Contacts of the helix formed by residues 5 - 21 (chain A) in PDB entry 2X9D
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 ASN 5 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A ARG* 3.6 42.2 + - - +
4A LEU* 1.3 76.2 - - - +
6A ARG* 1.3 67.5 + - - +
7A GLU* 4.0 14.3 + - - +
8A SER* 2.6 31.7 + - - -
9A VAL* 3.0 19.5 + - - +
1210A CL 4.4 3.2 - - - +
1212A CL 3.6 21.7 - - + +
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Residues in contact with ARG 6 (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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4A LEU 3.9 0.4 + - - -
5A ASN* 1.3 73.1 - - - +
7A GLU* 1.3 57.4 + - - +
9A VAL* 3.2 7.5 + - - +
10A ILE* 2.9 42.7 + - + +
54A ALA* 4.0 27.2 + - - +
57A VAL* 4.6 9.9 - - - +
58A GLU* 3.1 40.4 + - - +
108A LYS* 6.1 2.4 - - - +
1212A CL 3.8 9.9 - - + +
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Residues in contact with GLU 7 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ASN* 3.2 10.1 + - - +
6A ARG* 1.3 79.8 - - - +
8A SER* 1.3 59.1 + - - +
10A ILE* 3.5 0.8 + - - -
11A ASP* 3.0 43.0 + - - +
62A ARG* 3.5 21.1 + - - +
1212A CL 3.5 14.6 - - + +
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Residues in contact with SER 8 (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 ARG* 3.2 30.9 - - - +
5A ASN* 2.6 31.0 + - - -
7A GLU* 1.3 74.3 - - - +
9A VAL* 1.3 65.1 + - - +
11A ASP* 3.4 10.9 + - - +
12A ALA* 3.2 24.3 + - - +
34A LEU* 4.5 3.6 - - - +
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Residues in contact with VAL 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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4A LEU* 3.5 35.0 - - + +
5A ASN 3.0 16.8 + - - +
6A ARG* 3.6 8.3 - - - +
8A SER* 1.3 74.7 - - - +
10A ILE* 1.3 66.3 + - + +
12A ALA* 4.0 2.1 - - - +
13A ALA* 3.1 22.3 + - - +
30A LEU* 4.2 15.8 - - + +
34A LEU* 4.6 8.5 - - + -
41A LEU* 4.5 3.8 - - + -
44A HIS* 4.7 10.1 - - + -
45A VAL* 3.8 26.5 - - + -
51A LEU* 4.8 5.2 - - + -
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Residues in contact with ILE 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ARG* 2.9 35.3 + - + +
7A GLU* 4.8 0.2 - - - -
9A VAL* 1.3 80.4 - - + +
11A ASP* 1.3 56.2 + - - +
13A ALA* 3.2 2.7 + - - +
14A LEU* 2.8 55.1 + - + +
51A LEU* 5.0 7.2 - - + -
54A ALA* 3.9 28.3 - - + -
55A LEU* 3.8 15.0 - - + -
58A GLU* 3.8 27.6 - - + +
62A ARG* 3.8 17.9 - - - +
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Residues in contact with ASP 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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7A GLU* 3.0 38.6 + - - +
8A SER* 3.4 10.4 + - - +
10A ILE* 1.3 74.8 - - - +
12A ALA* 1.3 62.5 + - - +
14A LEU* 3.5 3.3 + - - +
15A GLU* 3.0 26.3 + - - +
62A ARG* 2.7 38.2 + - - +
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Residues in contact with ALA 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 SER 3.2 8.7 + - - +
9A VAL 4.0 0.9 - - - +
11A ASP* 1.3 77.9 - - - +
13A ALA* 1.3 53.4 + - - +
15A GLU* 3.2 4.8 + - - +
16A LEU* 2.8 35.5 + - - +
30A LEU* 3.8 17.5 - - + -
33A LYS* 3.5 27.3 - - + +
34A LEU* 3.8 24.9 - - + -
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Residues in contact with ALA 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 VAL 3.1 19.7 + - - +
10A ILE 3.2 0.4 + - - +
12A ALA* 1.3 75.6 - - - +
14A LEU* 1.3 57.1 + - - +
16A LEU* 3.5 7.1 + - - +
17A LEU* 2.9 27.4 + - - +
25A LEU* 3.8 5.1 - - + +
30A LEU* 3.7 14.3 - - + +
51A LEU* 3.6 24.5 - - + -
55A LEU* 3.6 26.7 - - + +
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Residues in contact with LEU 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ILE* 2.8 38.7 + - + +
11A ASP* 3.9 4.0 - - - +
13A ALA* 1.3 70.0 - - - +
15A GLU* 1.3 65.9 + - - +
17A LEU* 3.5 13.3 + - + +
18A ASN* 3.3 17.0 + - - -
55A LEU* 3.9 14.1 - - + +
58A GLU* 4.8 4.7 - - + -
59A ILE* 3.8 27.1 - - + -
62A ARG* 4.1 22.9 - - - +
63A HIS* 5.2 0.2 - - - +
93A TYR* 3.7 59.9 - - + +
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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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11A ASP 3.0 17.1 + - - +
12A ALA* 3.5 8.0 - - - +
14A LEU* 1.3 77.2 - - - +
16A LEU* 1.3 60.7 + - - +
18A ASN* 3.3 13.5 + - - +
19A GLU* 3.3 20.1 + - + +
33A LYS* 3.1 30.7 + - - +
93A TYR* 5.7 0.4 - - - -
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Residues in contact with LEU 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 ALA 2.8 19.5 + - - +
13A ALA* 3.6 3.8 - - - +
15A GLU* 1.3 70.3 - - - +
17A LEU* 1.3 55.9 + - - +
19A GLU* 3.0 20.3 + - - +
20A THR* 2.8 58.8 + - + +
25A LEU* 3.4 24.2 - - + -
26A THR 4.0 6.7 - - - +
29A LYS* 3.6 31.0 - - + +
30A LEU* 3.7 42.2 - - + +
33A LYS* 4.2 8.7 - - + +
51A LEU* 5.9 0.2 - - + -
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Residues in contact with LEU 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 ALA 2.9 17.4 + - - +
14A LEU* 3.5 19.3 - - + +
16A LEU* 1.3 76.7 - - - +
18A ASN* 1.3 58.1 + - - +
20A THR* 3.9 4.7 - - - -
21A GLY* 2.8 54.4 + - - +
22A ILE* 3.7 9.2 - - + +
25A LEU* 3.7 13.0 - - + +
52A LEU* 5.5 0.4 - - + -
55A LEU* 4.9 6.7 - - + -
59A ILE* 4.7 3.4 - - + -
93A TYR* 3.9 19.5 - - + -
94A ARG* 3.2 30.4 - - - +
95A ASP 4.9 0.2 - - - -
99A VAL* 3.7 26.9 - - + -
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Residues in contact with ASN 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 LEU 3.3 5.5 + - - -
15A GLU* 3.5 11.9 + - - +
16A LEU 3.2 0.6 - - - -
17A LEU* 1.3 80.3 - - - +
19A GLU* 1.3 62.1 + - - +
92A ARG 4.1 4.6 + - - +
93A TYR* 3.3 34.0 - - - -
94A ARG* 3.0 45.4 + - - +
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Residues in contact with GLU 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* 3.3 6.4 + - + +
16A LEU* 3.0 20.6 + - - +
18A ASN* 1.3 78.0 - - - +
20A THR* 1.3 60.6 + - + +
29A LYS* 3.0 25.0 + - - -
33A LYS* 2.6 32.5 + - - -
94A ARG* 2.7 20.0 + - - -
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Residues in contact with THR 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 LEU* 2.8 49.1 + - + +
19A GLU* 1.3 82.7 - - + +
21A GLY* 1.3 71.3 + - - +
23A ASP* 5.1 0.5 + - - +
24A GLY* 3.6 32.2 + - - +
25A LEU* 3.6 11.3 - - - +
29A LYS* 3.9 13.9 - - + +
94A ARG* 3.7 13.5 + - - -
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Residues in contact with GLY 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 LEU* 2.8 27.1 + - - +
20A THR* 1.3 92.2 + - - +
22A ILE* 1.3 63.7 + - - -
23A ASP 3.4 2.2 - - - -
25A LEU* 3.4 6.9 + - - +
94A ARG* 3.6 15.9 - - - +
95A ASP* 3.0 13.0 - - - -
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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