Contacts of the strand formed by residues 66 - 73 (chain A) in PDB entry 1Q9S
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 HIS 66 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57A TRP* 3.4 10.8 - - - -
58A ALA* 2.8 32.1 + - - +
59A SER* 5.8 0.2 - - - -
64A ASP* 3.6 41.3 + - + +
65A VAL* 1.3 74.6 + - - +
67A LYS* 1.3 64.9 + - - +
89A ILE* 3.6 22.9 - - + -
90A MET 4.4 3.5 + - - +
91A HIS* 3.1 54.8 + + + +
93A PHE* 4.6 7.6 - + - -
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Residues in contact with LYS 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A GLY 3.6 5.8 - - - -
57A TRP* 3.5 20.1 - - + -
66A HIS* 1.3 80.4 - - - +
68A MET* 1.3 62.3 + - - +
89A ILE* 3.3 3.8 - - - +
90A MET* 2.9 39.6 + - + +
134A LYS* 2.7 49.5 + - + +
137A LEU* 3.4 31.4 - - + -
138A GLU* 3.5 27.4 + - - -
143A LEU* 5.8 0.2 - - - -
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Residues in contact with MET 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A TYR* 3.3 5.2 - - - +
56A GLY* 2.8 46.1 + - - +
57A TRP 3.4 28.7 - - - +
58A ALA* 3.7 9.0 - - + -
67A LYS* 1.3 78.2 - - - +
69A VAL* 1.3 80.5 + - - +
70A VAL* 4.0 18.6 - - + -
87A THR* 3.7 12.6 - - + -
88A HIS 3.2 15.5 - - - +
89A ILE* 3.8 4.5 - - - -
90A MET* 3.5 9.0 - - - +
104A VAL* 3.7 24.7 - - + -
105A ALA 3.7 16.8 - - - +
106A ILE* 4.7 1.1 - - - -
137A LEU* 4.2 0.9 - - - +
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Residues in contact with VAL 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A TYR 3.2 13.5 - - - +
55A TYR* 4.3 1.1 - - + -
68A MET* 1.3 75.2 - - - +
70A VAL* 1.3 59.2 + - - +
86A GLU 4.0 0.2 - - - +
87A THR* 3.5 2.1 - - - +
88A HIS* 2.7 50.3 + - + +
90A MET* 4.1 5.4 - - + -
110A LEU* 4.3 4.9 - - + -
126A ILE* 5.6 0.2 - - + -
129A ASP* 3.9 15.3 - - + +
130A ILE* 4.1 15.7 - - + -
133A ALA* 3.5 32.3 - - + -
401A FMN 3.3 27.2 - - + +
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Residues in contact with VAL 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A GLY 3.9 0.9 - - - +
53A ILE* 3.6 4.8 - - - +
54A TYR* 2.8 55.1 + - + +
68A MET* 4.0 20.0 - - + -
69A VAL* 1.3 75.7 - - - +
71A SER* 1.3 72.7 + - - +
72A ILE* 4.2 3.3 + - + -
85A MET* 3.9 23.3 - - + -
86A GLU 3.1 14.1 - - - +
87A THR* 3.5 18.4 - - - +
106A ILE* 4.4 12.8 - - + -
401A FMN 4.9 1.6 - - - -
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Residues in contact with SER 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A GLY 3.8 4.0 - - - -
53A ILE* 3.7 12.8 - - - -
70A VAL* 1.3 74.5 - - - +
72A ILE* 1.3 62.0 + - - +
73A GLY 4.1 0.7 - - - -
75A ASN* 4.4 6.9 + - - -
84A SER* 3.5 1.0 + - - +
85A MET* 3.3 5.5 - - - -
86A GLU* 2.8 51.6 + - - +
113A GLU* 5.5 1.3 - - - -
401A FMN 3.5 45.9 - - - +
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Residues in contact with ILE 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A VAL* 5.4 0.2 - - + -
45A LEU* 3.9 30.7 - - + -
49A ILE* 4.0 16.6 - - + +
50A SER 4.2 11.0 - - - +
51A THR* 3.1 10.4 - - - -
52A GLY* 2.8 42.4 + - - +
54A TYR* 4.3 9.9 - - + -
70A VAL* 4.4 4.7 - - + -
71A SER* 1.3 77.4 - - - +
73A GLY* 1.3 60.2 + - - +
83A LYS* 4.3 15.5 - - + +
84A SER 3.3 6.5 - - - +
85A MET* 4.1 17.9 - - + -
106A ILE* 4.0 26.7 - - + -
113A GLU* 4.3 2.9 - - - -
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Residues in contact with GLY 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A THR* 4.3 1.8 - - - -
71A SER 4.1 0.8 - - - -
72A ILE* 1.3 76.8 - - - +
74A TRP* 1.3 68.1 + - - -
75A ASN* 3.6 1.9 - - - +
82A LYS 4.2 0.2 - - - +
83A LYS* 3.3 13.3 - - - +
84A SER* 2.7 43.8 + - - -
113A GLU* 3.2 16.9 + - - -
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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