Contacts of the helix formed by residues 81 - 89 (chain Q) 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 SER 81 (chain Q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76Q PHE* 4.9 0.3 - - - +
79Q SER 3.5 5.0 + - - -
80Q ILE* 1.3 79.6 - - - +
82Q LYS* 1.3 69.7 + - - +
83Q ALA* 4.4 4.3 - - - -
84Q LYS* 3.6 16.2 - - - +
85Q ALA* 3.4 13.9 + - - +
224i GLU* 5.4 14.8 - - - -
227i ASP* 4.9 2.5 - - - -
228i TYR* 6.1 1.6 - - - -
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Residues in contact with LYS 82 (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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81Q SER* 1.3 71.3 - - - +
83Q ALA* 1.3 57.7 + - - +
85Q ALA* 2.7 36.6 + - + +
86Q ALA 3.4 2.3 + - - -
116Q TRP* 6.4 1.8 - - + -
120Q GLU* 2.6 38.8 + - + +
122Q ARG* 2.9 22.4 + - - +
184i GLU* 3.7 20.8 + - + +
228i TYR* 4.3 3.4 - - - +
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Residues in contact with ALA 83 (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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81Q SER* 4.4 4.0 - - - -
82Q LYS* 1.3 78.5 - - - +
84Q LYS* 1.3 55.4 + - - +
86Q ALA* 2.7 30.0 + - - +
87Q ARG 3.3 8.0 + - - -
122Q ARG* 3.2 10.1 - - - +
224i GLU* 5.9 0.2 - - - -
227i ASP* 3.8 18.4 - - + +
228i TYR* 3.1 53.4 + - + +
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Residues in contact with LYS 84 (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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39Q ASP 5.8 0.9 - - - -
43Q VAL* 3.9 30.7 + - - +
46Q LYS* 5.5 0.2 - - - +
80Q ILE* 3.4 22.9 - - + -
81Q SER* 3.6 25.1 + - - +
82Q LYS 3.2 1.0 - - - -
83Q ALA* 1.3 74.6 - - - +
85Q ALA* 1.3 55.9 + - - +
87Q ARG* 3.3 33.3 + - - +
88Q LEU* 2.5 68.5 + - + +
227i ASP* 2.7 38.5 + - - +
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Residues in contact with ALA 85 (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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73Q VAL* 6.4 2.0 - - - -
76Q PHE* 5.2 9.2 - - + -
80Q ILE* 5.0 0.6 - - - +
81Q SER 3.4 6.9 + - - +
82Q LYS* 2.7 24.2 + - + +
84Q LYS* 1.3 70.4 - - - +
86Q ALA* 1.3 53.0 + - - +
88Q LEU* 4.2 4.5 - - - -
89Q VAL* 2.3 60.2 + - + +
116Q TRP* 3.9 20.6 - - + -
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Residues in contact with ALA 86 (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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82Q LYS 3.4 1.6 + - - +
83Q ALA* 2.7 18.6 + - - +
85Q ALA* 1.3 74.9 - - - +
87Q ARG* 1.3 55.1 + - - +
89Q VAL* 3.8 4.4 - - - -
90Q ARG* 2.8 34.3 + - - +
116Q TRP* 5.2 2.4 - - - -
122Q ARG* 4.4 25.8 - - - +
125Q LEU* 4.9 16.5 - - + +
227i ASP 5.4 3.4 - - - +
230i ALA 5.9 1.3 - - - -
231i ALA* 5.7 8.7 - - + -
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Residues in contact with ARG 87 (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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43Q VAL* 5.4 3.2 - - - +
83Q ALA 3.3 5.8 + - - +
84Q LYS* 3.3 33.0 - - - +
86Q ALA* 1.3 79.5 - - - +
88Q LEU* 1.3 61.6 + - - +
90Q ARG* 3.4 4.5 + - - +
91Q SER* 3.0 32.4 + - - +
223i THR* 4.6 2.6 + - - +
226i LYS* 4.3 24.0 - - - +
227i ASP* 2.1 50.1 + - - +
230i ALA* 3.7 31.4 - - + +
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Residues in contact with LEU 88 (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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42Q ALA 5.8 0.7 - - - -
43Q VAL* 5.1 0.4 - - - -
46Q LYS* 3.0 35.0 - - + -
49Q SER* 6.1 0.2 - - - -
76Q PHE* 5.6 8.7 - - + -
80Q ILE* 5.7 0.7 - - + -
84Q LYS* 2.5 73.6 + - + +
85Q ALA* 3.9 4.3 - - - +
87Q ARG* 1.3 77.8 - - - +
89Q VAL* 1.3 60.2 + - + +
90Q ARG 3.2 1.9 + - - -
91Q SER* 3.6 15.3 + - - -
92Q LEU* 3.8 13.5 + - - +
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Residues in contact with VAL 89 (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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73Q VAL* 6.0 7.2 - - + -
85Q ALA* 2.3 63.6 + - + +
86Q ALA* 3.8 4.3 - - - +
88Q LEU* 1.3 69.0 - - + +
90Q ARG* 1.3 57.8 + - - +
91Q SER 3.5 0.4 - - - -
92Q LEU* 4.3 6.4 - - + +
93Q LEU* 3.8 23.7 + - + +
113Q CYS* 4.8 17.9 - - + -
116Q TRP* 4.1 30.5 - - + -
125Q LEU* 5.4 12.9 - - + +
129Q LEU* 5.8 0.7 - - + -
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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