Contacts of the helix formed by residues 32 - 43 (chain Q) in PDB entry 5XS0
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 Q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208O CYS* 5.1 1.3 - - - -
203P ALA 4.2 0.3 + - - -
206P ASN 5.5 0.4 - - - +
207P SER* 3.2 43.8 + - - +
30Q GLN 3.4 5.3 + - - +
31Q TYR* 1.3 75.6 - - - +
33Q ALA* 1.3 58.5 + - - +
34Q GLU* 3.7 16.9 + - - +
35Q GLU* 3.2 16.0 + - - +
36Q TYR* 2.7 34.4 + - - +
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Residues in contact with ALA 33 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205O TYR* 3.4 40.9 - - + +
208O CYS* 3.7 34.3 - - + +
32Q THR* 1.3 72.4 - - - +
34Q GLU* 1.3 71.0 + - - +
36Q TYR* 3.8 0.3 - - - +
37Q GLN* 2.9 19.8 + - - +
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Residues in contact with GLU 34 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205O TYR* 4.8 10.5 - - - +
203P ALA* 3.6 24.6 - - + +
206P ASN* 4.8 12.1 - - - +
32Q THR* 3.7 19.2 + - - +
33Q ALA* 1.3 86.4 + - + +
35Q GLU* 1.3 55.3 + - - +
37Q GLN* 3.9 3.2 - - - +
38Q ALA* 2.9 30.5 + - - +
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Residues in contact with GLU 35 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200P VAL* 4.7 4.0 - - + +
203P ALA* 3.5 15.8 - - + +
204P ARG* 2.9 42.9 + - + +
207P SER* 3.6 16.5 + - - -
31Q TYR* 3.6 24.2 - - + -
32Q THR* 3.2 17.2 + - - +
34Q GLU* 1.3 75.7 - - - +
36Q TYR* 1.3 66.8 + - - +
38Q ALA* 3.7 2.9 - - - +
39Q ILE* 2.9 39.8 + - + +
79Q PHE 4.8 0.9 - - - +
116Q LYS* 3.2 22.2 + - - -
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Residues in contact with TYR 36 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201O GLU* 3.4 24.7 + - - -
204O ARG* 2.7 53.1 + - + -
205O TYR* 4.4 10.5 - - - -
208O CYS* 3.9 24.2 - - - -
80P GLY* 4.2 2.0 - - - -
81P TYR* 3.4 31.8 - + - -
82P ASN* 3.7 22.0 - - - -
31Q TYR* 4.0 12.7 - - + +
32Q THR 2.7 21.1 + - - +
33Q ALA 3.8 3.6 - - - +
35Q GLU* 1.3 73.0 - - - +
37Q GLN* 1.3 65.4 + - + +
40Q GLN* 2.9 38.8 + - + +
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Residues in contact with GLN 37 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201O GLU* 4.5 12.2 + - - +
205O TYR* 3.7 43.4 + - + +
33Q ALA 2.9 18.7 + - - +
34Q GLU* 4.0 3.6 - - - +
36Q TYR* 1.3 82.1 - - + +
38Q ALA* 1.3 62.9 + - - +
40Q GLN* 3.7 4.3 - - + +
41Q LYS* 2.9 53.5 + - + +
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Residues in contact with ALA 38 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199P SER* 4.2 15.0 - - - +
200P VAL* 3.6 35.1 - - + +
203P ALA* 4.7 1.1 - - + -
34Q GLU 2.9 18.8 + - - +
35Q GLU* 3.7 5.4 - - - +
37Q GLN* 1.3 78.3 + - - +
39Q ILE* 1.3 57.9 + - - +
41Q LYS* 3.4 6.7 + - - +
42Q ALA* 2.9 29.6 + - - +
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Residues in contact with ILE 39 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81P TYR* 3.4 30.1 - - + +
200P VAL* 3.5 20.2 - - + -
31Q TYR* 3.7 32.3 - - + -
35Q GLU* 2.9 30.6 + - + +
38Q ALA* 1.3 72.8 - - - +
40Q GLN* 1.3 67.5 + - - +
42Q ALA* 3.8 0.8 - - - +
43Q LEU* 2.9 33.3 + - + +
78Q MET* 3.5 36.8 - - + +
79Q PHE* 4.2 8.1 - - + -
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Residues in contact with GLN 40 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201O GLU* 3.4 28.7 + - - +
204O ARG* 3.7 3.6 - - - +
76P ASN* 3.4 23.2 + - - +
77P GLU* 4.2 13.7 + - - +
80P GLY* 3.6 6.0 - - - -
81P TYR* 3.3 27.7 + - + +
36Q TYR* 2.9 42.2 + - + +
37Q GLN* 3.7 5.6 - - - +
39Q ILE* 1.3 78.7 - - - +
41Q LYS* 1.3 62.9 + - + +
43Q LEU* 3.7 7.9 + - - +
44Q ARG* 3.9 27.0 + - - +
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Residues in contact with LYS 41 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201O GLU* 6.3 1.0 - - - +
37Q GLN* 2.9 50.3 + - + +
38Q ALA* 3.7 5.6 - - - +
40Q GLN* 1.3 78.4 - - + +
42Q ALA* 1.3 62.8 + - - +
44Q ARG* 3.1 45.0 + - - +
45Q GLN* 4.0 5.2 + - - +
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Residues in contact with ALA 42 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197P GLU* 3.4 28.9 - - - +
200P VAL* 4.1 4.9 - - + -
38Q ALA 2.9 18.6 + - - +
39Q ILE 3.2 3.6 + - - +
41Q LYS* 1.3 77.1 - - - +
43Q LEU* 1.3 62.8 + - - +
44Q ARG 3.2 0.9 + - - -
45Q GLN* 3.0 33.2 + - - +
78Q MET* 3.8 15.7 - - + +
161Q ALA* 3.4 9.0 - - - +
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Residues in contact with LEU 43 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81P TYR* 3.5 33.0 - - + -
39Q ILE* 2.9 26.1 + - + +
40Q GLN* 4.2 5.2 - - - +
41Q LYS 3.2 0.4 - - - -
42Q ALA* 1.3 75.4 - - - +
44Q ARG* 1.3 58.1 + - - +
45Q GLN 3.2 0.4 - - - -
78Q MET* 3.6 17.5 - - + -
79Q PHE* 4.5 2.7 - - + -
158Q PHE* 3.3 32.8 - - + +
159Q GLY* 4.0 1.7 - - - -
160Q ASN* 3.1 9.9 + - - -
161Q ALA* 2.9 39.6 + - + +
162Q LEU* 4.0 28.7 - - + +
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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