Contacts of the strand formed by residues 90 - 96 (chain A) in PDB entry 4REW
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 ASP 90 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48A ILE* 4.5 12.4 - - + +
49A LEU 3.2 16.4 - - - +
50A ASN* 3.0 28.0 + - - +
51A ARG* 3.9 5.2 - - - +
87A THR* 3.1 27.9 + - - +
89A SER* 1.3 94.5 + - - +
91A ILE* 1.3 65.1 + - - +
92A PHE* 3.1 32.9 - - + -
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Residues in contact with ILE 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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47A LYS 3.4 1.9 - - - +
49A LEU* 2.9 45.4 + - + +
51A ARG* 3.4 32.8 - - - +
54A ILE* 5.7 4.9 - - + -
63A ILE* 6.5 0.9 - - + -
67A ILE* 4.6 21.1 - - + -
84A VAL* 5.5 3.4 - - + -
85A ILE 4.1 5.6 - - - +
86A SER* 3.3 29.8 - - - +
87A THR 4.1 2.2 - - - +
90A ASP* 1.3 75.7 - - - +
92A PHE* 1.3 74.0 + - - +
93A MET* 5.2 3.4 - - + -
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Residues in contact with PHE 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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15A ILE* 3.4 49.8 - - + -
20A LEU* 4.8 7.2 - - + -
46A VAL* 5.2 2.7 - - + -
47A LYS 3.5 2.7 - - - -
48A ILE* 3.4 40.2 - - + -
84A VAL* 3.5 5.7 - - - +
85A ILE* 3.0 41.6 + - + +
87A THR* 4.1 12.6 - - + -
89A SER* 5.2 0.4 - - - -
90A ASP* 3.1 37.7 - - - -
91A ILE* 1.3 78.5 - - - +
93A MET* 1.3 72.4 + - - +
94A VAL* 5.7 1.6 - - + -
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Residues in contact with MET 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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45A ALA 3.3 3.8 - - - +
46A VAL* 3.1 5.0 - - - -
47A LYS* 3.0 42.2 + - + +
49A LEU* 4.5 20.6 - - + -
66A GLU* 5.2 12.3 - - + +
67A ILE* 4.6 22.4 - - + -
70A LEU* 4.1 19.1 - - + -
81A LEU* 3.7 30.5 - - + -
83A GLN 3.9 4.5 - - - -
84A VAL* 3.7 13.7 - - + -
91A ILE* 5.2 2.7 - - + -
92A PHE* 1.3 80.9 - - - +
94A VAL* 1.3 63.5 + - - +
95A MET* 4.0 12.6 - - + +
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Residues in contact with VAL 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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15A ILE* 5.3 5.8 - - + +
18A TYR* 4.5 19.5 - - + -
44A VAL* 4.6 8.5 - - + -
45A ALA 3.7 2.7 - - - -
46A VAL* 3.5 23.3 - - + -
81A LEU* 3.2 7.4 - - - +
82A TYR* 3.0 38.6 + - + -
83A GLN* 3.1 49.6 + - + +
85A ILE* 5.0 9.9 - - + -
92A PHE* 4.3 1.8 - - + -
93A MET* 1.3 73.9 - - - +
95A MET* 1.3 59.2 + - - +
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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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32A VAL* 5.0 1.1 - - + -
44A VAL* 3.4 8.3 - - - +
45A ALA* 2.8 44.1 + - + +
46A VAL 4.9 0.2 - - - -
47A LYS* 4.1 15.3 - - + +
70A LEU* 4.9 9.4 - - - -
79A ILE* 3.6 25.4 - - + -
80A LYS 3.6 4.5 - - - -
81A LEU* 3.6 18.8 - - + -
82A TYR* 3.7 6.7 - - - -
93A MET* 4.0 23.1 - - - +
94A VAL* 1.3 79.5 - - - +
96A GLU* 1.3 63.8 + - - +
97A TYR 3.3 0.7 + - - -
158A ALA 5.5 2.2 - - - +
601A STU 3.6 42.2 - - + -
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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 HIS 4.6 2.4 - - - +
78A ILE 3.9 3.6 - - - +
79A ILE* 3.4 17.7 - - + +
80A LYS* 3.1 47.6 + - - +
82A TYR* 3.0 28.9 + - + +
95A MET* 1.3 70.4 - - - +
97A TYR* 1.3 63.8 + - - +
98A VAL* 4.4 3.1 - - + +
156A LYS* 2.7 43.6 + - - +
601A STU 3.1 17.9 + - - -
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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