Contacts of the helix formed by residues 6 - 22 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A SER* 4.3 17.7 - - - -
4D GLN 3.8 3.0 + - - -
5D LEU* 1.3 80.1 - - - +
7D PRO* 1.3 75.6 - - - +
8D PHE* 3.7 2.9 + - - +
9D LEU* 3.3 17.1 + - + +
10D ILE* 2.9 24.1 + - - +
60D TYR* 2.9 38.5 + - + +
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Residues in contact with PRO 7 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D THR* 1.3 86.9 - - - +
8D PHE* 1.3 63.7 + - - +
10D ILE* 3.3 9.5 + - + +
11D LEU* 3.0 23.6 + - - +
114D MET* 5.0 21.1 - - + +
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Residues in contact with PHE 8 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D THR* 3.2 6.3 + - - +
7D PRO* 1.3 81.2 - - - +
9D LEU* 1.3 64.7 + - + +
11D LEU* 3.2 15.2 + - + +
12D LEU* 3.0 61.2 + - + +
60D TYR* 4.4 11.2 - + - +
62D TYR 3.3 24.9 - - - -
63D LEU 3.7 11.7 - - - -
64D ASN* 3.4 25.1 - - - -
65D PHE* 3.9 15.3 - + + -
111D ALA* 5.1 3.1 - - + -
116D ILE* 3.5 33.0 - - + +
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Residues in contact with LEU 9 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D GLN* 3.6 27.6 - - + +
6D THR* 3.2 17.4 + - + +
8D PHE* 1.3 81.8 - - + +
10D ILE* 1.3 61.0 + - - +
12D LEU* 3.9 9.4 - - + +
13D ARG* 2.9 54.3 + - - +
57D LEU* 3.7 29.1 - - + +
58D GLU 5.1 1.6 - - - +
60D TYR* 3.4 50.3 - - + -
62D TYR 4.5 4.3 - - - +
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Residues in contact with ILE 10 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D LEU* 4.0 19.7 - - + -
6D THR 2.9 23.4 + - - +
7D PRO* 3.6 12.3 - - + +
9D LEU* 1.3 78.2 - - - +
11D LEU* 1.3 63.6 + - - +
13D ARG* 3.4 26.8 + - + +
14D LYS* 3.1 24.6 + - + +
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Residues in contact with LEU 11 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D PRO 3.0 12.8 + - - +
8D PHE* 3.2 17.0 + - + +
10D ILE* 1.3 77.5 - - - +
12D LEU* 1.3 56.7 + - + +
14D LYS* 3.3 12.3 + - + +
15D THR* 2.7 47.9 + - - +
65D PHE* 4.7 8.1 - - + -
106D GLN* 5.6 1.1 - - - +
107D ALA* 3.8 13.7 - - + +
110D GLN* 4.2 19.3 - - + -
111D ALA* 3.6 42.2 - - + +
114D MET* 5.2 13.5 - - + -
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Residues in contact with LEU 12 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D PHE* 3.0 61.4 + - + +
9D LEU* 3.9 8.5 - - + +
10D ILE 3.3 0.2 - - - -
11D LEU* 1.3 75.6 - - + +
13D ARG* 1.3 59.5 + - - +
15D THR* 3.8 2.9 - - - +
16D LEU* 2.8 32.4 + - - +
57D LEU* 3.4 19.8 - - + +
62D TYR* 3.7 25.4 - - + +
65D PHE* 4.0 19.7 - - + -
68D PHE* 3.8 32.8 - - + -
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Residues in contact with ARG 13 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D LEU* 3.7 17.6 - - - +
4D GLN* 2.9 31.7 + - - +
5D LEU* 4.2 3.2 - - - +
9D LEU* 2.9 48.2 + - - +
10D ILE* 3.6 27.2 - - + +
12D LEU* 1.3 77.9 - - - +
14D LYS* 1.3 63.4 + - - +
16D LEU* 3.8 2.7 - - - +
17D GLU* 3.1 23.9 + - - +
54D LYS* 3.9 13.4 - - - +
57D LEU* 3.7 16.5 - - + +
58D GLU* 2.8 39.6 + - - +
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Residues in contact with LYS 14 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D ILE* 3.1 12.7 + - + +
11D LEU* 3.6 15.3 - - + +
13D ARG* 1.3 78.1 - - - +
15D THR* 1.3 58.2 + - - +
17D GLU* 3.3 6.7 + - - +
18D GLN* 2.9 55.6 + - + +
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Residues in contact with THR 15 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D LEU* 2.7 28.4 + - - +
12D LEU* 3.8 5.6 - - - -
14D LYS* 1.3 74.9 - - - +
16D LEU* 1.3 56.8 + - - +
18D GLN* 3.1 12.7 + - - +
19D LEU* 2.8 35.6 + - + +
65D PHE* 4.4 7.0 - - + -
68D PHE* 3.9 22.7 - - + -
103D VAL* 4.1 13.9 - - + -
104D LEU* 4.5 2.9 - - + -
107D ALA* 3.3 34.5 - - + +
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Residues in contact with LEU 16 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D LEU 2.8 22.8 + - - +
13D ARG* 3.8 3.8 - - - +
15D THR* 1.3 72.3 - - - +
17D GLU* 1.3 58.3 + - - +
19D LEU* 3.3 5.5 + - + +
20D GLN* 2.9 43.3 + - + +
50D PHE* 3.6 35.4 - - + +
53D MET* 4.2 25.4 - - + -
54D LYS* 3.8 46.2 - - + +
57D LEU* 4.1 10.3 - - + -
68D PHE* 4.0 10.9 - - + -
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Residues in contact with GLU 17 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D ARG 3.1 16.7 + - - +
14D LYS* 3.7 5.6 - - + +
16D LEU* 1.3 78.4 - - - +
18D GLN* 1.3 58.2 + - + +
20D GLN* 3.4 15.9 + - + +
21D GLU* 3.0 32.3 + - + +
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Residues in contact with GLN 18 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D LYS* 2.9 46.8 + - + +
15D THR* 3.4 21.2 + - - +
17D GLU* 1.3 75.4 - - + +
19D LEU* 1.3 62.8 + - - +
21D GLU* 3.4 28.1 - - - +
22D LYS* 3.6 15.6 - - - +
103D VAL* 3.7 25.5 - - + +
106D GLN* 4.7 12.5 + - - +
107D ALA* 5.1 0.7 - - - +
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Residues in contact with LEU 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D THR* 2.8 22.5 + - + +
16D LEU* 3.6 8.3 - - + +
18D GLN* 1.3 70.8 - - - +
20D GLN* 1.3 64.7 + - - +
22D LYS* 2.9 23.5 + - - +
23D ASP 3.7 2.4 + - - -
50D PHE* 3.9 19.1 - - + -
53D MET* 5.3 0.4 - - + -
68D PHE* 4.0 29.4 - - + -
72D PHE* 3.9 30.3 - - + -
96D LEU* 3.9 7.2 - - + +
100D GLY* 3.7 29.6 - - - +
103D VAL* 3.7 20.4 - - + -
104D LEU* 4.2 10.5 - - + -
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Residues in contact with GLN 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D LEU* 2.9 29.9 + - - +
17D GLU* 3.4 24.4 + - + +
19D LEU* 1.3 73.7 - - - +
21D GLU* 1.3 62.0 + - - +
23D ASP* 3.0 22.7 + - - +
26D ASN* 5.0 2.4 - - - +
29D SER* 6.4 0.2 - - - -
50D PHE* 3.7 53.9 + - + +
54D LYS* 5.4 3.6 - - - +
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Residues in contact with GLU 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D GLU* 3.0 19.7 + - + +
18D GLN* 3.4 23.8 - - - +
20D GLN* 1.3 79.2 - - - +
22D LYS* 1.3 70.5 + - + +
23D ASP 3.4 1.0 + - - -
24D THR* 3.9 15.1 + - - +
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Residues in contact with LYS 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D GLN 3.6 13.9 - - - +
19D LEU* 2.9 14.3 + - - +
21D GLU* 1.3 91.0 + - + +
23D ASP* 1.3 56.4 + - - +
24D THR* 3.1 13.9 + - - +
95D ARG* 5.8 0.9 - - - +
96D LEU* 3.8 17.9 + - + +
99D GLN* 3.5 60.2 + - + +
100D GLY 4.6 1.8 - - - +
103D VAL* 3.8 23.3 - - + +
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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