Contacts of the strand formed by residues 34 - 38 (chain o) in PDB entry 5GJQ
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 LEU 34 (chain o).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14o LEU* 4.0 16.6 - - + +
15o GLY 4.3 3.6 - - - -
16o ALA* 3.9 21.1 - - + -
32o ASP* 3.1 16.9 + - - +
33o LYS* 1.3 82.4 - - - +
35o THR* 1.3 60.6 + - - +
36o PRO* 3.8 6.6 - - - +
42o PHE* 4.0 12.8 - - + -
43o CYS 3.6 2.0 - - - +
44o CYS* 3.6 29.8 - - + -
175o ARG* 3.6 29.8 - - + +
176o LEU 4.2 1.8 - - - -
177o ALA* 4.0 26.0 - - + +
186o ARG* 3.4 22.0 + - - +
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Residues in contact with THR 35 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32o ASP 4.4 1.9 + - - -
33o LYS 3.8 0.2 + - - -
34o LEU* 1.3 73.8 + - - +
36o PRO* 1.3 82.7 - - + +
37o ILE* 3.3 1.8 + - + -
42o PHE* 3.4 4.3 - - - -
43o CYS* 2.8 56.8 + - - -
45o ARG* 3.4 28.6 + - - -
56o ALA* 4.4 15.5 - - + -
57o ASP* 6.2 0.2 - - - +
60o THR* 5.5 1.1 - - - +
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Residues in contact with PRO 36 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32o ASP* 5.9 0.2 - - - +
34o LEU 3.8 7.2 - - - +
35o THR* 1.3 97.4 - - + +
37o ILE* 1.3 61.5 + - - +
38o HIS 4.2 10.1 - - - +
41o ILE 3.7 5.6 - - - +
42o PHE* 3.8 26.6 - - + -
60o THR* 4.0 7.6 + - - +
186o ARG* 4.6 8.5 - - - +
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Residues in contact with ILE 37 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35o THR* 3.8 7.2 - - + +
36o PRO* 1.3 78.6 - - - +
38o HIS* 1.3 59.4 + - - +
41o ILE* 2.6 28.4 + - + +
43o CYS* 3.6 37.9 - - + +
56o ALA* 4.1 9.0 - - + +
59o VAL* 4.1 17.3 - - + -
60o THR* 3.7 40.3 + - - +
63o LEU* 3.6 27.5 - - + +
64o GLY* 5.7 0.7 + - - -
79o ALA* 4.3 2.2 - - + -
83o PHE* 3.9 16.2 - - + -
100o ILE* 5.7 0.2 - - + -
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Residues in contact with HIS 38 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74h GLU* 5.6 4.3 + - - +
36o PRO* 4.2 11.7 - - - +
37o ILE* 1.3 84.2 + - - +
39o ASP* 1.3 95.7 + - + +
40o ARG 3.2 5.7 + - - +
41o ILE* 3.0 24.8 + - + +
42o PHE* 4.7 2.3 - - - -
63o LEU* 4.3 7.9 - - + -
64o GLY* 5.0 11.0 - - - -
67o SER* 3.5 23.7 + - - -
73o PRO* 5.3 0.9 - - + -
74o PRO* 3.3 41.5 - - + +
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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