Contacts of the strand formed by residues 89 - 98 (chain A) in PDB entry 4A4F
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 CYS 89 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A MET* 4.1 34.1 - - + +
81A ALA 3.0 12.8 - - - +
82A VAL* 4.6 1.6 - - + -
88A GLN* 1.3 77.0 - - - +
90A TYR* 1.3 70.4 + - - +
123A LYS* 4.1 31.4 - - + -
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Residues in contact with TYR 90 (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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80A MET* 3.1 8.1 - - - -
81A ALA* 2.8 28.7 + - - +
83A TRP* 3.8 15.6 - + + -
86A ASP* 2.9 26.8 + - + +
88A GLN* 3.3 35.3 - - + +
89A CYS* 1.3 76.9 - - - +
91A GLU* 1.3 63.8 + - - +
92A ALA* 3.3 1.7 + - - +
108A PHE* 3.8 7.6 - - + -
111A TYR* 3.5 31.4 - + + -
201A 2MR 3.3 44.1 + - - -
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Residues in contact with GLU 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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78A LYS* 2.7 49.9 + - + +
79A CYS 3.4 10.1 - - - +
80A MET* 4.4 11.5 - - + +
90A TYR* 1.3 72.6 - - - +
92A ALA* 1.3 61.7 + - - +
108A PHE* 3.6 4.2 - - - +
109A ALA* 2.9 42.7 + - + +
111A TYR* 5.7 0.5 - - - -
125A VAL* 4.2 7.5 - - + +
126A GLU* 4.2 10.5 - - - +
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Residues in contact with ALA 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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78A LYS* 4.0 2.9 - - - -
79A CYS* 2.7 43.1 + - - +
81A ALA* 3.9 11.9 - - + -
90A TYR 3.3 0.4 + - - -
91A GLU* 1.3 76.8 - - - +
93A GLU* 1.3 60.2 + - - +
106A ILE* 3.4 34.8 - - + -
107A THR 3.1 10.3 - - - +
108A PHE* 3.7 11.9 - - + -
109A ALA* 4.2 0.9 - - - +
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Residues in contact with GLU 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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76A GLY* 3.8 24.8 - - - +
77A ASP 3.5 13.0 - - - +
78A LYS* 3.7 14.6 - - + +
92A ALA* 1.3 73.6 - - - +
94A ILE* 1.3 68.9 + - - +
95A GLU* 3.4 17.8 + - - +
106A ILE* 3.3 1.6 - - - -
107A THR* 2.7 41.0 + - - +
109A ALA* 4.9 4.9 - - + +
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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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73A TRP* 3.6 47.3 - - + -
74A LYS 3.7 15.0 - - - +
75A VAL* 4.1 2.1 - - - +
76A GLY* 3.0 29.8 + - - -
77A ASP 2.7 20.7 + - - +
79A CYS* 3.5 22.2 - - - -
93A GLU* 1.3 71.7 - - - +
95A GLU* 1.3 65.4 + - - +
96A GLU 3.8 10.3 - - - +
97A ILE* 3.7 28.9 - - + -
104A ALA* 4.1 4.5 - - + -
105A ALA 3.6 5.8 - - - +
106A ILE* 3.7 7.9 - - + -
122A LEU* 3.9 4.7 - - + -
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Residues in contact with GLU 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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75A VAL* 3.4 21.7 - - - +
93A GLU* 3.8 27.8 - - - +
94A ILE* 1.3 76.7 - - - +
96A GLU* 1.3 66.3 + - + +
105A ALA* 2.8 16.7 + - + +
106A ILE 4.5 0.9 - - - -
107A THR* 3.1 32.2 + - - +
114A ALA* 5.8 0.7 - - + -
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Residues in contact with GLU 96 (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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75A VAL* 4.0 7.4 - - + -
94A ILE* 3.6 1.3 - - - +
95A GLU* 1.3 83.3 - - + +
97A ILE* 1.3 73.8 + - - +
98A ASP* 5.9 1.9 - - - +
104A ALA* 3.3 4.7 - - - +
105A ALA* 2.7 41.4 + - + +
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Residues in contact with ILE 97 (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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73A TRP 3.3 28.7 - - - +
74A LYS* 3.4 25.1 - - - -
75A VAL* 3.6 11.6 - - + +
94A ILE* 3.7 14.1 - - + -
96A GLU* 1.3 88.7 - - - +
98A ASP* 1.3 69.4 + - - +
99A GLU* 3.7 19.7 + - + +
103A THR 3.7 9.4 - - - +
104A ALA* 4.2 4.7 - - + +
119A LEU* 4.3 22.9 - - + -
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Residues in contact with ASP 98 (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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96A GLU* 4.3 2.7 - - - +
97A ILE* 1.3 72.3 - - - +
99A GLU* 1.3 51.3 + - - +
100A GLU* 3.2 12.8 - - - +
101A ASN* 2.6 50.8 + - - +
102A GLY* 2.7 30.1 + - - -
103A THR* 2.6 31.2 + - - +
104A ALA* 5.6 0.2 - - - -
116A VAL* 5.8 1.8 - - + -
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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