Contacts of the strand formed by residues 81 - 89 (chain A) in PDB entry 4EEJ
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 81 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71A ASP* 2.8 37.4 + - + -
72A GLU 3.3 6.7 + - - -
73A TYR* 3.4 40.6 + + + -
80A ARG* 1.3 76.6 - - - +
82A VAL* 1.4 79.2 + - - +
83A LYS* 4.5 9.1 + - + +
98A LYS 4.5 1.4 - - - +
99A GLY* 4.6 6.1 - - - -
100A GLU 5.2 1.0 + - - -
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Residues in contact with VAL 82 (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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71A ASP* 3.6 1.4 - - - -
72A GLU* 2.9 61.1 + - + +
74A THR* 4.8 5.8 - - + -
80A ARG* 4.8 6.1 - - + +
81A HIS* 1.4 87.4 + - - +
83A LYS* 1.3 63.2 + - - +
84A ALA 4.7 1.3 - - - +
97A GLN* 3.8 33.4 - - + +
98A LYS 3.3 16.4 - - - +
99A GLY* 4.5 5.2 - - - -
100A GLU 5.4 1.3 - - - +
104A ARG* 4.1 26.9 - - - +
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Residues in contact with LYS 83 (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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69A GLU* 3.8 37.9 + - + +
70A PHE 3.6 2.5 - - - +
71A ASP* 2.8 37.8 + - - +
81A HIS* 4.8 7.8 + - + -
82A VAL* 1.3 71.1 - - - +
84A ALA* 1.3 61.7 + - - +
85A LEU* 5.3 0.3 - - - +
96A VAL 3.6 2.9 - - - +
97A GLN* 4.4 0.4 - - - -
98A LYS* 2.9 49.3 + - + +
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Residues in contact with ALA 84 (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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69A GLU* 3.2 5.9 - - - +
70A PHE* 2.8 67.5 + - + +
72A GLU* 3.6 20.9 - - + +
82A VAL* 3.8 1.0 - - + -
83A LYS* 1.3 72.1 - - - +
85A LEU* 1.3 61.6 + - - +
95A CYS* 4.4 3.6 - - - -
96A VAL 3.4 5.4 - - - +
97A GLN* 4.1 11.9 - - + +
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Residues in contact with LEU 85 (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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67A GLY* 3.8 33.9 - - - +
68A VAL 3.9 1.1 - - - +
69A GLU* 3.9 24.7 - - + +
70A PHE* 4.3 2.2 - - - -
83A LYS 5.3 0.4 - - - +
84A ALA* 1.3 76.4 - - - +
86A VAL* 1.3 64.7 + - - +
87A THR* 3.9 18.1 + - + +
94A VAL 3.6 1.7 - - - +
95A CYS* 3.2 2.3 - - - -
96A VAL* 3.0 39.4 + - + +
98A LYS* 6.3 2.0 - - - +
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Residues in contact with VAL 86 (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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64A PHE* 3.6 47.3 - - + -
65A THR 5.3 0.8 + - - +
66A VAL* 3.4 5.2 - - + -
67A GLY 2.8 26.9 + - - +
68A VAL 5.1 1.6 + - - -
70A PHE* 4.1 10.5 - - + -
85A LEU* 1.3 77.4 - - - +
87A THR* 1.3 64.9 + - - +
93A LEU* 3.5 32.8 - - + -
94A VAL 3.2 7.6 - - - +
95A CYS* 3.8 22.2 - - + -
106A TRP* 3.9 9.2 - - + -
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Residues in contact with THR 87 (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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66A VAL* 4.1 7.0 - - + -
67A GLY* 4.4 8.7 - - - -
85A LEU* 3.9 28.3 + - + -
86A VAL* 1.3 81.0 - - - +
88A TRP* 1.3 67.9 + - - +
89A GLU* 4.9 5.9 + - - +
93A LEU* 3.7 6.8 - - - +
94A VAL* 2.9 41.9 + - - +
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Residues in contact with TRP 88 (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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2A ARG* 3.1 78.6 + - + +
4A ARG* 3.8 7.2 - - + -
44A GLN* 4.0 11.4 - - - -
46A GLY 6.0 0.2 + - - -
47A ASP* 5.4 3.1 + - - -
49A PHE* 4.1 7.4 - + - -
66A VAL* 3.7 28.3 - - + +
87A THR* 1.3 77.4 - - - +
89A GLU* 1.3 64.9 + - - +
90A GLY 3.7 14.1 + - - +
91A ASP 3.8 10.5 - - - -
92A VAL 3.4 19.7 - - - -
93A LEU* 3.7 41.5 - - + -
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Residues in contact with GLU 89 (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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87A THR* 4.0 6.1 + - - +
88A TRP* 1.3 75.9 - - - +
90A GLY* 1.3 61.4 + - - +
91A ASP 3.2 0.5 + - - -
92A VAL* 2.9 31.6 + - + +
94A VAL* 3.7 36.4 - - + +
107A LYS* 4.7 9.4 + - - -
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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