Contacts of the helix formed by residues 15 - 27 (chain B) in PDB entry 1XR2
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 ARG 15 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11B ILE* 3.3 16.6 - - + -
12B GLY 3.2 9.4 + - - +
13B GLU 4.9 2.2 - - - +
14B LYS* 1.3 82.5 + - - +
16B GLU* 1.3 64.3 + - - +
17B PHE 3.0 3.1 - - - -
18B LYS* 3.1 38.5 + - + +
19B LYS* 3.2 12.8 + - - +
486B TRP* 3.1 65.3 - - + +
494B CYS* 4.5 13.1 - - - +
1201B C2F 4.3 11.1 + - - -
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Residues in contact with GLU 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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11B ILE 3.2 2.8 + - - -
12B GLY* 4.3 7.9 - - - -
13B GLU* 3.5 4.6 + - - +
14B LYS* 2.5 54.1 + - + +
15B ARG* 1.3 77.8 + - - +
17B PHE* 1.3 60.7 + - - +
19B LYS* 4.0 6.3 - - - +
20B ALA* 3.0 27.4 + - - +
37B GLU* 5.4 5.3 - - + +
40B LYS* 6.6 0.2 - - - -
41B LEU* 4.0 25.5 - - + +
44B TYR* 5.5 5.0 - - - +
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Residues in contact with PHE 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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10B LYS* 3.7 21.1 - - + +
11B ILE* 3.1 39.8 + - + +
15B ARG 3.0 0.6 - - - -
16B GLU* 1.3 76.1 - - - +
18B LYS* 1.3 69.7 + - + +
20B ALA* 3.5 1.2 + - - +
21B LEU* 3.2 46.1 + - + +
38B MET* 3.9 32.7 - - + +
41B LEU* 3.8 13.1 - - + +
61B LEU* 4.1 11.0 - - + -
62B SER 3.6 25.1 - - - -
63B TYR* 4.0 10.1 - - - -
64B TYR 4.6 0.2 - - - -
488B LEU* 4.9 1.3 - - + -
491B GLY 3.5 24.5 - - - -
492B SER* 4.8 0.7 - - - -
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Residues in contact with LYS 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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11B ILE* 5.4 1.5 - - + +
15B ARG* 3.1 43.4 + - + +
17B PHE* 1.3 86.5 - - + +
19B LYS* 1.3 62.7 + - - +
21B LEU* 3.7 1.0 - - - +
22B GLU* 2.7 60.8 + - - +
492B SER* 3.0 33.9 + - - +
493B ARG* 4.2 5.7 - - - +
494B CYS* 4.8 8.1 - - - -
1201B C2F 3.1 34.2 + - - +
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Residues in contact with LYS 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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14B LYS 5.8 0.7 - - - +
15B ARG 3.2 12.0 + - - +
16B GLU* 4.0 6.5 - - - +
18B LYS* 1.3 77.3 - - - +
20B ALA* 1.3 61.4 + - - +
22B GLU* 3.4 4.6 + - - +
23B ASP* 2.8 44.8 + - - +
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Residues in contact with ALA 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 GLU 3.0 18.3 + - - +
17B PHE 4.0 0.2 - - - +
19B LYS* 1.3 75.4 - - - +
21B LEU* 1.3 57.3 + - - +
23B ASP* 3.9 5.6 - - - +
24B PHE* 2.9 32.1 + - - +
29B ILE* 5.6 1.3 - - - +
34B PHE* 3.7 12.2 - - + +
37B GLU* 4.0 18.6 - - + -
38B MET* 3.7 23.8 - - + -
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Residues in contact with LEU 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 PHE* 3.2 43.9 + - + +
18B LYS 3.7 3.1 - - - +
20B ALA* 1.3 80.0 - - - +
22B GLU* 1.3 57.4 + - - +
24B PHE* 3.4 2.9 + - - +
25B TRP* 3.1 53.5 + - + -
34B PHE* 3.5 27.9 - - + -
63B TYR 3.5 22.0 - - - +
64B TYR* 4.8 0.2 - - + -
91B PHE* 3.5 15.3 - - + -
491B GLY* 3.9 8.7 - - - +
492B SER* 3.7 20.6 - - - -
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Residues in contact with GLU 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 LYS* 2.7 59.2 + - - +
19B LYS* 4.1 4.4 - - - +
21B LEU* 1.3 72.8 - - - +
23B ASP* 1.3 67.2 + - - +
25B TRP* 3.3 15.6 + - + +
26B LYS* 2.9 26.3 + - - +
492B SER* 3.0 21.7 + - - +
493B ARG* 4.9 3.6 + - - -
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Residues in contact with ASP 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 LYS* 2.8 34.9 + - - +
20B ALA* 3.9 5.1 + - - +
22B GLU* 1.3 73.6 - - - +
24B PHE* 1.3 58.7 + - - +
26B LYS* 3.3 4.4 + - - +
27B GLY 2.9 9.4 + - - -
28B LYS* 2.9 45.3 + - + +
29B ILE* 4.2 12.8 - - + -
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Residues in contact with PHE 24 (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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20B ALA 2.9 19.2 + - - +
21B LEU 3.6 3.4 - - - +
22B GLU 3.2 0.2 - - - -
23B ASP* 1.3 77.8 - - - +
25B TRP* 1.3 69.4 + + - +
27B GLY* 3.3 10.7 + - - -
29B ILE* 3.7 21.9 - - + +
30B THR* 3.8 10.1 - - - -
31B GLU* 3.5 30.5 - - + -
34B PHE* 3.9 20.0 - + + -
87B LEU* 4.3 19.7 - - + -
88B SER* 6.1 1.1 - - - -
91B PHE* 3.7 35.9 - + - -
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Residues in contact with TRP 25 (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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21B LEU* 3.1 49.1 + - + +
22B GLU* 3.8 16.2 - - + +
23B ASP 3.3 0.2 - - - -
24B PHE* 1.3 83.2 - + - +
26B LYS* 1.3 63.3 + - - +
27B GLY* 3.2 1.6 + - - -
64B TYR* 4.0 30.3 - + - -
91B PHE* 3.5 40.4 - + + +
95B ARG* 5.5 9.0 - - + -
492B SER* 3.6 26.2 - - - -
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Residues in contact with LYS 26 (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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22B GLU 2.9 18.8 + - - +
23B ASP* 3.8 7.0 - - - +
25B TRP* 1.3 76.4 - - - +
27B GLY* 1.3 59.6 + - - +
28B LYS* 3.4 6.4 + - + +
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Residues in contact with GLY 27 (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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23B ASP 2.9 4.5 + - - -
24B PHE 3.3 8.5 + - - -
25B TRP 3.1 5.5 - - - -
26B LYS* 1.3 79.1 - - - +
28B LYS* 1.3 62.5 + - - +
29B ILE 3.3 8.2 + - - +
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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