Contacts of the strand formed by residues 78 - 94 (chain B) in PDB entry 1WQ9
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 78 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69B MET* 4.0 26.9 - - - +
70B ARG 3.0 10.1 - - - -
71B MET* 3.6 22.3 - - - +
76B HIS 3.7 4.2 + - - -
77B SER* 1.3 77.2 + - - +
79B LYS* 1.3 63.3 + - - +
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Residues in contact with LYS 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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69B MET* 4.1 5.1 - - - +
70B ARG* 3.1 33.0 + - + +
77B SER* 5.6 2.5 - - - +
78B SER* 1.3 76.5 - - - +
80B MET* 1.3 80.1 + - + +
81B GLU* 3.6 1.4 + - - +
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Residues in contact with MET 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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5A PHE* 3.6 49.1 - - + -
67B GLN* 3.8 23.6 - - - +
68B ILE 3.3 9.2 - - - +
69B MET* 3.3 34.9 - - - +
79B LYS* 1.3 91.1 - - + +
81B GLU* 1.3 61.2 + - - +
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Residues in contact with GLU 81 (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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35B PHE* 4.7 1.8 - - - -
67B GLN* 3.3 4.8 - - - +
68B ILE* 2.8 39.5 + - + +
70B ARG* 2.7 57.4 + - - +
79B LYS 4.1 3.8 - - - +
80B MET* 1.3 77.7 - - - +
82B VAL* 1.3 75.5 + - - +
83B MET* 3.4 17.1 - - - +
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Residues in contact with VAL 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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2A VAL* 3.9 29.6 - - + -
65B ASP* 3.8 34.1 - - + +
66B ILE 3.5 8.3 - - - +
67B GLN* 4.7 8.3 - - + +
81B GLU* 1.3 83.4 - - - +
83B MET* 1.3 62.8 + - - +
84B LYS* 5.9 0.8 - - + +
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Residues in contact with MET 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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23B ILE* 3.8 11.2 - - - -
27B HIS* 3.6 26.0 - - + +
30B GLU* 3.8 24.0 - - + +
35B PHE* 3.8 19.3 - - + -
65B ASP* 3.7 0.3 - - - -
66B ILE 2.7 35.4 + - - +
68B ILE* 3.7 22.7 - - + -
81B GLU* 3.4 22.8 + - - +
82B VAL* 1.3 76.1 - - - +
84B LYS* 1.3 68.0 + - - +
85B PHE* 3.5 29.3 - - + -
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Residues in contact with LYS 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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27B HIS* 2.9 31.9 + - - +
63B THR* 3.6 23.3 + - + +
64B ALA 3.3 3.8 - - - -
65B ASP* 2.8 38.3 + - - +
82B VAL* 5.9 0.7 - - + -
83B MET* 1.3 76.8 - - - +
85B PHE* 1.3 61.2 + - - +
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Residues in contact with PHE 85 (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 VAL* 4.5 1.6 - - + -
23B ILE* 3.8 26.5 - - + -
26B GLU* 4.2 21.1 - - + -
27B HIS* 3.7 22.2 - + - -
40B VAL* 3.7 29.2 - - + -
42B VAL* 4.9 7.9 - - + -
44B ARG* 5.7 0.4 - - - +
63B THR* 3.4 5.9 - - - -
64B ALA* 2.8 34.6 + - + +
66B ILE* 3.7 33.2 - - + -
68B ILE* 4.7 2.7 - - + -
83B MET* 3.5 44.9 - - + -
84B LYS* 1.3 75.4 - - - +
86B MET* 1.3 66.5 + - - +
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Residues in contact with MET 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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26B GLU* 5.0 4.9 + - - +
42B VAL* 3.6 8.1 - - - +
44B ARG* 2.9 53.7 + - - +
61B LYS* 4.1 26.5 - - + +
62B HIS 3.7 6.7 - - - +
63B THR* 4.8 2.9 - - - +
85B PHE* 1.3 74.3 - - - +
87B GLU* 1.3 66.5 + - - +
88B HIS* 3.5 36.8 - - - +
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Residues in contact with GLU 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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3A ARG* 4.1 9.0 + - - -
42B VAL* 2.9 33.3 - - + +
43B LEU* 3.0 46.4 + - + +
61B LYS* 3.2 3.5 - - - +
62B HIS* 2.6 72.6 + - + +
64B ALA* 4.0 8.5 - - + +
85B PHE 4.6 2.9 - - - +
86B MET* 1.3 78.0 - - - +
88B HIS* 1.3 62.5 + - - +
89B THR* 5.5 0.2 - - + -
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Residues in contact with HIS 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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16B THR* 3.5 12.1 - - + +
43B LEU* 2.9 27.4 + - - +
44B ARG* 3.6 19.6 - - + -
45B CYS* 3.0 38.7 + - + -
58B PRO* 3.5 40.5 - - + +
60B GLY 3.6 4.3 - - - +
61B LYS* 4.5 7.4 - - + -
86B MET* 3.5 31.5 - - + +
87B GLU* 1.3 75.2 - - - +
89B THR* 1.3 63.4 + - - +
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Residues in contact with THR 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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16B THR* 3.6 14.4 + - - +
43B LEU* 6.0 1.1 - - + -
60B GLY* 2.8 30.8 + - - -
61B LYS 3.1 10.1 + - - +
62B HIS* 3.2 38.6 - - + -
88B HIS* 1.3 75.2 - - - +
90B ALA* 1.3 58.7 + - - +
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Residues in contact with ALA 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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16B THR* 4.6 0.2 - - - -
45B CYS* 3.5 2.3 - - - -
58B PRO* 3.4 6.1 - - - +
59B VAL* 2.9 41.1 + - + -
60B GLY* 3.6 7.7 + - - +
89B THR* 1.3 84.3 + - - +
91B CYS* 1.3 63.5 + - - +
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Residues in contact with CYS 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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14B CYS* 3.7 21.2 - - - +
15B GLN* 3.4 20.2 - - - -
16B THR* 3.4 23.1 - - - -
45B CYS* 2.0 45.3 - - + -
57B THR 3.3 6.1 - - - +
59B VAL* 4.2 4.1 - - - +
90B ALA* 1.3 72.2 - - - +
92B GLU* 1.3 65.1 + - - +
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Residues in contact with GLU 92 (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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14B CYS* 3.8 6.0 - - - -
57B THR* 2.8 32.1 + - - +
59B VAL* 4.1 14.8 - - + +
91B CYS* 1.3 79.5 - - - +
93B CYS* 1.3 76.4 + - - +
94B ARG* 2.7 40.9 + - + +
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Residues in contact with CYS 93 (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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14B CYS* 3.6 19.0 - - - -
48B CYS 4.8 0.7 - - - -
49B CYS* 2.0 54.7 - - + -
50B THR 4.8 1.1 - - - +
54B MET* 4.3 12.1 - - + +
55B LYS 3.4 5.6 - - - -
92B GLU* 1.3 79.8 - - - +
94B ARG* 1.3 63.0 + - - +
95B PRO* 4.6 0.9 - - - +
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Residues in contact with ARG 94 (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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54B MET* 3.5 4.7 - - - -
55B LYS 2.8 31.6 + - - +
57B THR* 3.7 25.4 - - + +
59B VAL* 3.6 25.1 - - - +
92B GLU* 2.7 36.3 + - + +
93B CYS* 1.3 78.8 - - - +
95B PRO* 1.3 76.2 - - + +
96B ALA* 3.1 7.8 + - - +
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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