Contacts of the helix formed by residues 6 - 23 (chain C) in PDB entry 4QYL
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 6 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35B SER* 4.3 16.6 - - - -
4C GLN 3.7 4.0 + - - -
5C LEU* 1.3 78.8 - - - +
7C PRO* 1.3 76.3 - - - +
8C PHE* 3.7 3.7 + - - +
9C LEU* 3.3 17.3 + - + +
10C ILE* 2.9 24.6 + - - +
60C TYR* 2.9 38.6 + - + +
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Residues in contact with PRO 7 (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 THR* 1.3 87.0 - - - +
8C PHE* 1.3 61.4 + - - +
10C ILE* 3.4 9.6 + - + +
11C LEU* 3.0 23.6 + - - +
114C MET* 3.6 23.9 - - + +
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Residues in contact with PHE 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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6C THR* 3.1 7.2 + - - +
7C PRO* 1.3 80.8 - - - +
9C LEU* 1.3 63.9 + - + +
11C LEU* 3.2 9.1 + - + +
12C LEU* 3.0 61.7 + - + +
60C TYR* 4.4 11.7 - + - +
62C TYR 3.3 24.9 - - - -
63C LEU 3.8 11.2 - - - -
64C ASN* 3.4 25.6 - - - -
65C PHE* 3.9 18.4 - + + -
111C ALA* 5.1 1.8 - - + -
114C MET* 3.9 16.9 - - - -
116C ILE 3.7 22.2 - - - +
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Residues in contact with LEU 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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4C GLN* 3.6 28.3 - - + +
6C THR* 3.2 18.1 + - + +
8C PHE* 1.3 83.7 - - + +
10C ILE* 1.3 57.5 + - - +
12C LEU* 3.8 9.7 - - + +
13C ARG* 2.9 54.6 + - - +
57C LEU* 3.8 28.4 - - + +
58C GLU 5.3 1.3 - - - +
60C TYR* 3.5 49.1 - - + -
62C TYR* 4.5 4.3 - - + +
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Residues in contact with ILE 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 LEU* 4.0 19.3 - - + -
6C THR 2.9 26.4 + - - +
7C PRO* 3.6 8.3 - - + +
9C LEU* 1.3 76.5 - - - +
11C LEU* 1.3 62.5 + - - +
13C ARG* 3.4 27.3 + - + +
14C LYS* 3.1 22.9 + - + +
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Residues in contact with LEU 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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7C PRO 3.0 13.6 + - - +
8C PHE* 3.2 12.5 + - + +
10C ILE* 1.3 77.7 - - - +
12C LEU* 1.3 56.8 + - + +
14C LYS* 3.3 11.8 + - + +
15C THR* 2.7 48.4 + - - +
65C PHE* 4.7 7.6 - - + -
106C GLN* 5.7 0.9 - - - +
107C ALA* 3.7 13.5 - - + +
110C GLN* 4.2 17.7 - - + -
111C ALA* 3.6 41.7 - - + +
114C MET* 4.0 17.9 - - + -
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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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8C PHE* 3.0 61.4 + - + +
9C LEU* 3.3 8.0 + - + +
11C LEU* 1.3 78.2 - - + +
13C ARG* 1.3 57.0 + - - +
15C THR* 3.8 2.9 - - - -
16C LEU* 2.9 32.7 + - - +
57C LEU* 3.5 19.5 - - + +
62C TYR* 3.7 26.0 - - + +
65C PHE* 4.0 19.1 - - + -
68C PHE* 3.8 32.8 - - + -
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Residues in contact with ARG 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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3C LEU* 3.7 17.7 - - - +
4C GLN* 3.0 32.3 + - - +
5C LEU* 4.2 3.4 - - - +
9C LEU* 2.9 40.2 + - - +
10C ILE* 3.5 32.9 - - - +
12C LEU* 1.3 74.1 - - - +
14C LYS* 1.3 66.2 + - - +
16C LEU* 3.8 2.5 - - - +
17C GLU* 3.1 37.0 + - - +
54C LYS* 3.9 15.2 - - - +
57C LEU* 3.7 16.5 - - + +
58C GLU* 2.8 38.5 + - - +
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Residues in contact with LYS 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 ILE* 3.1 11.2 + - + +
11C LEU* 3.6 15.3 - - + +
13C ARG* 1.3 78.4 - - - +
15C THR* 1.3 64.2 + - - +
17C GLU* 3.3 6.2 + - - +
18C GLN* 3.0 52.3 + - + +
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Residues in contact with THR 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 LEU* 2.7 31.6 + - - +
12C LEU* 3.8 6.0 - - - -
14C LYS* 1.3 73.3 - - - +
16C LEU* 1.3 57.2 + - - +
18C GLN* 3.2 12.5 + - - +
19C LEU* 2.8 35.8 + - + +
65C PHE* 4.4 6.3 - - + -
68C PHE* 3.8 23.8 - - + -
103C VAL* 4.1 13.0 - - + -
104C LEU* 4.5 2.9 - - + -
107C ALA* 3.3 34.7 - - + +
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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 LEU 2.9 19.1 + - - +
13C ARG* 3.8 3.4 - - - +
15C THR* 1.3 75.5 - - - +
17C GLU* 1.3 59.7 + - + +
19C LEU* 3.2 6.1 + - + +
20C GLN* 2.9 43.5 + - + +
50C PHE* 3.6 34.5 - - + +
53C MET* 4.1 26.2 - - + -
54C LYS* 3.8 42.8 - - + +
57C LEU* 4.1 13.7 - - + -
68C PHE* 4.0 10.7 - - + -
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Residues in contact with GLU 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 ARG* 3.1 25.1 + - - +
14C LYS* 3.8 5.6 - - - +
16C LEU* 1.3 78.8 - - + +
18C GLN* 1.3 60.1 + - + +
20C GLN* 3.3 19.7 + - - +
21C GLU* 3.0 26.8 + - - +
54C LYS* 5.1 8.3 + - - +
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Residues in contact with GLN 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 LYS* 3.0 47.1 + - + +
15C THR* 3.4 21.4 + - - +
17C GLU* 1.3 73.8 - - - +
19C LEU* 1.3 63.6 + - - +
21C GLU* 3.4 28.7 - - - +
22C LYS* 3.5 15.4 - - - +
103C VAL* 3.6 25.9 - - + +
106C GLN* 4.8 11.6 + - - +
107C ALA* 5.2 0.9 - - - +
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Residues in contact with LEU 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 THR* 2.8 24.0 + - + +
16C LEU* 3.2 7.8 + - + +
18C GLN* 1.3 69.9 - - - +
20C GLN* 1.3 65.9 + - - +
22C LYS* 2.9 23.2 + - - +
23C ASP 3.6 2.3 + - - -
50C PHE* 3.9 18.6 - - + -
53C MET* 5.4 0.4 - - + -
68C PHE* 4.0 28.5 - - + -
72C PHE* 3.9 28.9 - - + -
96C LEU* 3.9 7.0 - - + +
100C GLY* 3.7 33.2 - - - +
103C VAL* 3.7 17.9 - - + -
104C LEU* 4.2 12.6 - - + -
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Residues in contact with GLN 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 LEU* 2.9 26.0 + - - +
17C GLU* 3.3 32.5 + - - +
19C LEU* 1.3 75.6 - - - +
21C GLU* 1.3 57.1 + - - +
23C ASP* 2.9 28.2 + - - +
26C ASN* 5.0 3.1 - - - +
50C PHE* 3.8 52.3 + - + +
54C LYS* 5.4 3.6 - - - +
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Residues in contact with GLU 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 GLU 3.0 16.8 + - - +
18C GLN* 3.4 23.5 - - - +
20C GLN* 1.3 77.4 - - - +
22C LYS* 1.3 70.0 + - + +
23C ASP 3.5 0.9 + - - -
24C THR* 4.0 14.9 + - - +
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Residues in contact with LYS 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 GLN* 3.5 15.3 - - - +
19C LEU* 2.9 13.9 + - - +
21C GLU* 1.3 86.4 + - + +
23C ASP* 1.3 58.1 + - - +
24C THR* 3.1 14.4 + - - +
95C ARG* 5.9 1.4 - - - +
96C LEU* 3.8 18.7 + - + +
99C GLN* 3.4 56.2 + - + +
100C GLY* 4.6 1.3 - - - +
103C VAL* 3.8 23.8 - - + +
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Residues in contact with ASP 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 LEU 3.6 1.2 + - - -
20C GLN 2.9 16.0 + - - +
21C GLU 4.3 0.9 - - - -
22C LYS* 1.3 74.1 - - - +
24C THR* 1.3 62.2 + - - +
25C GLY 3.7 2.9 + - - -
26C ASN* 3.1 22.5 + - - +
27C ILE* 3.0 25.1 + - - +
28C PHE* 2.8 49.6 + - + +
29C SER* 3.7 4.0 + - - -
50C PHE* 4.0 18.3 - - + -
92C ALA* 5.7 0.5 - - - +
96C LEU* 4.2 6.7 - - + +
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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