Contacts of the helix formed by residues 7 - 19 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A GLU 5.0 3.4 - - - +
6A LEU* 1.3 74.9 - - - +
8A PRO* 1.3 75.1 - - - +
9A ALA* 3.6 7.1 + - - +
10A GLN* 2.6 45.2 + - - +
11A ARG* 2.9 21.2 + - - +
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Residues in contact with PRO 8 (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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7A THR* 1.3 87.2 - - - +
9A ALA* 1.3 62.8 + - - +
11A ARG* 3.0 32.8 + - - +
12A THR* 3.0 26.5 + - - -
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Residues in contact with ALA 9 (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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7A THR* 3.3 7.0 + - - +
8A PRO* 1.3 79.2 - - - +
10A GLN* 1.3 58.2 + - + +
12A THR* 3.5 7.9 + - - -
13A GLU* 3.0 26.2 + - - +
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Residues in contact with GLN 10 (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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5A GLU 4.4 0.9 - - - +
6A LEU* 3.1 24.7 - - + +
7A THR* 2.6 54.9 + - - +
9A ALA* 1.3 75.9 - - + +
11A ARG* 1.3 66.0 + - - +
13A GLU* 3.0 11.7 + - - +
14A VAL* 2.9 27.9 + - - +
27A VAL* 4.0 21.5 - - + +
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Residues in contact with ARG 11 (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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6A LEU* 3.0 37.0 + - + +
7A THR* 2.9 16.6 + - - +
8A PRO* 3.4 28.2 - - - +
10A GLN* 1.3 75.7 - - - +
12A THR* 1.3 52.1 + - - +
14A VAL* 3.2 7.9 + - - +
15A GLU* 2.8 35.1 + - - +
44A LEU* 4.1 5.8 - - - +
49A VAL* 4.3 35.8 - - + +
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Residues in contact with THR 12 (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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8A PRO 3.0 13.3 + - - -
9A ALA* 3.7 11.6 - - - +
11A ARG* 1.3 73.9 - - - +
13A GLU* 1.3 59.3 + - - +
15A GLU* 3.1 16.5 + - - +
16A LEU* 2.7 56.3 + - + +
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Residues in contact with GLU 13 (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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9A ALA 3.0 14.9 + - - +
10A GLN* 3.0 11.4 + - - +
12A THR* 1.3 78.8 - - - +
14A VAL* 1.3 59.7 + - - +
16A LEU* 3.4 14.1 + - - +
17A LEU* 3.4 11.6 + - - +
22A ALA* 5.2 0.7 - - - +
24A LYS 4.8 5.0 - - - +
25A SER* 2.6 30.8 + - - +
26A ARG* 3.3 19.1 + - - +
27A VAL* 3.0 29.6 + - - +
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Residues in contact with VAL 14 (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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6A LEU* 4.0 9.9 - - + -
10A GLN 2.9 16.6 + - - +
11A ARG* 3.5 7.2 - - - +
13A GLU* 1.3 76.3 - - - +
15A GLU* 1.3 58.0 + - - +
17A LEU* 3.1 7.8 + - - +
18A ALA* 2.9 23.6 + - - +
25A SER* 4.0 4.7 - - - +
27A VAL* 3.9 21.8 - - + -
28A LEU* 3.5 23.1 - - + -
40A ALA* 3.5 28.4 - - + +
43A LEU* 4.6 6.5 - - + -
44A LEU* 3.6 23.3 - - + -
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Residues in contact with GLU 15 (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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11A ARG 2.8 16.8 + - - +
12A THR* 3.1 19.3 + - - +
14A VAL* 1.3 74.8 - - - +
16A LEU* 1.3 68.3 + - + +
18A ALA* 3.0 1.9 + - - +
19A ARG* 2.9 55.5 + - - +
44A LEU* 4.0 11.2 - - + -
49A VAL* 4.7 7.8 - - + +
50A TRP* 2.7 41.4 + - + +
54A ARG* 3.1 9.4 + - - -
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Residues in contact with LEU 16 (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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12A THR* 2.7 56.1 + - + +
13A GLU* 3.7 8.5 - - - +
15A GLU* 1.3 75.5 - - + +
17A LEU* 1.3 60.0 + - - +
19A ARG* 3.6 7.6 + - + +
20A GLY 3.3 1.9 + - - -
21A ARG* 2.8 62.2 + - + +
22A ALA* 3.1 17.5 + - + -
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Residues in contact with LEU 17 (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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13A GLU 3.4 8.2 + - - +
14A VAL 3.1 9.1 + - - +
15A GLU 3.1 0.4 - - - -
16A LEU* 1.3 78.1 - - - +
18A ALA* 1.3 60.3 + - - +
20A GLY* 2.9 17.3 + - - -
22A ALA* 3.2 23.5 - - - +
23A ASP* 3.9 17.3 - - - +
24A LYS 4.2 11.2 - - - +
25A SER* 3.7 24.9 - - - -
28A LEU* 4.4 4.0 - - + -
35A GLU* 3.9 7.9 - - - -
36A THR* 3.7 33.0 - - - +
37A PRO* 3.5 26.0 - - + +
40A ALA* 3.8 8.7 - - + -
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Residues in contact with ALA 18 (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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14A VAL 2.9 8.2 + - - +
15A GLU 3.0 7.2 + - - +
17A LEU* 1.3 76.0 - - - +
19A ARG* 1.3 57.6 + - - +
20A GLY 3.2 0.2 - - - -
37A PRO 3.7 13.0 - - - +
40A ALA* 3.7 9.8 - - + +
41A HIS* 3.9 8.1 - - + +
44A LEU* 3.6 19.7 - - + -
50A TRP* 3.6 23.1 - - + -
56A PRO* 3.5 6.1 - - - +
60A ARG* 2.8 32.2 + - - -
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Residues in contact with ARG 19 (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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15A GLU* 2.9 39.3 + - - +
16A LEU* 4.0 10.1 - - - +
18A ALA* 1.3 77.8 - - - +
20A GLY* 1.3 62.2 + - - +
21A ARG* 3.3 7.9 + - + +
50A TRP* 4.2 13.9 - - + -
54A ARG* 2.7 30.3 - - - +
56A PRO* 4.5 4.5 - - + -
59A ASP* 3.2 40.2 + - + +
60A ARG* 3.5 26.2 + - - -
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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