Contacts of the strand formed by residues 78 - 91 (chain B) in PDB entry 3QS1
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 GLY 78 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73B MET 3.9 0.3 - - - +
75B TYR* 2.9 33.1 + - - +
76B VAL 3.2 4.7 - - - -
77B SER* 1.3 79.0 - - - +
79B THR* 1.3 64.4 + - - -
109B PHE* 3.5 22.1 + - - -
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Residues in contact with THR 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B GLU* 3.7 15.3 - - + +
73B MET 3.6 3.4 - - - -
74B ASN* 2.6 30.9 + - - +
75B TYR 5.2 0.2 + - - -
78B GLY* 1.3 75.7 - - - -
80B VAL* 1.3 82.8 + - - +
81B SER* 5.0 2.9 - - - -
106B ASP* 4.5 1.9 - - - +
109B GLY* 2.8 43.1 + - - -
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Residues in contact with VAL 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B TRP* 3.7 38.1 - - + +
72B GLU* 3.3 3.3 - - - -
73B MET* 2.7 54.3 + - + +
75B TYR* 4.6 4.4 - - + -
79B THR* 1.3 82.4 - - - +
81B SER* 1.3 61.4 + - - +
102B ILE* 6.2 0.7 - - + -
104B VAL* 4.0 13.5 - - + -
106B ASP 3.7 12.3 - - - +
107B THR* 4.2 11.7 - - + -
109B PHE* 3.7 28.9 + - + -
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Residues in contact with SER 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B VAL 3.0 15.4 + - - -
72B GLU* 4.2 15.5 + - - -
79B THR* 5.0 4.3 - - - -
80B VAL* 1.3 78.6 - - - +
82B GLY* 1.3 54.1 + - - +
102B ILE* 4.6 0.6 - - - +
104B VAL* 3.4 7.0 - - - +
105B THR* 2.7 28.6 + - - -
106B ASP* 2.9 37.1 + - - +
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Residues in contact with GLY 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70B LYS* 3.2 8.1 - - - +
71B VAL 2.6 36.1 + - - +
81B SER* 1.3 77.4 + - - +
83B PHE* 1.3 58.6 + - - -
102B ILE* 3.8 8.9 - - - +
103B GLU 3.0 15.5 - - - -
105B THR* 3.5 12.6 - - - -
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Residues in contact with PHE 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B SER* 4.2 2.0 - - - -
44B GLN* 4.3 16.2 - - + -
64B TYR* 5.3 4.7 - - - -
68B GLY* 3.5 25.4 - - - +
69B THR 3.1 13.5 - - - +
70B LYS* 4.1 6.5 - - + -
71B VAL* 4.2 1.3 - - - -
82B GLY* 1.3 78.3 - - - +
84B PHE* 1.3 73.1 + - - +
85B SER* 3.5 3.1 - - - -
102B ILE* 3.4 6.3 - - - +
103B GLU* 2.8 71.5 + - + -
105B THR* 3.8 26.9 - - + -
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Residues in contact with PHE 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B ASN* 4.1 9.9 - - - -
67B ASP* 3.1 25.6 + - + +
68B GLY 2.9 26.9 + - - -
69B THR* 2.8 32.7 + - - +
71B VAL* 3.2 33.9 - - + -
83B PHE* 1.3 73.8 - - - +
85B SER* 1.3 64.5 + - - +
100B LYS* 3.7 32.8 - - + -
101B PHE* 3.3 18.4 - - - -
102B ILE* 4.2 11.4 - - + +
130B ILE* 3.1 31.4 - - + -
131B GLY* 4.5 6.3 - - - -
133B VAL* 4.5 5.6 - - + -
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Residues in contact with SER 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B TYR* 3.6 21.4 + - - -
65B GLU 4.2 3.1 - - - -
67B ASP* 4.3 3.9 + - - +
83B PHE* 3.5 8.6 + - - -
84B PHE* 1.3 77.4 + - - +
86B LYS* 1.3 64.2 + - - +
100B LYS* 3.4 6.8 - - - +
101B PHE* 2.8 46.9 + - - +
103B GLU* 2.3 34.8 + - - +
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Residues in contact with LYS 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B TYR* 3.4 3.5 - - - -
65B GLU* 2.9 59.9 + - + +
66B LYS 5.1 4.0 - - - +
67B ASP* 4.7 15.0 - - + +
85B SER* 1.3 76.5 - - - +
87B ASP* 1.3 66.5 + - - +
98B PRO* 6.6 0.2 - - + -
99B TYR 3.2 13.0 - - - +
100B LYS* 4.3 30.9 - - + +
101B PHE* 4.1 0.7 - - - -
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Residues in contact with ASP 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B GLY* 3.3 15.4 - - - +
56B TYR* 2.7 24.7 + - - +
61B SER* 2.8 20.8 + - - -
63B THR* 3.0 27.2 + - - +
64B TYR* 3.5 8.4 - - - +
86B LYS* 1.3 75.7 - - - +
88B ILE* 1.3 78.3 + - - +
89B VAL 3.7 0.6 + - - -
98B PRO* 3.2 4.4 - - - +
99B TYR* 2.5 41.6 + - - +
101B PHE* 3.5 22.4 - - + -
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Residues in contact with ILE 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B ILE* 3.7 0.5 - - - -
21B GLY 2.8 33.2 + - - +
22B ASP* 4.3 10.8 - - + +
63B THR* 3.1 35.2 - - + +
87B ASP* 1.3 87.2 + - - +
89B VAL* 1.3 59.2 + - - +
90B THR* 3.9 2.3 + - - +
95B SER* 3.6 23.3 - - - +
96B PHE* 3.4 34.3 - - - +
98B PRO* 3.9 11.2 - - + -
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Residues in contact with VAL 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B ALA* 5.5 2.0 - - + -
19B GLN 3.5 10.1 - - - +
20B ILE* 4.0 25.8 - - + +
29B PHE* 6.2 1.3 - - + -
38B LEU* 4.0 16.6 - - + -
87B ASP 3.7 1.1 + - - +
88B ILE* 1.3 74.5 - - - +
90B THR* 1.3 63.5 + - - +
91B ILE* 3.4 29.8 - - + -
96B PHE* 2.8 51.6 + - + +
99B TYR* 3.7 20.4 - - + -
101B PHE* 4.3 10.8 - - + -
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Residues in contact with THR 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B ALA* 3.6 2.4 - - - +
19B GLN* 2.8 56.6 + - - +
21B GLY 5.0 2.3 + - - -
24B LYS* 3.7 24.8 - - - +
88B ILE* 4.4 5.5 + - - +
89B VAL* 1.3 73.5 - - - +
91B ILE* 1.3 60.4 + - - +
93B ASN* 3.6 21.5 - - + +
94B LEU 3.0 22.4 - - - +
95B SER* 2.8 22.7 + - - +
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Residues in contact with ILE 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B VAL* 4.2 15.3 - - + -
18B ALA* 4.0 20.4 - - + +
19B GLN* 4.9 0.2 - - - -
31B PHE* 4.4 15.5 - - + -
38B LEU* 4.6 9.2 - - + -
89B VAL* 3.4 32.3 - - + -
90B THR* 1.3 70.1 - - - +
92B ALA* 1.3 73.6 + - - +
94B LEU* 3.0 25.6 + - + +
96B PHE* 3.6 21.1 - - + -
121B VAL* 5.1 6.3 - - + -
136B VAL* 4.4 12.6 - - + -
140B LEU* 5.9 0.9 - - + -
165B LEU* 5.2 0.9 - - + -
167B ILE* 3.3 31.2 - - + -
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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