (chain A) in PDB entry 3CQ6
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 ALA 68 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A GLU* 3.0 6.8 + - - -
66A ARG 3.4 4.8 - - - +
67A ASP* 1.3 78.4 - - - +
69A VAL* 1.3 58.6 + - - +
70A GLU 3.4 2.4 + - - -
71A LEU* 3.5 9.2 + - + -
72A ARG* 3.0 35.6 + - + +
93A TRP* 5.9 1.6 - - + -
94A ALA* 5.4 1.8 - - + +
258A HIS* 6.1 2.5 - - + -
259A LEU* 4.4 19.3 - - + -
264A GLN* 3.3 35.2 - - + +
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Residues in contact with VAL 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A GLU* 2.9 18.9 + - - +
67A ASP* 3.1 19.8 + - + +
68A ALA* 1.3 76.1 - - - +
70A GLU* 1.3 63.8 + - - +
72A ARG* 3.3 11.7 + - - +
73A ASP* 2.9 28.3 + - - +
89A ARG* 3.9 38.6 - - - +
264A GLN* 4.9 0.2 - - - +
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Residues in contact with GLU 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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65A GLU* 4.7 1.0 + - - -
68A ALA 3.4 0.4 - - - -
69A VAL* 1.3 78.4 - - - +
71A LEU* 1.3 63.1 + - - +
73A ASP* 3.1 14.6 + - + +
74A GLU* 3.1 30.8 + - + +
264A GLN* 5.6 2.0 - - - +
268A ILE* 3.8 31.1 - - + +
272A ARG* 5.6 1.2 + - - -
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Residues in contact with LEU 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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68A ALA* 3.5 14.4 + - + +
69A VAL 3.4 0.2 - - - -
70A GLU* 1.3 77.7 - - - +
72A ARG* 1.3 58.0 + - - +
74A GLU* 3.2 2.6 + - - +
75A LEU* 2.9 41.1 + - + +
94A ALA* 3.8 24.2 - - + -
237A LEU* 4.0 17.0 - - + -
259A LEU* 4.0 11.0 - - + -
264A GLN* 4.3 21.4 - - + +
267A ALA* 3.6 24.2 - - + -
268A ILE* 3.7 21.6 - - + +
271A LEU* 3.9 17.7 - - + -
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Residues in contact with ARG 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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67A ASP* 2.9 41.0 + - - +
68A ALA* 3.0 18.5 + - + +
69A VAL* 3.8 12.1 - - - +
71A LEU* 1.3 77.3 - - - +
73A ASP* 1.3 56.6 + - - +
75A LEU* 3.7 11.1 - - + +
76A ALA* 2.9 31.2 + - - +
89A ARG* 3.0 47.4 + - + +
90A ASP* 4.2 6.9 + - - +
92A LEU* 2.8 32.7 + - + +
93A TRP* 4.0 21.6 - - - +
94A ALA* 4.5 11.4 - - + +
247A ILE* 3.9 18.6 - - - +
251A MET* 5.9 1.8 - - - -
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Residues in contact with ASP 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 VAL* 2.9 22.4 + - - +
70A GLU* 3.1 14.8 + - + +
72A ARG* 1.3 75.7 - - - +
74A GLU* 1.3 66.1 + - - +
76A ALA* 3.3 5.5 + - - +
77A ALA* 3.0 25.3 + - - +
89A ARG* 3.0 43.9 + - - +
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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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70A GLU* 3.1 21.7 + - + +
71A LEU* 3.2 4.0 + - - +
73A ASP* 1.3 80.2 - - - +
75A LEU* 1.3 60.4 + - - +
77A ALA* 3.3 12.9 + - - +
78A TYR* 2.9 28.8 + - - +
268A ILE* 4.5 20.6 - - + +
271A LEU* 3.7 27.8 - - + +
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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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71A LEU* 2.9 39.6 + - + +
72A ARG* 3.7 9.0 - - + +
74A GLU* 1.3 77.0 - - - +
76A ALA* 1.3 55.0 + - - +
78A TYR* 3.3 6.2 + - + +
79A ILE* 2.9 33.1 + - - +
92A LEU* 3.1 19.7 - - + -
94A ALA* 3.8 21.5 - - + +
226A MET* 4.6 3.4 - - - -
230A PHE* 6.3 0.2 - - + -
237A LEU* 4.4 8.5 - - + -
239A TYR* 3.8 41.7 - - + -
271A LEU* 3.9 25.6 - - + -
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Residues in contact with ALA 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 ARG 2.9 15.2 + - - +
73A ASP* 3.5 5.4 - - - +
75A LEU* 1.3 74.9 - - - +
77A ALA* 1.3 63.7 + - - +
79A ILE 3.4 0.5 + - - -
80A THR* 2.9 31.4 + - - -
87A VAL* 3.6 7.0 - - - +
88A THR* 3.3 43.5 - - - +
89A ARG 3.6 1.1 - - - +
92A LEU* 3.6 14.3 - - + +
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Residues in contact with ALA 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 ASP 3.0 14.6 + - - +
74A GLU* 3.3 20.2 + - - +
76A ALA* 1.3 75.6 - - - +
78A TYR* 1.3 63.4 + - - +
80A THR* 3.5 5.9 + - - +
81A LYS* 3.1 24.3 + - - +
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Residues in contact with TYR 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 2.9 16.7 + - - +
75A LEU* 3.3 5.4 + - + +
77A ALA* 1.3 75.5 - - - +
79A ILE* 1.3 63.1 + - + +
81A LYS* 3.3 8.4 + - + +
82A GLN* 2.7 66.8 + - + +
202A GLU* 2.6 37.9 + - - +
230A PHE* 3.5 25.7 - + - -
239A TYR* 3.6 24.9 - + - -
271A LEU* 4.0 14.8 - - + +
274A SER* 4.3 11.9 - - - +
278A LEU* 3.5 25.9 - - + +
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Residues in contact with ILE 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 2.9 19.6 + - - +
76A ALA 3.9 3.4 - - - +
78A TYR* 1.3 84.8 - - + +
80A THR* 1.3 56.3 + - - +
82A GLN* 4.3 1.3 - - - -
83A THR* 2.8 57.2 + - + +
85A VAL* 4.5 1.8 - - + +
87A VAL* 3.6 21.1 - - + -
92A LEU* 4.3 2.2 - - + -
210A THR* 4.5 5.8 - - + -
224A ARG* 4.0 21.8 - - - +
239A TYR* 3.8 27.6 - - + +
241A VAL* 3.8 35.0 - - + -
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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 ALA 2.9 22.0 + - - -
77A ALA* 3.6 6.7 - - - -
79A ILE* 1.3 75.6 - - - +
81A LYS* 1.3 59.7 + - - +
84A GLY* 3.0 29.3 + - - -
85A VAL 3.2 15.3 - - - +
86A ALA* 4.1 11.9 - - + -
87A VAL 3.1 27.4 + - - -
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Residues in contact with LYS 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 ALA 3.1 14.9 + - - +
78A TYR* 3.8 6.3 - - + +
80A THR* 1.3 83.4 - - + +
82A GLN* 1.3 63.4 + - - +
84A GLY* 4.1 3.5 + - - -
274A SER* 5.0 7.5 + - - +
275A ALA* 4.4 20.2 - - - +
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Residues in contact with GLN 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 TYR* 2.7 58.7 + - + +
79A ILE* 3.9 2.5 - - - +
81A LYS* 1.3 75.9 - - - +
83A THR* 1.3 64.4 + - + +
201A ALA 5.3 1.2 + - - -
202A GLU* 3.8 27.4 + - - +
204A SER 5.9 0.4 + - - -
224A ARG* 4.0 14.8 - - - +
278A LEU* 4.8 4.5 - - - +
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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 ILE* 2.8 34.8 + - + +
82A GLN* 1.3 83.6 - - + +
84A GLY* 1.3 61.5 + - - +
85A VAL* 3.4 18.0 + - - +
208A SER* 3.6 28.8 + - - +
210A THR* 3.0 22.8 + - + +
211A THR* 4.5 8.5 - - - +
224A ARG* 3.9 13.7 - - - +
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Residues in contact with GLY 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* 3.0 18.3 + - - -
81A LYS 4.1 4.0 + - - -
82A GLN 3.6 1.4 - - - -
83A THR* 1.3 78.0 - - - +
85A VAL* 1.3 60.6 + - - +
86A ALA 3.9 2.0 + - - -
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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