Contacts of the strand formed by residues 81 - 89 (chain Q) in PDB entry 5HJD
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 PHE 81 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17I ARG* 3.2 14.6 + - - +
18I KCR 4.0 25.1 - - + +
19I GLN 5.9 0.7 - - - -
32Q TRP* 4.0 13.0 - + - -
55Q LEU* 3.9 14.8 - - + -
56Q HIS* 3.7 31.0 - + + -
59Q PHE* 3.7 32.1 - + - -
79Q ALA 3.9 11.4 - - - -
80Q GLY* 1.3 80.0 - - - +
82Q ILE* 1.3 73.6 + - - +
83Q LEU* 3.6 29.0 + - + -
104Q LEU* 2.9 43.2 + - + +
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Residues in contact with ILE 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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17I ARG* 4.5 11.4 - - - +
54Q HIS 4.4 0.7 - - - +
55Q LEU 5.8 0.2 - - - -
56Q HIS* 6.0 0.7 - - - -
81Q PHE* 1.3 82.2 - - - +
83Q LEU* 1.3 59.8 + - - +
84Q PRO* 3.2 16.5 - - + +
101Q ASP* 4.0 30.3 - - + +
102Q TYR 3.5 2.7 - - - +
103Q ASP* 4.0 31.6 - - + +
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Residues in contact with LEU 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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34Q VAL* 4.0 19.5 - - + -
53Q PHE* 3.9 12.6 - - + -
54Q HIS 3.3 37.0 - - - +
55Q LEU* 3.6 20.2 - - + -
81Q PHE* 3.6 12.5 + - + -
82Q ILE* 1.3 72.2 - - - +
84Q PRO* 1.3 67.1 - - - +
85Q ILE* 3.3 10.0 + - + +
101Q ASP 4.4 0.4 - - - -
102Q TYR* 2.5 49.5 + - + +
104Q LEU* 3.6 32.1 - - + -
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Residues in contact with PRO 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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54Q HIS* 2.9 67.3 + - + +
82Q ILE* 3.2 15.9 - - + +
83Q LEU* 1.3 81.3 - - - +
85Q ILE* 1.3 59.4 + - - +
99Q ARG* 4.2 20.0 - - + +
100Q PHE 3.5 6.7 - - - +
101Q ASP* 3.7 19.1 - - - +
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Residues in contact with ILE 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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13Q LEU* 4.0 21.8 - - + -
34Q VAL* 4.6 4.5 - - + -
35Q PHE 5.2 0.2 - - - +
36Q VAL* 3.9 20.6 - - + -
51Q VAL* 3.9 12.8 - - + -
52Q VAL 3.4 8.5 - - - +
53Q PHE* 4.0 19.7 - - + -
83Q LEU* 3.5 22.4 - - + +
84Q PRO* 1.3 74.8 - - - +
86Q GLU* 1.3 65.5 + - - +
87Q VAL* 4.2 3.5 + - + -
98Q VAL 3.7 0.9 - - - +
99Q ARG* 3.3 4.4 - - - +
100Q PHE* 2.6 48.7 + - + +
102Q TYR* 3.7 28.7 - - + -
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Residues in contact with GLU 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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50Q LYS 3.9 0.9 - - - +
51Q VAL* 3.4 4.7 - - - +
52Q VAL* 2.8 43.2 + - + +
54Q HIS* 3.4 26.5 + - + +
63Q LYS* 5.9 0.9 + - - -
84Q PRO* 6.0 0.2 - - + -
85Q ILE* 1.3 77.8 - - - +
87Q VAL* 1.3 62.6 + - - +
88Q TYR* 3.2 34.5 + - + -
97Q LYS* 3.4 26.4 + - + -
98Q VAL 3.4 4.3 - - - +
99Q ARG* 4.3 24.2 - - + +
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Residues in contact with VAL 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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11Q LEU* 4.3 21.5 - - + -
13Q LEU* 5.5 0.2 - - + -
36Q VAL* 4.4 13.0 - - + -
48Q VAL* 4.0 30.3 - - + -
50Q LYS 3.8 2.5 - - - -
51Q VAL* 4.3 16.2 - - + +
85Q ILE* 4.7 6.3 - - + -
86Q GLU* 1.3 75.0 - - - +
88Q TYR* 1.3 62.9 + - - +
89Q PHE* 3.8 20.6 - - + -
97Q LYS* 3.3 3.9 - - - -
98Q VAL* 3.0 44.2 + - + +
100Q PHE* 4.5 8.7 - - + -
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Residues in contact with TYR 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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48Q VAL* 3.5 6.2 - - - +
49Q GLU* 2.6 50.6 + - + +
50Q LYS* 2.8 49.5 + - + +
52Q VAL* 4.1 13.6 - - + +
63Q LYS* 5.8 2.3 + - - -
86Q GLU* 3.2 39.5 + - + -
87Q VAL* 1.3 76.3 - - - +
89Q PHE* 1.3 55.8 + - - +
96Q ARG* 3.7 18.4 - - + -
97Q LYS* 3.4 37.9 + - + -
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Residues in contact with PHE 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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11Q LEU* 5.4 0.2 - - + -
47Q PHE* 3.2 28.9 - + - +
48Q VAL* 5.1 0.2 - - + -
49Q GLU* 3.4 16.5 - - - +
87Q VAL* 3.8 20.2 - - + -
88Q TYR* 1.3 76.8 - - - +
90Q LYS* 1.3 53.1 + - - +
91Q ASN* 2.6 31.1 + - + +
95Q PRO* 3.6 24.7 - - + -
96Q ARG* 3.1 20.9 + - - +
97Q LYS* 3.7 21.8 - - - -
98Q VAL* 3.6 25.6 - - + -
122Q LEU* 4.0 11.7 - - + -
124Q PHE* 3.5 31.6 - + - -
131Q PHE* 3.8 7.9 - + + -
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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