Contacts of the helix formed by residues 7 - 19 (chain C) in PDB entry 2R7D
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 THR 7 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C GLU 5.4 1.3 - - - +
6C LEU* 1.3 75.2 - - - +
8C PRO* 1.3 76.3 - - + +
9C ALA* 3.5 9.0 + - - +
10C GLN* 2.9 50.4 + - - +
11C ARG* 3.0 12.0 + - - +
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Residues in contact with PRO 8 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C THR* 1.3 86.9 - - - +
9C ALA* 1.3 61.0 + - - +
11C ARG* 3.3 33.7 + - - +
12C THR* 3.1 25.9 + - - -
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Residues in contact with ALA 9 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C THR* 3.1 8.4 + - - +
8C PRO* 1.3 79.8 - - - +
10C GLN* 1.3 58.5 + - + +
12C THR* 3.3 8.4 + - - -
13C GLU* 3.0 26.0 + - - +
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Residues in contact with GLN 10 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C GLU 4.1 3.1 - - - +
6C LEU* 3.3 27.5 - - + +
7C THR* 2.9 46.4 + - - +
9C ALA* 1.3 74.0 - - + +
11C ARG* 1.3 66.1 + - - +
13C GLU* 3.1 12.4 + - - +
14C VAL* 3.0 26.9 + - - +
27C VAL* 3.8 21.9 - - + +
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Residues in contact with ARG 11 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C LEU* 2.8 44.2 + - + +
7C THR* 3.0 12.4 + - - +
8C PRO* 3.3 34.3 + - - +
10C GLN* 1.3 74.9 - - - +
12C THR* 1.3 57.5 + - - +
14C VAL* 3.3 4.3 + - - +
15C GLU* 2.8 31.5 + - - +
44C LEU* 4.3 4.6 - - - +
49C VAL* 4.1 38.1 - - + +
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Residues in contact with THR 12 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C PRO 3.1 14.1 + - - -
9C ALA* 3.6 11.1 - - - -
11C ARG* 1.3 75.7 - - - +
13C GLU* 1.3 56.2 - - - +
15C GLU* 3.2 14.0 + - - +
16C LEU* 2.7 56.7 + - + +
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Residues in contact with GLU 13 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C ALA 3.0 13.6 + - - +
10C GLN* 3.1 11.6 + - - +
12C THR* 1.3 78.7 - - - +
14C VAL* 1.3 59.8 + - - +
16C LEU* 3.4 12.8 + - - +
17C LEU* 3.4 12.1 + - - +
22C ALA* 5.1 1.2 - - - +
24C LYS 4.8 3.9 - - - +
25C SER* 2.8 28.3 + - - +
26C ARG* 3.0 17.5 + - - +
27C VAL* 2.8 34.8 + - - +
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Residues in contact with VAL 14 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C LEU* 4.0 9.0 - - + -
10C GLN 3.0 16.6 + - - +
11C ARG* 3.7 6.5 - - - +
13C GLU* 1.3 73.2 - - - +
15C GLU* 1.3 61.1 + - - +
17C LEU* 3.1 6.3 + - - +
18C ALA* 2.9 24.6 + - - +
25C SER* 3.9 5.4 - - - +
27C VAL* 3.8 21.5 - - + -
28C LEU* 3.6 24.7 - - + -
40C ALA* 3.6 28.4 - - + +
43C LEU* 4.3 6.5 - - + -
44C LEU* 3.7 23.6 - - + -
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Residues in contact with GLU 15 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C ARG 2.8 18.6 + - - +
12C THR* 3.2 18.5 + - - +
14C VAL* 1.3 78.4 - - - +
16C LEU* 1.3 58.5 + - + +
18C ALA* 3.2 1.0 + - - +
19C ARG* 2.9 63.4 + - - +
44C LEU* 3.9 13.0 - - + +
49C VAL* 4.9 6.4 - - + +
50C TRP* 2.7 40.3 + - + +
54C ARG* 3.2 10.0 + - - -
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Residues in contact with LEU 16 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C THR* 2.7 51.9 + - + +
13C GLU* 3.6 8.1 - - - +
14C VAL 3.2 0.2 - - - -
15C GLU* 1.3 82.7 - - + +
17C LEU* 1.3 59.8 + - - +
19C ARG* 3.5 10.8 + - + +
20C GLY 3.3 2.1 + - - -
21C ARG* 2.8 61.3 + - + +
22C ALA* 3.1 16.3 + - + -
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Residues in contact with LEU 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C GLU 3.4 6.0 + - - +
14C VAL 3.1 9.0 + - - +
16C LEU* 1.3 77.8 - - - +
18C ALA* 1.3 66.1 + - - +
20C GLY* 2.9 12.6 + - - -
22C ALA* 3.1 23.3 - - - +
23C ASP* 3.7 21.3 - - - +
24C LYS 4.0 11.7 - - - +
25C SER* 3.6 25.8 - - - -
28C LEU* 3.6 22.0 - - + -
35C GLU* 3.9 5.6 - - - +
36C THR 3.8 21.1 - - - +
37C PRO* 3.5 24.2 - - + +
40C ALA* 4.0 1.8 - - + -
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Residues in contact with ALA 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C VAL 2.9 13.8 + - - +
15C GLU 3.2 7.6 + - - +
17C LEU* 1.3 77.2 - - - +
19C ARG* 1.3 53.8 + - - +
20C GLY 3.2 0.2 - - - -
37C PRO 3.7 12.3 - - - +
40C ALA* 3.7 9.1 - - + +
41C HIS* 3.9 8.3 - - + +
44C LEU* 3.8 13.7 - - + -
50C TRP* 3.6 24.5 - - + -
56C PRO* 3.7 2.6 - - - +
60C ARG* 2.7 37.1 + - - -
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Residues in contact with ARG 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C GLU* 2.9 48.5 + - - +
16C LEU* 4.0 14.3 - - - +
17C LEU 3.1 0.2 - - - -
18C ALA* 1.3 76.2 - - - +
20C GLY* 1.3 61.4 + - - +
21C ARG* 3.4 7.6 + - + +
50C TRP* 4.1 14.6 - - + -
54C ARG* 3.7 21.1 - - - +
56C PRO* 4.5 6.5 - - + -
59C ASP* 3.1 33.9 + - + +
60C ARG* 3.4 29.1 + - - -
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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