Contacts of the helix formed by residues 8 - 23 (chain A) in PDB entry 2D99
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 LEU 8 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A GLY* 1.3 73.5 - - - +
9A ARG* 1.3 62.5 + - - +
11A MET* 3.1 26.0 + - + +
12A VAL* 3.3 10.2 - - - +
63A PRO* 3.6 14.4 - - + +
66A LEU* 3.8 14.6 - - + -
67A MET* 3.1 54.1 - - + +
70A LEU* 3.6 24.2 - - + +
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Residues in contact with ARG 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 GLY* 4.4 0.2 - - - -
8A LEU* 1.3 74.8 - - - +
10A LYS* 1.3 63.4 + - - +
11A MET 3.0 4.9 - - - -
12A VAL* 3.0 10.2 - - - +
13A GLU* 2.5 71.0 + - + +
58A PRO 3.4 19.5 - - - +
59A ALA* 3.2 34.0 - - - +
66A LEU* 3.4 16.0 - - + +
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Residues in contact with LYS 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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3A SER* 3.8 9.2 - - - +
4A GLY* 3.2 41.5 - - - +
5A SER 4.4 5.8 - - - +
6A SER 5.0 1.8 - - - +
7A GLY* 3.0 20.9 + - - +
9A ARG* 1.3 93.0 - - - +
11A MET* 1.3 60.4 + - + +
13A GLU* 3.7 22.6 + - + +
14A GLU* 3.6 15.2 + - + +
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Residues in contact with MET 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 SER* 5.5 1.8 - - - -
7A GLY 2.5 31.9 + - - +
8A LEU* 3.2 22.9 - - + +
10A LYS* 1.3 78.3 - - + +
12A VAL* 1.3 58.1 + - - +
14A GLU* 3.5 17.8 - - - +
15A VAL* 3.0 20.6 - - - +
70A LEU* 3.2 34.8 - - + +
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Residues in contact with VAL 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 LEU 3.3 12.3 - - - +
9A ARG 3.0 15.5 - - - +
11A MET* 1.3 74.9 - - - +
13A GLU* 1.3 66.9 + - - +
14A GLU 3.0 3.9 + - - -
15A VAL* 3.0 16.3 + - + -
16A PHE* 3.2 46.2 + - + -
58A PRO* 3.3 6.5 - - + -
66A LEU* 3.3 28.3 - - + -
69A ILE* 3.6 20.9 - - + -
70A LEU* 3.6 13.9 - - + -
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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 ARG* 2.5 76.2 + - + +
10A LYS* 3.7 21.1 - - + +
11A MET 3.4 0.2 - - - -
12A VAL* 1.3 73.9 - - - +
14A GLU* 1.3 58.1 + - - +
16A PHE* 4.9 1.4 - - - +
17A ASP* 3.2 27.9 + - - +
34A TYR* 5.5 2.9 + - - -
58A PRO* 3.4 24.7 - - + +
59A ALA* 5.3 0.2 - - - +
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Residues in contact with GLU 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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10A LYS* 3.6 18.6 + - + +
11A MET* 3.5 16.1 - - - +
12A VAL 3.0 0.2 - - - -
13A GLU* 1.3 79.8 - - - +
15A VAL* 1.3 62.1 + - + +
16A PHE 3.5 0.2 - - - -
17A ASP* 3.0 8.9 + - - +
18A VAL* 2.5 51.3 + - + +
29A VAL* 5.6 2.7 - - + -
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Residues in contact with VAL 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 MET 3.0 25.4 - - - +
12A VAL* 3.4 15.9 - - + +
14A GLU* 1.3 84.2 - - + +
16A PHE* 1.3 71.9 + - + +
18A VAL* 2.7 19.7 + - - +
19A LEU* 2.7 39.3 + - + +
69A ILE* 5.3 0.7 - - + -
70A LEU* 4.1 11.0 - - + -
73A SER* 4.4 20.9 - - - +
76A ILE* 4.9 4.9 - - + -
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Residues in contact with PHE 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 VAL* 3.2 36.4 + - + +
13A GLU 4.9 1.1 - - - +
15A VAL* 1.3 79.7 - - + +
17A ASP* 1.3 58.5 + - - +
20A TYR* 2.8 27.9 + - - +
32A LEU* 3.7 13.9 - - + -
34A TYR* 2.8 31.9 - + - +
46A VAL* 4.6 5.8 - - + -
49A LEU* 4.3 13.9 - - + -
55A PHE* 5.4 5.6 - + - -
56A ARG 4.1 7.9 - - - -
58A PRO* 4.4 6.3 - - + -
61A TYR* 3.9 28.7 - + - -
69A ILE* 4.1 7.9 - - + -
76A ILE* 4.2 22.7 - - + -
78A PHE* 2.9 32.3 - + - -
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Residues in contact with ASP 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 3.2 20.5 + - - +
14A GLU* 3.0 12.2 + - - +
15A VAL 3.0 0.6 - - - -
16A PHE* 1.3 77.4 - - - +
18A VAL* 1.3 55.8 - - - +
20A TYR* 3.2 5.1 - - - +
21A SER* 2.7 36.4 + - - -
29A VAL* 3.7 13.6 - - + +
30A VAL 3.3 21.1 - - - +
31A PRO* 3.1 12.8 - - - +
32A LEU* 2.9 28.6 + - - +
34A TYR* 5.4 0.9 + - - -
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Residues in contact with VAL 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 GLU* 2.5 36.7 + - + +
15A VAL* 2.7 8.0 + - - +
17A ASP* 1.3 68.3 - - - +
19A LEU* 1.3 65.5 + - + +
21A SER* 2.8 7.0 + - - -
22A GLU* 2.6 53.3 + - + +
29A VAL* 4.2 25.4 - - + -
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Residues in contact with LEU 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 VAL* 2.7 36.3 + - + +
18A VAL* 1.3 82.1 - - + +
20A TYR* 1.3 56.7 + - - +
22A GLU* 2.9 11.8 + - + +
23A ALA* 2.8 30.1 + - - +
73A SER* 4.9 3.1 - - - +
76A ILE* 3.2 49.8 - - + +
77A ARG* 4.9 0.7 - - - -
78A PHE* 3.2 28.6 - - + +
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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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16A PHE 2.8 21.0 + - - +
17A ASP* 3.2 2.9 - - - +
19A LEU* 1.3 76.8 - - - +
21A SER* 1.3 50.6 + - - +
23A ALA* 3.1 3.9 + - + +
24A LEU* 2.7 68.1 + - + +
30A VAL* 3.8 18.6 - - + -
31A PRO 3.2 30.5 - - - -
32A LEU* 4.4 4.7 - - + -
33A PRO* 4.3 12.4 - - + +
37A LEU* 4.1 13.6 - - + +
44A LEU* 3.3 33.7 - - + -
78A PHE* 3.4 16.3 - + + -
80A LEU* 4.5 7.2 - - + -
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Residues in contact with SER 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 ASP 2.7 19.3 + - - -
18A VAL* 2.8 6.0 + - - -
20A TYR* 1.3 75.1 - - - +
22A GLU* 1.3 58.9 + - - +
24A LEU* 3.5 7.4 - - - -
25A GLY 2.7 29.3 + - - -
26A ARG* 3.1 24.4 + - - +
28A SER 2.8 27.8 + - - -
29A VAL* 3.9 7.1 - - - +
30A VAL* 4.0 16.3 + - - -
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Residues in contact with GLU 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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18A VAL* 2.6 37.7 + - + +
19A LEU* 3.1 14.6 - - + +
21A SER* 1.3 78.6 + - - +
23A ALA* 1.3 60.9 + - - +
25A GLY* 3.2 13.6 + - - -
26A ARG 5.0 6.1 - - - +
86A GLY* 3.6 24.5 - - - +
87A PRO 4.9 1.6 - - - +
88A SER* 4.3 25.2 + - - +
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Residues in contact with ALA 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 LEU 2.8 12.3 + - - +
20A TYR* 3.7 7.2 - - + +
22A GLU* 1.3 76.7 - - - +
24A LEU* 1.3 60.9 + - - +
25A GLY* 3.5 0.3 + - - -
78A PHE* 4.0 27.6 - - + +
80A LEU* 3.4 26.8 - - + +
84A SER 5.3 0.9 - - - +
85A SER* 4.8 11.9 - - - -
86A GLY 4.3 18.3 + - - +
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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