Contacts of the helix formed by residues 32 - 44 (chain B) in PDB entry 5XRZ
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 32 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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203A ALA 4.5 0.3 + - - -
207A SER* 3.2 36.6 + - - +
30B GLN 3.6 4.7 + - - +
31B TYR* 1.3 77.0 - - - +
33B ALA* 1.3 60.4 + - - +
34B GLU* 3.7 19.1 + - - +
35B GLU* 3.4 20.2 + - - +
36B TYR* 2.9 28.6 + - - +
208K CYS* 4.2 2.5 - - - -
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Residues in contact with ALA 33 (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 THR* 1.3 73.6 - - - +
34B GLU* 1.3 66.8 + - + +
36B TYR* 3.3 3.3 + - - +
37B GLN* 2.9 31.0 + - - +
205K TYR* 3.6 32.6 - - + +
208K CYS* 3.7 32.2 - - + +
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Residues in contact with GLU 34 (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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203A ALA* 3.6 25.4 - - + +
206A ASN* 5.3 8.1 - - - +
207A SER* 5.4 0.3 - - - -
32B THR* 3.7 18.2 + - - +
33B ALA* 1.3 87.7 + - + +
35B GLU* 1.3 63.4 + - - +
37B GLN* 3.3 3.6 + - - +
38B ALA* 2.9 25.8 + - - +
205K TYR* 4.8 11.4 - - - +
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Residues in contact with GLU 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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200A VAL* 5.0 2.2 - - + -
203A ALA* 3.4 14.8 - - + +
204A ARG* 3.1 42.1 + - + +
207A SER* 3.1 24.4 + - - -
31B TYR* 3.2 32.8 - - + -
32B THR* 3.4 16.1 + - - +
34B GLU* 1.3 78.1 - - - +
36B TYR* 1.3 64.1 + - - +
38B ALA* 3.8 1.9 - - - +
39B ILE* 2.9 43.7 + - + +
116B LYS* 3.4 11.1 + - - -
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Residues in contact with TYR 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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80A GLY* 5.0 2.0 - - - -
81A TYR* 3.4 33.8 + + - +
82A ASN* 3.8 17.7 - - - +
116A LYS* 6.2 0.2 - - - -
31B TYR* 4.6 8.5 - - + +
32B THR 2.9 19.8 + - - +
33B ALA* 3.5 8.7 - - - +
35B GLU* 1.3 77.8 - - - +
37B GLN* 1.3 71.0 + - + +
39B ILE* 3.8 1.2 - - - +
40B GLN* 2.9 37.4 + - + +
201K GLU* 3.6 27.8 + - - -
204K ARG* 2.8 48.5 + - + -
205K TYR* 4.2 22.9 - + + -
208K CYS* 5.1 7.2 - - - -
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Residues in contact with GLN 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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33B ALA 2.9 17.8 + - - +
34B GLU* 3.9 4.0 - - - +
36B TYR* 1.3 80.7 - - - +
38B ALA* 1.3 63.5 + - - +
40B GLN* 3.4 4.9 + - + +
41B LYS* 3.0 65.1 + - + +
201K GLU* 4.4 13.7 + - - +
205K TYR* 3.1 46.0 + - + +
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Residues in contact with ALA 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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199A SER* 3.6 29.1 - - - +
200A VAL* 3.6 23.2 - - + +
203A ALA* 4.8 1.1 - - + -
34B GLU 2.9 17.5 + - - +
35B GLU* 3.8 5.2 - - - +
37B GLN* 1.3 77.7 - - - +
39B ILE* 1.3 57.5 + - - +
41B LYS* 3.9 4.6 - - - +
42B ALA* 2.9 31.4 + - - +
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Residues in contact with ILE 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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81A TYR* 3.4 41.7 - - + +
200A VAL* 3.6 20.0 - - + -
204A ARG* 5.2 0.2 - - - +
31B TYR* 3.8 14.8 - - + +
35B GLU* 2.9 39.1 + - + +
36B TYR 3.8 2.9 - - - +
38B ALA* 1.3 75.5 - - - +
40B GLN* 1.3 57.2 + - - +
42B ALA 3.4 0.3 + - - -
43B LEU* 2.9 44.2 + - + +
78B MET* 3.6 28.0 - - + +
79B PHE* 4.2 8.5 - - + -
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Residues in contact with GLN 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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76A ASN* 3.4 22.6 + - - +
77A GLU* 4.1 7.4 + - - +
80A GLY* 4.0 1.6 - - - -
81A TYR* 3.8 26.3 + - + +
36B TYR* 2.9 30.1 + - + +
37B GLN* 3.7 6.5 - - + +
39B ILE* 1.3 76.6 - - - +
41B LYS* 1.3 64.2 + - + +
43B LEU* 3.0 17.9 + - - +
44B ARG* 3.0 46.0 + - - +
201K GLU* 4.0 9.6 + - - +
204K ARG* 3.6 21.4 - - - +
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Residues in contact with LYS 41 (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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37B GLN* 3.0 56.5 + - + +
38B ALA* 4.1 3.4 - - - +
40B GLN* 1.3 75.5 - - + +
42B ALA* 1.3 62.9 + - - +
44B ARG* 3.3 44.4 + - - +
45B GLN* 3.8 9.0 + - - +
201K GLU* 5.0 8.9 - - - +
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Residues in contact with ALA 42 (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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192A LYS* 4.9 0.5 - - - +
197A GLU* 3.5 24.0 - - - +
200A VAL* 4.0 6.1 - - + -
38B ALA 2.9 19.0 + - - +
41B LYS* 1.3 76.3 - - - +
43B LEU* 1.3 59.8 + - - +
45B GLN* 3.3 29.9 - - - +
78B MET* 3.7 27.6 - - + +
161B ALA* 3.4 9.3 - - - +
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Residues in contact with LEU 43 (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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81A TYR* 3.6 25.1 - - + -
39B ILE* 2.9 35.0 + - + +
40B GLN* 3.0 8.2 + - - +
42B ALA* 1.3 72.1 - - - +
44B ARG* 1.3 60.9 + - - +
45B GLN 3.1 2.2 - - - -
78B MET* 3.7 18.6 - - + -
79B PHE* 4.6 4.0 - - + -
158B PHE* 3.5 30.5 - - + +
159B GLY* 4.0 1.9 - - - -
160B ASN 3.3 9.5 + - - -
161B ALA* 3.1 32.5 + - + -
162B LEU* 3.9 33.9 - - + +
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Residues in contact with ARG 44 (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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77A GLU* 2.8 44.3 + - - +
40B GLN* 3.0 37.6 + - + +
41B LYS* 3.3 51.4 + - - +
42B ALA 3.3 0.8 - - - -
43B LEU* 1.3 76.5 - - - +
45B GLN* 1.3 63.3 + - - +
46B ARG* 3.8 6.9 + - - +
160B ASN* 3.7 18.9 + - - +
195K ASP* 6.3 0.7 - - - -
196K LEU* 3.4 29.8 - - - +
201K GLU* 4.0 9.3 + - - -
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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