Contacts of the helix formed by residues 13 - 23 (chain A) in PDB entry 6JGW
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 13 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A ALA* 4.9 0.9 - - - -
12A CYS* 1.3 77.6 - - - +
14A VAL* 1.3 64.8 + - - +
15A GLU* 4.3 10.3 - - + +
16A THR* 3.3 19.6 + - - +
17A ILE* 3.2 18.7 + - - +
17C T 4.6 10.8 - - + +
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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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3A ILE* 3.8 21.0 - - + +
4A GLY* 4.3 11.7 - - - +
7A ALA* 3.9 20.2 - - + -
13A ALA* 1.3 73.4 - - - +
15A GLU* 1.3 65.4 + - - +
17A ILE* 3.0 10.5 + - - +
18A ARG* 2.9 63.9 + - - +
6D C 4.7 6.3 - - - +
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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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13A ALA* 3.4 6.9 - - + +
14A VAL* 1.3 82.3 + - - +
16A THR* 1.3 52.4 + - - +
18A ARG* 3.3 29.6 + - + +
19A TYR* 2.7 37.1 + - - +
22A ARG* 4.7 1.6 + - - +
17C T 4.1 26.0 - - + +
18C A 3.9 28.9 + - - +
19C C 4.0 18.4 + - - +
9D G 5.4 0.9 - - - +
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Residues in contact with THR 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 CYS* 3.7 14.3 - - - -
13A ALA* 3.3 25.5 + - - +
15A GLU* 1.3 77.3 - - - +
17A ILE* 1.3 52.9 + - - +
19A TYR* 3.1 8.5 + - - +
20A TYR* 2.7 68.5 + - + +
51A ARG* 4.2 6.2 + - - +
16C C 3.7 22.2 - - - +
17C T 3.9 16.7 + - - +
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Residues in contact with ILE 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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3A ILE* 3.9 16.8 - - + +
6A LEU* 3.9 23.1 - - + -
7A ALA* 4.0 18.6 - - + +
12A CYS* 3.9 23.6 - - - +
13A ALA 3.2 9.2 + - - +
14A VAL* 3.0 8.7 + - - +
16A THR* 1.3 73.3 - - - +
18A ARG* 1.3 68.3 + - - +
20A TYR* 3.3 8.1 + - - +
21A GLU* 3.1 20.3 + - - +
26A LEU* 3.9 15.3 - - + +
39A TYR* 3.7 22.7 - - - +
47A LEU* 3.9 20.9 - - + -
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Residues in contact with ARG 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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3A ILE* 3.9 10.3 - - - +
14A VAL* 2.9 38.5 + - - +
15A GLU* 3.5 30.3 + - - +
17A ILE* 1.3 77.4 - - - +
19A TYR* 1.3 62.2 + - - +
21A GLU* 3.2 21.9 - - - +
22A ARG* 3.3 26.5 + - - +
37A ARG* 3.9 34.0 + - - +
19C C 5.7 1.6 - - - +
6D C 4.5 3.8 - - - -
7D C 2.6 43.5 + - - +
8D T 3.7 33.6 + - + +
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Residues in contact with TYR 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 2.7 21.8 + - - +
16A THR* 3.3 5.8 - - - +
18A ARG* 1.3 71.5 - - - +
20A TYR* 1.3 83.0 + + - +
22A ARG* 2.9 45.8 + - - +
23A GLU* 3.0 39.3 + - + +
60A LEU* 3.5 20.1 - - + +
14C G 5.4 0.2 - - - +
15C G 3.7 35.2 + + + -
16C C 3.8 37.5 - + - -
17C T 4.2 4.5 - - + -
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Residues in contact with TYR 20 (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 CYS* 5.4 0.2 - - - -
16A THR* 2.7 38.9 + - + +
17A ILE* 3.3 6.7 + - - +
19A TYR* 1.3 89.7 - + - +
21A GLU* 1.3 59.1 + - - +
23A GLU* 3.4 4.4 + - + +
24A GLN 3.1 4.2 + - - -
25A LEU* 2.9 48.1 + - + +
26A LEU* 3.4 10.8 + - + -
47A LEU* 3.9 22.9 - - + -
50A ILE* 3.7 23.3 - - + -
51A ARG* 2.5 38.5 + - - -
54A ARG* 3.8 5.8 - - + +
60A LEU* 4.3 11.0 - - + -
16C C 2.7 22.9 + - - -
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Residues in contact with GLU 21 (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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17A ILE 3.1 10.3 + - - +
18A ARG* 3.2 13.4 - - - +
19A TYR 3.1 0.4 - - - -
20A TYR* 1.3 76.3 - - - +
22A ARG* 1.3 63.1 + - + +
24A GLN* 3.1 14.4 + - - +
26A LEU* 4.0 20.1 - - + +
27A PRO 4.1 3.3 - - - +
28A GLU* 3.4 40.1 - - + +
29A PRO* 3.5 10.9 - - - +
31A ARG* 4.6 3.8 + - - -
37A ARG* 3.1 31.0 + - - +
39A TYR* 3.2 24.1 + - - -
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Residues in contact with ARG 22 (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 4.7 1.8 + - - -
18A ARG* 3.3 29.4 + - - +
19A TYR* 2.9 43.2 + - - +
21A GLU* 1.3 78.1 - - + +
23A GLU* 1.3 72.2 + - - +
24A GLN* 3.2 14.4 + - - +
17C T 4.7 12.1 + - - +
18C A 5.9 0.4 - - - +
9D G 5.8 3.0 + - - -
10D T 4.8 24.2 + - - +
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Residues in contact with GLU 23 (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 TYR* 3.0 51.8 + - + +
20A TYR* 3.4 7.2 + - + +
21A GLU 3.3 0.4 - - - -
22A ARG* 1.3 89.1 - - - +
24A GLN* 1.3 72.4 + - - +
25A LEU* 3.2 8.4 + - + +
60A LEU* 4.6 8.2 - - + +
64A ARG* 2.8 40.5 + - - +
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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