Contacts of the strand formed by residues 85 - 93 (chain B) in PDB entry 2FIU
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 85 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10B VAL* 3.9 20.9 - - + -
11B ASP 3.4 13.7 - - - +
12B VAL* 4.0 2.5 - - - -
13B ARG* 4.0 4.6 - - - +
18B TYR* 4.0 15.9 - - + -
81B ARG* 2.8 21.0 + - + +
82B GLN* 3.6 14.4 + - - +
83B GLU 3.6 1.4 + - - -
84B VAL* 1.3 80.9 - - - +
86B ASP* 1.3 68.7 + - - +
87B ALA* 4.1 1.4 + - - +
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Residues in contact with ASP 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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10B VAL* 3.3 3.6 - - - +
11B ASP 2.8 32.5 + - - +
13B ARG* 2.3 42.1 + - - +
51B ARG* 3.8 27.8 - - - +
82B GLN 5.7 0.2 - - - +
85B ALA* 1.3 76.6 - - - +
87B ALA* 1.3 61.6 + - - +
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Residues in contact with ALA 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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47A GLU* 4.1 15.6 - - - +
48A GLY* 4.9 1.6 + - - -
9B GLN 3.0 11.7 - - - +
10B VAL* 3.8 17.7 - - + -
51B ARG* 4.5 1.3 - - - +
81B ARG* 4.2 26.5 - - + +
85B ALA 4.1 1.2 + - - +
86B ASP* 1.3 77.1 - - - +
88B GLU* 1.3 68.4 + - - +
89B MSE 4.1 11.4 + - + -
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Residues in contact with GLU 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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47A GLU 3.3 9.4 - - - +
48A GLY* 4.5 8.7 - - - -
49A THR 4.4 17.5 - - - +
7B ILE 3.8 1.2 - - - +
8B ALA* 3.5 0.7 - - - -
9B GLN* 2.9 55.3 + - - +
51B ARG* 2.7 48.0 + - - +
87B ALA* 1.3 74.1 - - - +
89B MSE 1.3 66.0 + - - +
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Residues in contact with MSE 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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45A GLU* 4.3 0.7 - - - -
46A LEU* 3.0 36.9 + - + -
47A GLU* 2.8 26.4 + - + +
48A GLY 4.9 0.9 - - - +
6B TRP* 3.1 50.0 - - + +
7B ILE 3.3 4.9 - - - +
8B ALA* 3.7 17.0 - - + -
21B TYR* 4.5 2.7 - - - +
69B TYR* 4.8 1.6 - - + -
74B TYR* 3.4 10.1 - - + +
81B ARG* 3.3 38.1 - - - +
87B ALA* 4.3 9.0 - - + -
88B GLU* 1.3 80.6 - - - +
90B MSE 1.3 64.2 + - - +
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Residues in contact with MSE 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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7A ILE* 5.3 1.6 - - + -
9A GLN* 4.0 23.6 - - + +
43A VAL* 3.8 17.7 - - + -
44A THR 3.3 13.2 - - - +
45A GLU* 4.6 2.5 - - - -
46A LEU* 4.1 5.2 - - - +
50A ALA* 4.0 16.6 - - + -
54A ASN* 3.5 36.1 - - + +
5B TYR 3.6 0.3 - - - +
6B TRP* 3.4 3.8 - - - +
7B ILE* 2.9 69.9 + - + +
9B GLN* 4.4 4.0 - - - +
89B MSE 1.3 78.1 - - - +
91B ILE* 1.3 65.6 + - - +
92B VAL* 4.1 10.1 - - + -
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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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42A SER 3.6 1.6 - - - +
43A VAL* 3.3 4.9 - - - +
44A THR* 2.8 42.7 + - - -
46A LEU* 3.8 28.9 - - + -
4B GLY* 4.3 0.2 - - - -
5B TYR 3.3 11.2 - - - +
6B TRP* 4.4 8.1 - - + -
62B VAL* 4.2 29.2 - - + -
65B ALA* 3.6 39.0 - - + +
66B ILE* 3.6 28.0 - - + +
69B TYR* 5.1 0.2 - - + -
90B MSE 1.3 79.4 - - - +
92B VAL* 1.3 66.1 + - - +
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Residues in contact with VAL 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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38A ALA* 3.7 20.0 - - + -
41A GLY 3.8 17.5 - - - +
42A SER 3.5 3.1 - - - -
43A VAL* 4.7 2.9 - - + -
54A ASN* 3.9 33.9 - - + +
56A VAL* 5.5 0.9 - - + -
4B GLY 3.8 0.5 - - - -
5B TYR* 2.9 35.2 + - + +
7B ILE* 3.8 26.5 - - + -
90B MSE 4.1 13.0 - - + -
91B ILE* 1.3 79.1 - - - +
93B GLU* 1.3 75.3 + - - +
94B GLY 3.5 0.5 + - - -
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Residues in contact with GLU 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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38A ALA* 3.8 4.3 - - - +
39A ARG 4.9 0.2 + - - -
41A GLY* 3.6 17.6 + - - -
42A SER* 3.0 37.5 + - - +
2B ALA* 3.9 18.2 - - + +
3B LYS 4.3 0.2 - - - +
62B VAL* 3.7 30.4 - - + +
92B VAL* 1.3 78.8 - - - +
94B GLY* 1.3 74.6 + - - +
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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