Contacts of the helix formed by residues 66 - 74 (chain A) in PDB entry 7CE1
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 ASN 66 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A ARG* 3.6 25.9 + - - +
64A GLN 3.4 1.8 + - - -
65A PRO* 1.3 69.6 - - - +
67A ARG* 1.3 66.9 + - - +
68A ALA* 3.1 18.4 + - - +
69A GLY* 3.2 10.2 + - - +
70A VAL* 3.1 16.9 + - - +
71B ARG* 5.3 2.8 + - - -
72B LEU* 4.5 6.4 - - - +
11a G 3.4 45.4 + - - +
12a T 3.0 11.1 + - - +
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Residues in contact with ARG 67 (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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19A ARG* 5.0 0.2 - - - +
65A PRO 3.0 8.5 + - - +
66A ASN* 1.3 72.0 + - - +
68A ALA* 1.3 52.2 + - - +
69A GLY 2.8 5.3 + - - -
70A VAL* 2.9 8.5 + - - +
71A ARG* 2.7 40.2 + - + +
77A THR 3.6 14.8 + - - +
78A ASN* 3.1 35.1 + - + +
79A VAL* 3.8 9.3 - - - +
109A GLN* 3.5 24.4 + - - +
111A HIS* 3.5 38.2 + - - -
71B ARG* 3.7 29.8 - - - +
129B TYR* 4.7 4.3 + - - -
133B THR* 4.8 9.9 - - + -
135B SER* 4.8 4.7 - - - -
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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
----------------------------------------------------------
66A ASN* 3.1 11.6 + - - +
67A ARG* 1.3 77.3 - - - +
69A GLY* 1.3 57.1 + - - +
71A ARG* 3.8 7.6 - - - +
72A LEU* 3.2 26.5 + - - +
68B ALA* 4.0 11.6 - - - +
71B ARG* 3.7 43.4 - - + +
72B LEU* 3.9 18.2 - - + +
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Residues in contact with GLY 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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66A ASN* 3.2 11.3 + - - -
67A ARG 2.8 0.8 - - - -
68A ALA* 1.3 78.9 - - - +
70A VAL* 1.3 64.1 + - - +
71A ARG 3.1 0.4 + - - -
72A LEU 3.5 3.1 + - - -
73A ARG* 3.5 3.5 + - - +
72B LEU* 3.8 9.8 - - - +
11a G 3.1 42.0 + - - -
12a T 3.8 14.3 + - - -
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Residues in contact with VAL 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A PRO* 4.0 14.6 - - + -
66A ASN 3.1 21.1 - - - +
67A ARG* 2.9 6.7 + - - +
69A GLY* 1.3 78.1 - - - +
71A ARG* 1.3 59.1 + - - +
73A ARG* 5.1 0.7 - - - -
74A THR* 2.7 47.1 + - - +
76A LYS* 4.1 11.4 - - + +
78A ASN* 5.5 10.8 - - - +
12a T 3.8 31.0 - - - +
13a T 4.2 11.4 - - - +
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Residues in contact with ARG 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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67A ARG* 2.7 19.7 + - + +
68A ALA* 4.2 2.2 - - - +
70A VAL* 1.3 78.2 - - - +
72A LEU* 1.3 62.4 + - - +
74A THR 3.0 12.4 - - - +
75A GLY* 4.6 4.2 - - - +
76A LYS 3.4 19.7 - - - +
77A THR* 3.8 35.3 + - + +
79A VAL* 4.4 13.3 - - - +
133A THR 4.9 3.4 + - - -
134A GLY 4.5 2.2 + - - -
135A SER* 3.6 31.3 + - - +
66B ASN* 5.6 4.5 - - - +
67B ARG* 3.9 33.6 - - - +
68B ALA* 3.7 24.7 - - + +
71B ARG* 5.9 3.0 - - - +
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Residues in contact with LEU 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 3.2 16.7 + - - +
70A VAL 3.4 0.4 - - - -
71A ARG* 1.3 80.2 - - - +
73A ARG* 1.3 60.6 + - - +
66B ASN* 4.0 13.8 - - - +
68B ALA* 3.9 4.0 - - + +
69B GLY* 4.1 10.8 - - - +
72B LEU* 3.4 31.4 - - + -
11a G 3.4 10.1 - - - +
10b C 3.2 54.2 + - + +
11b G 3.5 43.7 - - + +
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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 GLY 3.5 6.6 + - - +
70A VAL* 4.4 1.1 - - - +
71A ARG 3.4 0.2 - - - -
72A LEU* 1.3 83.2 - - - +
74A THR* 1.3 68.2 + - + +
75A GLY 4.1 0.5 + - - -
11a G 3.8 3.1 - - - +
12a T 3.6 21.3 - - + +
13a T 3.2 42.8 + - - +
14a G 2.4 47.2 + - - -
8b A 4.6 3.6 + - - -
9b A 3.7 27.0 + - - -
10b C 3.2 29.1 + - - +
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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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70A VAL* 2.7 44.4 + - + +
71A ARG 3.0 11.0 - - - +
73A ARG* 1.3 79.2 - - + +
75A GLY* 1.3 58.1 + - - +
76A LYS* 2.8 18.3 + - - +
13a T 3.6 42.8 - - - +
14a G 4.8 6.1 - - - +
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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