Contacts of the helix formed by residues 8 - 23 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6B ALA 4.1 6.7 - - - +
7B LEU* 1.3 76.4 - - - +
9B GLN* 1.3 56.1 + - - +
10B GLU* 2.6 44.8 + - - +
11B GLN* 2.7 37.0 + - - +
12B LYS* 3.1 12.3 + - - +
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Residues in contact with GLN 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364A SO4 3.3 26.4 + - - -
7B LEU 4.1 0.6 + - - -
8B THR* 1.3 71.7 - - - +
10B GLU* 1.3 59.1 + - - +
12B LYS* 3.5 34.7 - - + +
13B LYS* 3.5 18.7 + - - +
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Residues in contact with GLU 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B THR* 2.6 20.4 + - - +
9B GLN* 1.3 78.7 - - - +
11B GLN* 1.3 65.6 + - + +
13B LYS* 2.9 28.2 - - + +
14B GLU* 3.4 5.7 + - - +
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Residues in contact with GLN 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B ALA 4.5 0.5 - - - +
7B LEU* 3.3 19.1 - - + +
8B THR* 2.7 46.7 + - - +
10B GLU* 1.3 76.4 - - + +
12B LYS* 1.3 57.5 + - - +
13B LYS 3.1 1.3 - - - -
14B GLU* 3.1 13.9 + - - +
15B LEU* 2.6 41.9 + - + +
178B GLN 4.1 8.6 + - - +
179B GLN* 4.0 22.2 + - - +
181B GLY* 5.3 3.9 - - - +
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Residues in contact with LYS 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258A ARG* 5.1 1.2 - - - +
364A SO4 2.9 31.6 + - - +
7B LEU* 4.1 32.9 + - + -
8B THR 3.1 13.1 + - - +
9B GLN* 3.5 31.0 - - + +
11B GLN* 1.3 73.9 - - - +
13B LYS* 1.3 70.5 + - - +
15B LEU* 4.2 2.0 - - - +
16B SER* 2.9 25.7 + - - -
220B HIS* 5.8 4.1 + - - -
222B TYR* 3.4 56.9 - - + +
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Residues in contact with LYS 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B GLN 3.5 13.3 + - - +
10B GLU* 2.9 20.4 + - + +
12B LYS* 1.3 80.6 - - - +
14B GLU* 1.3 61.0 + - - +
16B SER* 3.6 4.2 - - - -
17B GLU* 3.0 45.8 + - + +
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Residues in contact with GLU 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B GLU 3.4 4.9 + - - +
11B GLN* 3.1 18.1 + - - +
13B LYS* 1.3 75.5 - - - +
15B LEU* 1.3 72.2 + - - +
16B SER 2.6 3.9 + - - -
17B GLU* 2.8 27.2 + - - +
18B ILE* 3.0 29.0 + - + +
138B LYS* 2.7 35.4 + - - -
181B GLY* 3.8 17.1 - - - -
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Residues in contact with LEU 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B LEU* 3.6 18.6 - - + -
11B GLN* 2.6 24.2 + - + +
12B LYS* 3.8 4.5 - - - +
14B GLU* 1.3 75.4 - - + +
16B SER* 1.3 57.6 + - - +
18B ILE* 4.8 0.7 - - + -
19B ALA* 2.8 24.4 + - - +
178B GLN* 3.2 48.2 - - + +
181B GLY* 4.2 7.0 - - - -
182B LEU 3.0 39.7 - - - +
183B VAL* 3.1 16.6 - - + +
222B TYR* 4.2 9.4 - - + -
225B GLY* 3.9 13.7 - - - +
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Residues in contact with SER 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B LYS 2.9 16.7 + - - -
13B LYS* 3.6 4.5 - - - -
14B GLU 2.6 4.4 + - - -
15B LEU* 1.3 70.9 - - - +
17B GLU* 1.3 60.7 + - - -
18B ILE 2.9 1.8 - - - -
19B ALA 2.5 22.7 + - - -
20B GLN* 2.7 32.3 + - - +
222B TYR* 4.5 9.5 + - - -
224B GLU* 3.5 26.7 + - - +
225B GLY* 4.3 0.2 - - - -
265B PRO* 5.8 0.2 - - - +
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Residues in contact with GLU 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B LYS* 3.0 42.5 - - + +
14B GLU* 2.8 21.3 + - - +
16B SER* 1.3 73.5 - - - +
18B ILE* 1.3 59.8 + - + +
20B GLN* 4.1 8.7 - - - +
21B SER* 2.8 33.6 + - - -
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Residues in contact with ILE 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B GLU* 3.0 37.6 + - + +
15B LEU* 3.7 2.0 - - - +
16B SER 2.7 3.4 + - - -
17B GLU* 1.3 75.1 - - + +
19B ALA* 1.3 64.6 + - - +
20B GLN 3.1 0.2 - - - -
21B SER* 2.9 14.1 + - - +
22B ILE* 2.9 35.6 + - + +
103B VAL* 4.6 7.2 - - + -
138B LYS* 4.2 2.0 - - - +
143B ASP* 3.3 57.9 - - + +
181B GLY 4.4 3.6 - - - +
183B VAL* 3.5 15.9 - - + -
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Residues in contact with ALA 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B LEU 2.8 19.7 + - - +
16B SER* 2.5 10.7 + - - +
18B ILE* 1.3 73.5 - - - +
20B GLN* 1.3 58.3 + - - +
22B ILE* 3.8 7.6 - - - +
23B VAL* 3.6 14.9 - - - +
183B VAL* 4.0 13.9 - - + -
224B GLU 3.7 20.2 - - - +
225B GLY* 4.0 4.9 - - - -
226B THR 3.9 9.4 - - - +
227B LEU* 3.7 11.9 - - - +
265B PRO* 3.9 14.1 - - + +
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Residues in contact with GLN 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B SER* 2.7 35.3 + - - +
17B GLU* 4.1 5.8 - - - +
19B ALA* 1.3 72.0 - - - +
21B SER* 1.3 54.8 + - - +
22B ILE 2.7 16.1 + - - -
23B VAL* 2.8 20.9 + - + -
24B ALA* 3.1 12.7 + - - -
265B PRO* 3.9 23.3 - - + +
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Residues in contact with SER 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B GLU 2.8 21.8 + - - -
18B ILE* 2.9 19.9 + - - -
20B GLN* 1.3 72.5 - - - +
22B ILE* 1.3 59.9 + - - +
24B ALA* 4.0 10.4 + - - +
27B LYS* 4.2 13.9 + - - -
74B GLY 4.0 8.4 - - - +
103B VAL* 4.1 17.0 - - - +
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Residues in contact with ILE 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B ILE* 2.9 34.3 - - + +
19B ALA* 3.8 7.2 - - - +
20B GLN 2.7 5.7 + - - -
21B SER* 1.3 79.6 - - - +
23B VAL* 1.3 57.0 + - + +
24B ALA 3.5 1.6 + - - -
27B LYS* 3.7 10.4 - - - +
28B GLY 4.1 1.0 - - - +
29B ILE* 3.2 36.6 - - + -
74B GLY* 3.6 22.3 - - - +
75B GLY* 4.5 9.6 - - - -
103B VAL* 4.8 7.9 - - + -
144B PHE* 3.4 39.5 - - + -
183B VAL* 4.9 1.6 - - + -
227B LEU* 3.9 19.5 - - + -
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Residues in contact with VAL 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B ALA 3.6 18.8 - - - +
20B GLN* 2.8 16.5 + - + +
22B ILE* 1.3 78.1 - - + +
24B ALA* 1.3 67.0 + - - +
25B ASN 4.0 0.2 - - - -
26B GLY 4.9 0.5 + - - -
27B LYS 3.5 20.9 - - - +
28B GLY* 5.0 0.7 - - - -
227B LEU* 4.1 11.2 - - + -
265B PRO* 4.2 16.8 - - + +
266B GLY* 4.4 1.8 - - - -
268B CYS* 3.2 35.2 - - - -
296B LYS* 3.5 26.3 - - + +
298B SER* 3.9 7.2 - - - +
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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