Contacts of the strand formed by residues 90 - 95 (chain A) in PDB entry 4FG8
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 90 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50A CYS* 3.5 27.0 - - - -
51A ILE 3.4 6.7 - - - +
52A ALA* 3.7 26.5 - - + +
53A LYS* 4.0 7.1 - - - +
86A GLU* 3.7 1.7 - - - -
87A SER* 2.9 35.2 + - - +
89A GLY* 1.3 96.5 - - - +
91A LEU* 1.3 66.5 + - - +
92A TYR* 3.8 28.9 + - + -
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Residues in contact with LEU 91 (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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10A TRP* 4.8 11.2 - - + +
49A LYS 3.1 5.2 - - - +
50A CYS* 3.6 2.6 - - - -
51A ILE* 2.8 61.4 + - + +
52A ALA 5.1 2.5 - - - +
53A LYS* 4.6 17.5 - - + -
84A ILE* 4.9 9.9 - - + -
85A TYR 3.9 3.1 - - - +
86A GLU* 3.9 27.6 - - + +
90A HIS* 1.3 75.3 - - - +
92A TYR* 1.3 63.0 + - - +
93A LEU* 4.0 4.0 - - + +
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Residues in contact with TYR 92 (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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16A ILE* 3.8 47.1 - - + +
22A PHE* 3.8 22.8 - + - -
48A ILE* 3.5 24.0 - - + -
49A LYS 3.5 1.6 - - - -
50A CYS* 4.0 22.6 - - + -
84A ILE* 3.4 5.2 - - - +
85A TYR 2.8 44.4 + - - +
86A GLU 5.1 0.2 - - - -
87A SER* 3.7 26.8 + - - -
90A HIS* 3.8 29.4 + + + -
91A LEU* 1.3 74.7 - - - +
93A LEU* 1.3 63.9 + - - +
94A ILE* 3.7 5.8 + - + +
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Residues in contact with LEU 93 (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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47A ALA 3.6 0.2 - - - +
48A ILE* 3.4 2.9 - - - -
49A LYS* 2.9 48.9 + - + +
51A ILE* 3.7 31.0 - - + -
67A ILE* 6.1 0.2 - - + -
70A LEU* 5.6 11.0 - - + -
81A LEU* 3.7 16.6 - - + -
83A ASP 3.7 1.8 - - - -
84A ILE* 3.7 36.1 - - + -
91A LEU* 5.2 4.7 - - + +
92A TYR* 1.3 71.4 - - - +
94A ILE* 1.3 64.7 + - - +
95A MET* 3.5 7.7 + - + +
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Residues in contact with ILE 94 (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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20A TYR* 3.4 42.4 - - + +
46A VAL* 3.8 34.1 - - + -
47A ALA 3.9 1.8 - - - -
48A ILE* 3.8 23.6 - - + -
81A LEU* 3.6 1.7 - - - +
82A ASP* 2.8 38.1 + - + -
83A ASP* 2.7 29.8 + - + +
85A TYR* 3.7 16.2 - - + -
92A TYR* 4.0 13.7 - - + +
93A LEU* 1.3 74.8 - - - +
95A MET* 1.3 54.9 + - - +
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Residues in contact with MET 95 (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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34A VAL* 3.8 26.0 - - + -
46A VAL* 3.6 7.8 - - - +
47A ALA* 2.6 45.5 + - + +
49A LYS* 3.7 35.4 - - + +
79A VAL* 4.1 13.5 - - + -
80A ALA 3.6 4.9 - - - +
81A LEU* 4.4 13.7 - - + -
82A ASP* 3.6 5.1 - - - +
93A LEU* 3.9 9.4 - - + +
94A ILE* 1.3 77.9 - - - +
96A GLN* 1.3 71.3 + - - +
97A LEU 3.3 0.7 + - - -
161A SER 4.8 8.7 - - - +
401A ATP 3.9 19.5 - - - +
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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