Contacts of the helix formed by residues 8 - 25 (chain C) in PDB entry 6Q3W
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 GLN 8 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6C GLN* 3.3 12.7 + - + +
7C PRO* 1.3 82.3 - - - +
9C VAL* 1.3 64.4 + - - +
11C GLU* 3.3 29.4 - - + +
12C LEU* 3.2 20.3 + - - +
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Residues in contact with VAL 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 PRO* 3.9 16.6 - - + +
8C GLN* 1.3 71.8 - - - +
10C ALA* 1.3 63.9 + - - +
12C LEU* 3.2 17.2 + - - +
13C LEU* 3.3 12.7 + - + +
58C GLU* 3.8 35.7 - - + +
60C MET* 3.7 32.0 - - + +
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Residues in contact with ALA 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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8C GLN 3.4 0.4 - - - -
9C VAL* 1.3 80.3 - - - +
11C GLU* 1.3 69.4 + - - +
13C LEU* 3.3 10.0 + - - +
14C ALA* 3.1 22.3 + - - +
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Residues in contact with GLU 11 (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 GLN* 3.3 36.4 - - + +
10C ALA* 1.3 81.4 + - - +
12C LEU* 1.3 57.2 + - - +
14C ALA* 3.3 7.9 + - - +
15C GLU* 2.9 31.9 + - - +
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Residues in contact with LEU 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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7C PRO 5.5 0.9 - - - +
8C GLN 3.2 9.4 + - - +
9C VAL* 3.2 13.8 + - - +
11C GLU* 1.3 79.8 - - - +
13C LEU* 1.3 61.8 + - - +
15C GLU* 3.5 7.1 + - + +
16C ALA* 3.1 23.2 + - - +
60C MET* 3.8 42.2 - - + +
62C VAL* 3.9 11.7 - - + -
130C VAL* 3.7 32.2 - - + +
131C SER 4.1 14.6 - - - +
132C SER* 3.9 15.0 - - - +
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Residues in contact with LEU 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 VAL* 3.3 7.4 + - + +
10C ALA* 3.3 12.0 + - - +
12C LEU* 1.3 80.6 - - - +
14C ALA* 1.3 62.5 + - - +
16C ALA* 3.3 4.7 + - - +
17C ARG* 3.0 55.3 + - + +
31C ALA* 3.9 26.2 - - + -
62C VAL* 4.3 17.4 - - + +
64C VAL* 4.2 4.9 - - + -
390C LEU* 4.2 23.6 - - + -
392C LEU* 5.3 0.2 - - + -
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Residues in contact with ALA 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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10C ALA 3.1 12.8 + - - +
11C GLU* 3.7 9.9 - - - +
13C LEU* 1.3 76.6 - - - +
15C GLU* 1.3 57.8 + - - +
17C ARG* 3.2 9.8 + - - +
18C ARG* 2.9 31.4 + - - +
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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 GLU 2.9 17.7 + - - +
12C LEU* 3.8 8.3 - - + +
14C ALA* 1.3 76.4 - - - +
16C ALA* 1.3 57.6 + - - +
18C ARG* 3.7 5.9 - - - +
19C ALA* 2.9 31.9 + - - +
78C THR* 5.8 2.0 - - - +
130C VAL* 5.2 5.8 - - + -
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Residues in contact with ALA 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 LEU 3.1 14.3 + - - +
13C LEU 3.5 8.7 - - - +
15C GLU* 1.3 78.4 - - - +
17C ARG* 1.3 57.1 + - - +
19C ALA* 3.5 1.7 + - - +
20C PHE* 3.0 28.1 + - - +
62C VAL* 4.4 8.3 - - + +
64C VAL* 3.7 19.6 - - + +
128C VAL* 3.9 10.9 - - + +
130C VAL* 3.8 31.1 - - + +
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Residues in contact with ARG 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 LEU* 3.0 44.8 + - - +
14C ALA* 3.7 7.6 - - - +
16C ALA* 1.3 73.8 - - - +
18C ARG* 1.3 66.7 + - - +
20C PHE* 3.3 2.6 + - - +
21C ARG* 3.1 23.7 + - - +
27C GLU* 4.9 10.5 + - - +
28C PRO* 4.4 11.9 - - + +
64C VAL* 3.9 24.2 - - + -
390C LEU* 5.3 1.6 - - - +
392C LEU* 3.5 45.0 + - + +
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Residues in contact with ARG 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 ALA 2.9 16.4 + - - +
15C GLU* 3.7 7.4 - - - +
17C ARG* 1.3 77.0 - - - +
19C ALA* 1.3 62.6 + - - +
21C ARG* 3.3 6.9 + - - +
22C GLU* 3.2 35.0 + - - +
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Residues in contact with ALA 19 (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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15C GLU 2.9 19.4 + - - +
16C ALA 3.8 3.4 - - - +
18C ARG* 1.3 76.0 - - - +
20C PHE* 1.3 58.7 + - - +
22C GLU* 3.4 9.4 + - - +
23C GLU* 3.0 31.2 + - - +
76C LEU* 4.4 4.4 - - + +
78C THR* 4.1 26.5 - - + -
128C VAL* 4.1 11.2 - - + -
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Residues in contact with PHE 20 (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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16C ALA 3.0 18.9 + - - +
17C ARG 3.7 4.0 - - - +
18C ARG 3.3 0.4 - - - -
19C ALA* 1.3 77.7 - - - +
21C ARG* 1.3 56.1 + - - +
24C PHE* 2.9 67.2 + + + +
26C ALA* 3.2 22.7 - - + -
27C GLU 4.0 2.0 - - - -
28C PRO* 3.5 23.8 - - + -
64C VAL* 3.5 24.7 - - + -
65C GLY* 3.6 6.5 - - - -
66C SER* 3.7 19.7 - - - -
126C SER* 3.4 30.5 - - - -
128C VAL* 3.5 12.3 - - + +
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Residues in contact with ARG 21 (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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17C ARG 3.1 14.4 + - - +
18C ARG* 3.7 7.0 - - - +
20C PHE* 1.3 79.8 - - - +
22C GLU* 1.3 59.3 + - + +
25C GLY* 2.9 29.6 + - - -
26C ALA 3.3 18.7 + - - +
27C GLU* 4.3 19.7 - - - +
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Residues in contact with GLU 22 (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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18C ARG* 3.2 25.6 + - - +
19C ALA* 3.8 7.8 - - - +
21C ARG* 1.3 80.3 - - + +
23C GLU* 1.3 61.8 + - - +
25C GLY* 4.1 3.1 + - - -
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Residues in contact with GLU 23 (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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19C ALA 3.0 18.0 + - - +
20C PHE 4.0 2.2 - - - +
22C GLU* 1.3 79.8 - - - +
24C PHE* 1.3 89.4 + - + +
75C LEU 5.5 0.2 - - - +
76C LEU* 3.8 19.6 - - + +
87C ARG* 2.5 54.4 + - - +
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Residues in contact with PHE 24 (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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20C PHE* 2.9 62.7 + + + +
23C GLU* 1.3 103.1 - - + +
25C GLY* 1.3 62.3 + - - +
26C ALA* 3.3 5.6 + - + +
68C ARG* 4.8 4.0 - - - -
74C SER* 3.5 42.2 - - - -
75C LEU 4.9 0.9 - - - -
76C LEU* 4.9 3.8 - - + -
126C SER* 3.6 19.5 - - - -
127C ALA 4.0 11.2 - - - -
128C VAL* 4.2 4.9 - - + -
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Residues in contact with GLY 25 (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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21C ARG* 2.9 16.8 + - - -
22C GLU 4.1 2.6 + - - -
23C GLU 3.7 1.2 - - - -
24C PHE* 1.3 77.3 - - - +
26C ALA* 1.3 61.3 + - - +
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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