Contacts of the strand formed by residues 70 - 77 (chain Q) in PDB entry 1S72
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 ALA 70 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24030 C 3.7 18.8 + - - +
24040 G 3.8 1.8 + - - -
66Q LYS* 3.0 8.5 - - - +
67Q GLN 2.9 32.5 + - - +
69Q ASP* 1.3 82.8 - - - +
71Q TYR* 1.3 60.5 + - - +
85Q ILE* 3.7 24.2 - - + -
86Q VAL 3.8 7.9 - - - +
87Q THR* 4.0 16.7 - - + +
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Residues in contact with TYR 71 (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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31Q GLU 3.5 7.9 + - - -
32Q GLU* 3.1 17.5 + - - -
33Q PHE* 2.8 62.2 + + + -
63Q VAL* 3.8 19.7 - - + -
65Q GLY 4.2 0.4 - - - -
66Q LYS* 3.4 43.0 + - + -
67Q GLN 4.8 0.2 - - - -
69Q ASP 4.2 5.8 - - - -
70Q ALA* 1.3 76.5 - - - +
72Q LYS* 1.3 63.9 + - - +
73Q VAL* 3.8 7.4 - - + -
84Q ILE 3.3 0.9 - - - +
85Q ILE* 3.2 6.8 - - - +
86Q VAL 2.6 44.8 + - - +
88Q ALA* 4.2 17.3 - - + -
91Q LEU* 4.2 14.4 - - + -
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Residues in contact with LYS 72 (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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23860 U 4.4 8.4 + - - +
23870 U 6.0 0.7 - - - -
63Q VAL* 3.8 1.0 - - - -
64Q GLU* 2.8 41.6 + - + +
65Q GLY* 3.0 14.5 + - - +
66Q LYS* 3.8 25.2 + - - +
67Q GLN* 3.9 26.7 + - + +
71Q TYR* 1.3 73.5 - - - +
73Q VAL* 1.3 61.1 + - - +
74Q ASP* 5.0 1.3 - - - +
83Q THR* 4.4 15.5 - - + -
84Q ILE 3.4 4.7 - - - -
85Q ILE* 3.5 22.4 - - + -
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Residues in contact with VAL 73 (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 VAL* 4.0 23.1 - - + -
41Q LEU* 4.1 9.9 - - + -
61Q GLY* 3.6 29.6 - - - -
62Q THR 3.5 8.5 - - - +
63Q VAL* 4.3 8.5 - - + -
71Q TYR* 4.4 2.9 - - + -
72Q LYS* 1.3 76.6 - - - +
74Q ASP* 1.3 67.3 + - - +
75Q ILE* 3.9 3.6 + - + -
83Q THR* 3.4 1.1 - - - -
84Q ILE* 2.7 48.2 + - + +
86Q VAL* 3.7 26.0 - - + -
91Q LEU* 4.1 8.5 - - + -
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Residues in contact with ASP 74 (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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61Q GLY* 3.2 4.9 - - - -
62Q THR* 2.9 35.8 + - - +
64Q GLU* 2.9 34.8 - - + +
72Q LYS* 4.9 0.9 - - - +
73Q VAL* 1.3 75.8 - - - +
75Q ILE* 1.3 60.9 + - - +
81Q GLU* 6.2 3.4 - - + -
82Q LYS 3.4 4.9 - - - +
83Q THR* 3.1 26.9 + - - +
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Residues in contact with ILE 75 (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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41Q LEU* 4.5 2.5 - - + -
56Q PHE* 3.6 26.5 - - + -
59Q GLN* 3.7 31.4 - - + +
60Q THR 5.3 1.3 - - - +
61Q GLY* 3.8 21.1 - - - +
73Q VAL* 3.9 7.8 + - + +
74Q ASP* 1.3 81.3 - - - +
76Q VAL* 1.3 68.9 + - - +
77Q ASP* 4.7 5.6 - - + +
81Q GLU* 3.6 3.8 - - - +
82Q LYS* 2.8 46.1 + - + +
84Q ILE* 3.1 40.4 - - + -
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Residues in contact with VAL 76 (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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10180 A 4.7 6.8 - - - +
10190 C 4.5 15.9 + - - +
59Q GLN* 3.7 18.7 + - - +
75Q ILE* 1.3 80.8 - - - +
77Q ASP* 1.3 59.2 + - - +
78Q GLY 3.3 23.7 + - - +
79Q GLY* 4.0 11.9 - - - +
80Q LYS 3.2 10.1 - - - +
81Q GLU* 4.5 15.0 - - + -
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Residues in contact with ASP 77 (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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23040 G 5.5 0.7 + - - -
23920 C 2.7 28.3 + - - +
23930 C 3.5 15.9 - - - +
56Q PHE* 3.5 19.4 - - + -
59Q GLN* 5.0 8.0 + - - +
75Q ILE* 4.1 4.6 - - + +
76Q VAL* 1.3 67.0 - - - +
78Q GLY* 1.3 63.1 + - - +
79Q GLY 2.8 0.9 + - - -
80Q LYS* 2.7 31.0 + - - +
82Q LYS* 2.6 47.4 + - + +
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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