Contacts of the strand formed by residues 93 - 109 (chain B) in PDB entry 4FAO
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 PRO 93 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B ILE* 4.0 23.8 - - + -
85B LEU* 4.0 13.9 - - + -
86B TYR 3.6 6.5 - - - +
87B LYS* 4.7 1.8 - - + -
91B GLY 3.6 8.3 - - - +
92B VAL* 1.3 86.7 - - + +
94B THR* 1.3 61.2 + - - +
21F GLU* 3.9 0.7 - - - +
46F ARG* 3.9 19.5 - - - +
55F VAL* 3.8 27.1 - - + +
56F LYS* 3.0 22.3 + - - +
81F VAL* 4.2 18.4 - - + -
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Residues in contact with THR 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B LEU* 3.1 6.6 - - - +
86B TYR* 2.9 66.6 + - - -
88B ASP* 3.7 19.6 + - - +
92B VAL* 3.1 16.3 + - + +
93B PRO* 1.3 72.6 - - - +
95B LEU* 1.3 62.4 + - - +
21F GLU* 3.1 31.6 - - + +
56F LYS* 3.8 6.1 - - - +
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Residues in contact with LEU 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B SER* 4.4 1.3 - - - -
84B VAL 3.2 25.6 - - - +
85B LEU* 4.3 6.7 - - + +
86B TYR* 4.3 3.1 - - - -
94B THR* 1.3 77.2 - - - +
96B LYS* 1.3 78.4 + - - +
97B TYR* 3.4 18.7 + - + +
13F TYR* 6.5 1.1 - - + -
42F TYR* 3.2 38.6 - - + +
56F LYS* 4.3 7.3 - - - +
59F CYS 4.1 9.0 - - - +
60F TRP* 4.0 16.4 - - + -
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Residues in contact with LYS 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B ILE 4.0 1.7 - - - +
83B SER* 3.4 1.4 - - - -
84B VAL* 2.9 41.1 + - + +
86B TYR* 3.9 16.2 - - + -
95B LEU* 1.3 79.5 + - - +
97B TYR* 1.3 78.6 + - - +
98B HIS* 3.2 46.2 - - - +
99B TYR* 3.9 19.0 - - + +
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Residues in contact with TYR 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B ILE 3.4 5.5 - - - +
83B SER* 2.8 36.0 + - - -
95B LEU* 3.4 18.4 + - + +
96B LYS* 1.3 86.1 - - - +
98B HIS* 1.3 83.9 + + - +
99B TYR 3.5 0.2 - - - -
29F GLU* 5.9 3.8 - - - -
31F CYS* 4.1 5.2 - - - +
32F GLU* 2.5 42.2 + - + -
39F LEU* 3.9 7.3 - - - +
59F CYS* 3.6 24.4 - - + +
60F TRP 3.7 19.7 + - - -
61F LEU* 3.2 40.8 - - + +
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Residues in contact with HIS 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B PRO* 4.1 17.6 - - + +
96B LYS* 3.2 23.9 - - - +
97B TYR* 1.3 109.5 - + + +
99B TYR* 1.3 55.9 + - - +
100B GLU* 3.0 36.6 + - + +
32F GLU* 4.6 11.9 + - + +
33F GLY* 5.6 2.2 - - - -
61F LEU* 4.2 9.2 - - + +
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Residues in contact with TYR 99 (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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53A LYS* 3.8 21.0 - - + +
17B PHE* 6.2 1.3 - + - -
22B TRP* 4.5 9.5 - + - -
25B TRP* 4.0 17.3 - + - -
26B ILE* 5.4 1.3 - - + -
81B PRO* 3.1 17.4 - - - +
82B ILE 3.1 24.0 + - - +
84B VAL* 3.9 32.3 - - + -
96B LYS* 3.9 23.3 - - + +
97B TYR 3.5 0.4 - - - -
98B HIS* 1.3 69.1 - - - +
100B GLU* 1.3 70.1 + - - +
102B MET* 3.7 30.5 - - + +
75D GLU* 2.5 38.7 + - - +
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Residues in contact with GLU 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A LYS* 3.6 22.3 - - - +
79B LEU 4.3 5.7 - - - +
81B PRO* 3.4 21.9 - - - +
98B HIS* 3.0 39.2 + - - +
99B TYR* 1.3 80.0 - - - +
101B GLY* 1.3 67.2 + - - +
102B MET* 3.6 1.6 + - - +
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Residues in contact with GLY 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A THR* 5.8 0.4 - - - -
53A LYS* 3.2 7.0 + - - +
54A HIS* 2.8 32.6 + - - +
79B LEU* 3.8 25.1 - - - +
80B SER 3.7 9.9 + - - -
99B TYR 3.7 1.0 + - - -
100B GLU* 1.3 81.8 + - - +
102B MET* 1.3 59.5 + - - +
103B SER 3.6 1.6 - - - -
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Residues in contact with MET 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A LYS* 4.0 18.6 - - - -
54A HIS* 3.5 10.8 - - - +
57A VAL* 4.2 19.5 - - + -
17B PHE* 4.4 12.1 - - + -
22B TRP* 4.8 2.9 - - + -
32B TYR* 2.9 57.1 + - + +
34B ALA* 3.3 7.3 - - - +
80B SER 3.1 3.6 + - - +
82B ILE* 3.8 27.6 - - + -
99B TYR* 3.7 45.3 - - + +
100B GLU 3.8 4.7 - - - +
101B GLY* 1.3 79.3 - - - +
103B SER* 1.3 60.6 + - - +
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Residues in contact with SER 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A HIS* 4.2 1.1 - - - -
33B GLU 3.0 23.5 + - - -
34B ALA* 4.2 4.5 - - - +
35B TYR* 3.6 14.0 - - - -
79B LEU* 3.0 18.1 - - - +
80B SER* 3.1 32.9 + - - -
82B ILE* 4.2 16.2 - - - -
101B GLY 3.6 0.4 - - - -
102B MET* 1.3 83.4 - - - +
104B VAL* 1.3 63.7 + - - +
37F LYS* 4.4 7.4 + - - -
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Residues in contact with VAL 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A HIS* 3.4 32.5 - - + +
10B LYS* 3.8 20.9 + - + -
35B TYR* 3.1 47.7 - - + +
36B GLU* 4.4 1.6 - - - +
37B CYS* 3.9 14.6 - - - -
76B PRO* 4.1 17.3 - - + -
79B LEU* 3.8 3.8 - - + -
80B SER* 4.8 1.6 - - - -
103B SER* 1.3 77.2 + - - +
105B ALA* 1.3 64.0 + - - +
106B GLU 3.7 20.6 - - - +
37F LYS* 5.6 2.1 + - - -
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Residues in contact with ALA 105 (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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10B LYS* 3.1 24.4 + - - +
78B LYS* 2.7 47.3 + - + +
79B LEU 4.0 1.3 - - - +
80B SER* 4.0 19.7 - - - +
103B SER 3.5 1.0 + - - -
104B VAL* 1.3 74.4 - - - +
106B GLU* 1.3 66.6 + - + +
37F LYS* 5.8 2.5 - - - +
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Residues in contact with GLU 106 (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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10B LYS* 5.1 0.9 - - - +
50B THR* 5.6 2.1 + - - -
76B PRO* 3.7 4.7 - - - +
77B THR* 2.8 36.8 + - - +
78B LYS* 3.4 39.0 + - + +
104B VAL* 3.7 6.2 - - - +
105B ALA* 1.3 85.8 - - + +
107B CYS* 1.3 62.6 + - - +
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Residues in contact with CYS 107 (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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8B CYS* 4.7 2.2 - - - -
9B GLN* 3.7 22.7 - - - -
10B LYS* 3.7 23.8 - - + +
37B CYS* 2.0 52.9 - - + -
48B ASP 4.4 9.3 - - - +
49B VAL* 5.3 1.1 - - - -
50B THR* 4.2 8.7 + - - -
74B CYS* 4.6 5.4 - - - -
75B VAL 3.6 4.5 - - - -
77B THR* 3.3 11.2 + - - +
104B VAL* 4.1 0.4 - - - -
106B GLU* 1.3 76.5 - - - +
108B GLY* 1.3 58.8 + - - +
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Residues in contact with GLY 108 (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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8B CYS* 4.6 4.3 - - - -
49B VAL* 3.4 19.1 - - - -
50B THR* 4.9 0.2 - - - -
73B CYS 3.3 0.2 - - - +
74B CYS* 3.2 7.2 - - - -
75B VAL* 2.9 35.0 + - - +
77B THR* 3.4 14.6 - - - -
107B CYS* 1.3 78.8 - - - +
109B CYS* 1.3 61.3 + - - -
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Residues in contact with CYS 109 (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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8B CYS* 4.3 8.5 - - - -
41B CYS* 2.0 54.7 - - + -
45B LEU* 4.8 14.4 - - + -
49B VAL* 3.1 33.2 + - + -
51B PRO* 4.0 4.9 - - + +
52B THR 4.0 0.2 + - - -
55B ALA* 3.9 10.7 - - + +
72B ALA* 4.3 5.4 - - + -
73B CYS 3.4 2.2 - - - -
108B GLY* 1.3 74.5 - - - -
110B ARG* 1.3 84.7 + - - +
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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