Contacts of the helix formed by residues 34 - 40 (chain B) in PDB entry 1XOX
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 34 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B TRP* 5.0 0.2 - - - -
27B PHE 3.4 4.5 - - - -
28B LEU 2.8 25.6 - - - +
31B CYS 3.1 19.5 - - - +
33B CYS* 1.3 75.1 - - - +
35B PRO* 1.3 68.3 - - - +
36B GLU* 3.5 5.2 + - - +
37B ARG* 2.9 31.4 + - + +
38B MET* 2.6 36.2 + - - +
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Residues in contact with PRO 35 (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 ILE* 3.8 12.1 - - + +
22B PHE* 2.9 46.2 - - + -
24B ASN 5.2 2.7 - - - +
25B TRP* 5.0 4.0 - - + -
27B PHE 4.1 4.7 - - - +
28B LEU* 3.6 33.4 - - + -
34B THR* 1.3 90.4 - - - +
36B GLU* 1.3 58.2 + - + +
39B ALA* 2.9 27.0 + - - +
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Residues in contact with GLU 36 (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 LYS* 4.1 17.9 + - - +
19B ILE* 3.4 34.4 - - + +
34B THR* 3.3 4.5 + - - +
35B PRO* 1.3 78.8 - - + +
37B ARG* 1.3 64.0 + - - +
40B GLU* 3.3 24.6 + - - +
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Residues in contact with ARG 37 (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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32B ALA* 3.1 36.8 - - - +
34B THR* 2.9 30.7 + - + +
36B GLU* 1.3 79.5 - - - +
38B MET* 1.3 60.1 + - - +
40B GLU* 3.7 18.5 - - - +
41B ALA 4.2 0.5 + - - -
72B ASP* 5.9 1.8 - - - -
73B PRO* 2.9 26.8 - - + +
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Residues in contact with MET 38 (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 PHE* 3.7 15.9 - - + -
25B TRP* 3.2 27.1 - - + -
33B CYS* 3.1 36.6 - - + +
34B THR 2.6 17.7 + - - +
37B ARG* 1.3 70.4 - - - +
39B ALA* 1.3 53.5 + - - +
40B GLU 2.9 4.3 - - - -
41B ALA* 2.6 34.1 + - - +
42B GLY 3.5 2.8 + - - -
43B PHE* 3.6 15.0 + - + +
55B ALA* 3.3 34.1 - - + -
67B TRP* 3.6 28.3 - - + -
73B PRO* 3.6 15.0 - - + -
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Residues in contact with ALA 39 (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 LYS* 4.9 2.3 - - + +
18B ARG* 3.5 36.9 + - + -
19B ILE* 3.4 26.9 - - + -
22B PHE* 3.7 8.6 - - + -
35B PRO 2.9 21.3 + - - +
38B MET* 1.3 76.7 - - - +
40B GLU* 1.3 60.8 + - - +
41B ALA 3.0 0.2 - - - -
42B GLY 3.1 10.3 + - - -
43B PHE 3.4 12.6 - - - -
86B PHE* 3.9 1.0 - - - -
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Residues in contact with GLU 40 (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 LYS* 3.2 31.2 - - - +
36B GLU 3.3 19.2 + - - +
37B ARG* 3.7 15.5 - - - +
38B MET 2.9 0.6 + - - -
39B ALA* 1.3 78.8 - - - +
41B ALA* 1.3 55.1 + - - +
74B ILE* 4.0 24.3 - - + +
86B PHE* 2.8 24.8 - - - -
87B LEU 4.5 2.3 - - - +
89B VAL 4.4 12.5 - - - +
90B LYS* 5.8 1.7 - - - +
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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