Contacts of the helix formed by residues 32 - 43 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208G CYS* 5.0 2.0 - - - -
207H SER* 3.1 38.8 + - - +
30I GLN 3.4 6.0 + - - +
31I TYR* 1.3 77.5 - - - +
33I ALA* 1.3 67.3 + - - +
34I GLU* 3.2 21.2 + - - +
35I GLU* 3.3 10.2 + - - +
36I TYR* 2.8 22.2 + - - +
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Residues in contact with ALA 33 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205G TYR* 3.7 34.5 - - + +
208G CYS* 3.8 31.8 - - + +
32I THR* 1.3 73.1 - - - +
34I GLU* 1.3 70.9 + - - +
36I TYR* 3.4 1.4 + - - +
37I GLN* 2.9 27.0 + - - +
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Residues in contact with GLU 34 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205G TYR* 5.0 9.4 - - - +
203H ALA* 3.6 26.8 - - + +
206H ASN* 4.9 12.2 - - + +
207H SER* 5.2 0.3 - - - -
32I THR* 3.6 20.1 + - - +
33I ALA* 1.3 86.9 + - + +
35I GLU* 1.3 56.0 + - - +
37I GLN* 3.9 2.3 - - - +
38I ALA* 3.0 30.0 + - - +
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Residues in contact with GLU 35 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200H VAL* 4.8 3.4 - - + +
203H ALA* 3.6 17.2 - - + +
204H ARG* 2.8 49.4 + - + +
207H SER* 4.0 11.3 + - - -
31I TYR* 3.3 29.6 + - + -
32I THR* 3.3 14.3 + - - +
34I GLU* 1.3 75.5 + - - +
36I TYR* 1.3 67.6 + - - +
38I ALA* 3.7 1.3 - - - +
39I ILE* 2.9 39.9 + - + +
79I PHE 4.6 0.9 - - - +
116I LYS* 3.6 14.7 + - - -
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Residues in contact with TYR 36 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201G GLU* 3.4 25.3 + - - -
204G ARG* 2.6 53.0 + - + +
205G TYR* 4.4 12.6 - + - -
208G CYS* 3.9 21.8 - - - -
80H GLY* 4.7 1.8 - - - -
81H TYR* 3.4 37.2 - + - -
82H ASN* 3.8 19.1 - - - -
31I TYR* 4.2 13.1 - - + +
32I THR 2.8 18.3 + - - +
33I ALA 3.7 5.2 - - - +
35I GLU* 1.3 77.5 - - - +
37I GLN* 1.3 63.5 + - + +
40I GLN* 2.9 34.3 + - + +
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Residues in contact with GLN 37 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201G GLU* 4.2 19.3 + - - +
205G TYR* 3.1 36.0 + - + +
33I ALA 2.9 17.8 + - - +
34I GLU* 4.0 2.7 - - - +
36I TYR* 1.3 80.2 - - + +
38I ALA* 1.3 68.2 + - - +
40I GLN* 3.6 3.9 - - + +
41I LYS* 2.9 57.0 + - + +
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Residues in contact with ALA 38 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199H SER* 4.1 15.3 - - - +
200H VAL* 3.7 35.8 - - + +
203H ALA* 4.3 3.8 - - + -
34I GLU 3.0 19.0 + - - +
35I GLU 3.7 3.8 - - - +
37I GLN* 1.3 76.1 - - - +
39I ILE* 1.3 58.8 + - - +
41I LYS* 3.8 5.3 - - - +
42I ALA* 2.9 30.0 + - - +
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Residues in contact with ILE 39 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81H TYR* 3.4 39.0 - - + +
200H VAL* 3.5 20.2 - - + -
31I TYR* 4.0 7.6 - - + +
35I GLU* 2.9 40.9 + - + +
38I ALA* 1.3 72.2 - - - +
40I GLN* 1.3 65.8 + - - +
43I LEU* 2.9 34.3 + - + +
78I MET* 3.5 37.0 - - + +
79I PHE* 4.0 13.7 - - + -
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Residues in contact with GLN 40 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201G GLU* 3.2 31.2 + - - +
204G ARG* 3.3 19.0 - - - +
76H ASN* 3.7 11.1 + - - +
77H GLU* 4.6 10.9 + - - +
80H GLY* 3.6 11.6 - - - -
81H TYR* 3.5 26.3 + - + +
36I TYR* 2.9 31.2 + - + +
37I GLN* 3.6 7.4 - - + +
39I ILE* 1.3 79.3 - - - +
41I LYS* 1.3 62.0 + - + +
43I LEU* 3.8 7.8 + - - +
44I ARG* 3.8 26.9 + - - +
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Residues in contact with LYS 41 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201G GLU* 6.2 1.8 - - - +
37I GLN* 2.9 52.4 + - + +
38I ALA* 3.8 5.8 - - - +
40I GLN* 1.3 74.9 - - + +
42I ALA* 1.3 64.8 + - - +
44I ARG* 3.2 44.4 + - - +
45I GLN* 4.1 4.9 + - - +
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Residues in contact with ALA 42 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197H GLU* 3.6 24.2 - - - +
200H VAL* 3.9 5.6 - - + -
38I ALA 2.9 18.8 + - - +
39I ILE 3.9 2.2 - - - +
41I LYS* 1.3 77.3 - - - +
43I LEU* 1.3 61.5 + - - +
44I ARG 3.2 1.0 + - - -
45I GLN* 3.2 29.6 + - - +
78I MET* 3.9 21.2 - - + +
161I ALA* 3.3 11.9 - - - +
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Residues in contact with LEU 43 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81H TYR* 3.5 28.3 - - + -
39I ILE* 2.9 31.8 + - + +
40I GLN* 4.2 5.8 - - - +
41I LYS 3.2 0.4 - - - -
42I ALA* 1.3 76.1 - - - +
44I ARG* 1.3 57.4 + - - +
45I GLN 3.3 0.2 - - - -
78I MET* 3.7 19.1 - - + -
79I PHE* 4.6 3.4 - - + -
158I PHE* 3.3 33.0 - - + +
159I GLY* 4.5 1.8 - - - -
160I ASN 3.0 11.3 + - - -
161I ALA* 2.8 33.5 + - + -
162I LEU* 4.0 33.7 - - + +
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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