Contacts of the helix formed by residues 8 - 21 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6D ALA 4.2 6.3 - - - +
7D LEU* 1.3 76.3 - - - +
9D GLN* 1.3 67.8 + - - +
10D GLU* 3.9 9.6 + - - +
11D GLN* 3.0 44.9 + - - +
12D LYS* 3.0 17.4 + - - +
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Residues in contact with GLN 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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364C SO4 4.6 10.1 + - - -
8D THR* 1.3 74.0 - - - +
10D GLU* 1.3 61.9 + - - +
12D LYS* 3.5 27.0 + - - +
13D LYS* 3.0 25.0 + - + +
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Residues in contact with GLU 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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8D THR* 3.0 9.2 + - - +
9D GLN* 1.3 80.0 - - - +
11D GLN* 1.3 64.9 + - + +
13D LYS* 3.3 18.8 - - + +
14D GLU* 3.3 21.3 + - + +
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Residues in contact with GLN 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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6D ALA 4.4 1.9 - - - +
7D LEU* 3.6 18.7 - - + +
8D THR* 3.0 37.7 + - - +
10D GLU* 1.3 78.2 - - + +
12D LYS* 1.3 68.7 + - - +
14D GLU* 3.4 11.1 + - - +
15D LEU* 3.2 25.6 + - + +
178D GLN 3.5 20.6 + - - +
179D GLN* 3.7 24.4 + - - +
181D GLY* 5.0 5.6 - - - +
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Residues in contact with LYS 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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364C SO4 2.9 38.6 + - - +
7D LEU* 4.1 31.9 + - + -
8D THR 3.0 13.1 + - - +
9D GLN* 3.6 24.3 - - - +
11D GLN* 1.3 73.8 - - - +
13D LYS* 1.3 54.0 + - - +
15D LEU* 2.6 31.5 + - - +
16D SER* 2.6 18.8 + - - -
222D TYR* 3.1 50.4 - - + +
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Residues in contact with LYS 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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9D GLN* 3.0 12.7 + - + +
10D GLU* 3.3 22.6 - - + +
12D LYS* 1.3 78.9 - - - +
14D GLU* 1.3 56.6 + - - +
16D SER* 3.4 9.9 + - - -
17D GLU* 3.0 40.0 + - + +
222D TYR* 4.9 0.2 + - - -
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Residues in contact with GLU 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 GLU* 3.3 9.7 + - + +
11D GLN* 3.8 11.8 - - - +
12D LYS 2.8 4.9 + - - -
13D LYS* 1.3 75.3 - - - +
15D LEU* 1.3 60.9 + - + +
17D GLU* 3.3 13.0 - - + +
18D ILE* 2.8 48.2 + - + +
138D LYS* 2.6 37.7 + - - -
143D ASP* 4.3 1.4 - - - +
181D GLY* 4.3 10.6 - - - +
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Residues in contact with LEU 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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7D LEU* 4.0 16.4 - - + -
11D GLN 3.2 17.7 + - - +
12D LYS* 2.6 13.5 + - - +
14D GLU* 1.3 71.2 - - + +
16D SER* 1.3 55.4 + - - +
18D ILE* 5.2 0.2 - - + -
19D ALA* 2.7 37.6 + - - +
178D GLN* 3.6 39.3 - - + +
181D GLY* 3.9 15.9 - - - +
182D LEU 3.2 35.0 - - - +
183D VAL* 3.6 13.6 - - + +
222D TYR* 4.5 2.7 - - + -
225D GLY* 3.8 17.3 - - - +
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Residues in contact with SER 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 LYS 2.6 16.4 + - - -
13D LYS* 3.4 13.4 - - - -
15D LEU* 1.3 72.1 - - - +
17D GLU* 1.3 66.0 + - - +
19D ALA* 3.3 0.7 - - - +
20D GLN* 2.8 48.3 + - - +
222D TYR* 3.2 25.8 + - - -
224D GLU* 4.1 13.8 - - - +
225D GLY* 4.1 1.4 - - - -
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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 LYS* 3.0 31.9 + - + +
14D GLU* 3.3 17.4 - - + +
16D SER* 1.3 79.7 - - - +
18D ILE* 1.3 55.3 + - + +
20D GLN* 4.1 2.9 - - - +
21D SER* 2.8 41.5 + - - -
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Residues in contact with ILE 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 GLU* 2.8 36.2 + - + +
17D GLU* 1.3 70.5 - - + +
19D ALA* 1.3 54.3 + - - +
21D SER* 2.5 22.5 + - - -
22D ILE* 2.8 34.2 - - + +
103D VAL* 4.1 13.5 - - + -
143D ASP* 3.5 55.4 - - + +
144D PHE* 4.8 0.7 - - + -
181D GLY 3.8 8.7 - - - +
183D VAL* 3.5 22.2 - - + -
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Residues in contact with ALA 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 LEU 2.7 24.3 + - - +
16D SER 3.3 3.6 - - - +
18D ILE* 1.3 73.7 - - - +
20D GLN* 1.3 68.0 + - - +
22D ILE* 3.3 13.4 + - - +
23D VAL* 4.2 2.3 - - - +
183D VAL* 3.9 11.2 - - + +
224D GLU 3.7 19.3 - - - +
225D GLY* 3.8 8.7 - - - -
226D THR 3.8 11.0 - - - +
227D LEU* 4.1 11.8 - - - +
265D PRO* 3.9 9.4 - - + -
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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 SER* 2.8 42.8 + - - +
17D GLU* 4.2 2.4 - - - +
19D ALA* 1.3 73.3 - - + +
21D SER* 1.3 53.2 + - - +
22D ILE 2.7 13.5 + - - -
23D VAL* 2.9 12.2 + - - +
24D ALA* 2.8 25.1 + - - -
224D GLU 5.1 2.2 + - - +
265D PRO* 4.0 20.0 - - + -
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Residues in contact with SER 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 2.8 19.2 + - - -
18D ILE* 2.5 30.5 + - - -
20D GLN* 1.3 75.2 - - - +
22D ILE* 1.3 61.1 + - - +
24D ALA* 3.9 17.8 - - - +
27D LYS* 3.9 14.2 + - - -
74D GLY 4.3 4.6 - - - +
103D VAL* 4.1 11.2 - - - +
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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