Contacts of the helix formed by residues 8 - 22 (chain Z) in PDB entry 1XDM
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 8 (chain Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6Z ALA 4.2 7.4 - - - +
7Z LEU* 1.3 77.2 - - - +
9Z GLN* 1.3 68.4 + - - +
10Z GLU* 2.9 11.3 + - - +
11Z GLN* 2.7 42.0 + - - +
12Z LYS* 3.3 10.5 + - - +
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Residues in contact with GLN 9 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364Y SO4 5.1 6.1 + - - -
8Z THR* 1.3 73.3 - - - +
10Z GLU* 1.3 56.5 + - - +
12Z LYS* 3.2 36.3 + - - +
13Z LYS* 3.0 29.1 + - + +
222Z TYR* 5.3 2.5 + - - -
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Residues in contact with GLU 10 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8Z THR* 3.0 10.8 - - - +
9Z GLN* 1.3 76.4 - - - +
11Z GLN* 1.3 66.6 + - + +
13Z LYS* 3.2 15.9 + - + +
14Z GLU* 3.1 21.1 + - - +
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Residues in contact with GLN 11 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6Z ALA 3.7 2.9 - - - +
7Z LEU* 2.8 33.2 + - + +
8Z THR* 2.7 39.9 + - - +
10Z GLU* 1.3 77.8 - - + +
12Z LYS* 1.3 54.0 + - - +
14Z GLU* 3.4 9.2 + - - +
15Z LEU* 2.8 40.9 + - + +
178Z GLN 4.3 2.1 + - - +
179Z GLN* 4.0 31.9 + - - +
181Z GLY* 5.7 2.1 - - - +
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Residues in contact with LYS 12 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199Y GLU* 5.8 1.2 + - - -
364Y SO4 3.3 26.1 + - - +
7Z LEU* 3.6 34.1 + - + -
8Z THR 3.5 7.4 - - - +
9Z GLN* 3.2 35.0 - - - +
10Z GLU 3.2 0.2 - - - -
11Z GLN* 1.3 75.1 - - - +
13Z LYS* 1.3 68.7 + - - +
15Z LEU* 2.9 8.2 + - - +
16Z SER* 2.7 28.8 + - - -
222Z TYR* 3.3 50.6 - - + +
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Residues in contact with LYS 13 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9Z GLN* 3.0 16.5 + - + +
10Z GLU* 3.3 18.4 - - + +
12Z LYS* 1.3 75.6 - - - +
14Z GLU* 1.3 65.2 + - - +
16Z SER* 3.5 5.0 - - - -
17Z GLU* 2.9 51.2 + - + +
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Residues in contact with GLU 14 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10Z GLU* 3.1 8.6 + - + +
11Z GLN* 3.5 11.4 - - - +
13Z LYS* 1.3 82.6 - - - +
15Z LEU* 1.3 64.5 + - - +
17Z GLU* 3.2 16.0 + - - +
18Z ILE* 3.0 34.5 + - + +
138Z LYS* 4.0 23.0 + - - +
181Z GLY* 3.9 21.5 - - - +
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Residues in contact with LEU 15 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7Z LEU* 3.7 31.0 - - + -
11Z GLN* 2.8 37.0 + - + +
12Z LYS* 2.9 8.0 + - - +
14Z GLU* 1.3 71.6 - - + +
16Z SER* 1.3 64.4 + - - +
18Z ILE* 3.1 5.3 + - - -
19Z ALA* 3.1 20.6 + - - +
178Z GLN* 3.9 21.1 - - + +
181Z GLY* 4.3 7.2 - - - -
182Z LEU 2.9 40.6 - - - +
183Z VAL* 3.2 17.0 - - + +
222Z TYR* 5.0 2.0 - - + -
225Z GLY* 3.9 16.2 - - - +
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Residues in contact with SER 16 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12Z LYS 2.7 22.3 + - - -
13Z LYS* 3.5 5.4 - - - -
15Z LEU* 1.3 74.0 - - - +
17Z GLU* 1.3 63.6 + - - +
19Z ALA* 3.4 0.5 + - - +
20Z GLN* 3.0 46.1 + - - +
222Z TYR* 4.5 14.1 - - - -
224Z GLU* 4.6 10.8 + - - +
225Z GLY* 4.2 9.3 - - - -
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Residues in contact with GLU 17 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13Z LYS* 2.9 60.2 + - + +
14Z GLU* 3.4 11.5 + - - +
16Z SER* 1.3 75.7 + - - +
18Z ILE* 1.3 54.1 + - + +
20Z GLN* 3.9 8.9 - - - +
21Z SER* 2.5 36.5 + - - -
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Residues in contact with ILE 18 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14Z GLU* 3.0 30.7 - - + +
15Z LEU* 3.3 9.0 - - - +
16Z SER 3.1 0.6 - - - -
17Z GLU* 1.3 72.9 - - + +
19Z ALA* 1.3 58.8 + - - +
20Z GLN 3.1 0.4 - - - -
21Z SER* 2.6 20.9 + - - +
22Z ILE* 2.7 42.4 + - + +
103Z VAL* 4.3 7.4 - - + -
138Z LYS* 3.8 25.8 - - - +
143Z ASP* 3.7 38.6 - - + +
181Z GLY 4.5 2.7 - - - +
183Z VAL* 3.9 5.6 - - + -
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Residues in contact with ALA 19 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15Z LEU 3.1 8.9 + - - +
16Z SER 4.1 0.7 - - - +
18Z ILE* 1.3 78.5 - - - +
20Z GLN* 1.3 61.6 + - - +
22Z ILE* 3.3 17.3 + - - +
23Z VAL* 3.6 12.5 - - - +
183Z VAL* 3.8 19.7 - - + -
224Z GLU 3.9 15.7 - - - +
226Z THR 3.3 28.0 - - - +
227Z LEU* 3.9 9.4 - - + +
265Z PRO* 3.9 4.9 - - + +
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Residues in contact with GLN 20 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16Z SER* 3.0 34.5 + - - +
17Z GLU* 3.9 7.2 - - - +
19Z ALA* 1.3 80.7 - - - +
21Z SER* 1.3 55.1 + - - +
22Z ILE 3.2 0.2 - - - -
23Z VAL* 3.4 8.9 + - + +
24Z ALA* 2.8 28.5 + - - -
224Z GLU 5.9 0.7 - - - +
265Z PRO* 4.4 17.2 - - + +
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Residues in contact with SER 21 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17Z GLU 2.5 25.2 + - - -
18Z ILE* 2.6 21.0 + - - +
20Z GLN* 1.3 72.2 - - - +
22Z ILE* 1.3 58.8 + - - +
23Z VAL 3.1 6.4 + - - -
24Z ALA* 3.8 11.4 - - - -
27Z LYS* 3.6 20.5 + - - -
74Z GLY 3.6 9.9 - - - +
103Z VAL* 4.7 9.1 - - - +
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Residues in contact with ILE 22 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18Z ILE* 2.7 41.7 + - + +
19Z ALA* 3.7 7.0 - - - +
20Z GLN 3.2 1.2 - - - -
21Z SER* 1.3 78.3 - - - +
23Z VAL* 1.3 57.3 + - + +
27Z LYS 2.6 22.4 - - - +
28Z GLY 3.9 4.2 - - - +
29Z ILE* 3.5 33.7 - - + -
74Z GLY* 3.7 23.1 - - - +
75Z GLY* 4.3 4.7 - - - +
103Z VAL* 4.6 5.6 - - + -
144Z PHE* 4.0 28.7 - - + -
183Z VAL* 4.5 0.4 - - + -
227Z LEU* 3.7 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