Contacts of the strand formed by residues 88 - 96 (chain E) in PDB entry 3ZXR
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 THR 88 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18E VAL* 4.4 4.5 - - - -
20E TYR* 3.2 19.2 - - + +
22E ASP* 3.9 10.8 - - + +
80E ILE* 3.6 7.4 - - - +
81E ASP* 2.8 34.7 + - - +
84E ARG* 3.2 47.8 + - - +
86E ALA 2.6 21.4 + - - -
87E LYS* 1.3 77.0 + - - +
89E LEU* 1.3 61.3 + - - +
90E ASN* 3.9 14.6 - - - +
200F ASP* 4.4 0.5 + - - -
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Residues in contact with LEU 89 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9E VAL* 3.8 29.4 - - + +
12E LEU* 3.8 21.5 - - + -
13E ALA* 4.2 20.2 - - + -
18E VAL* 3.9 17.9 - - + +
20E TYR 2.9 9.0 + - - +
21E VAL* 3.3 9.9 - - + +
22E ASP 2.8 29.2 + - - -
42E PHE* 4.3 4.9 - - + -
78E ALA* 4.1 2.0 - - + -
79E ARG 3.5 28.7 - - - +
80E ILE* 3.7 13.2 - - + -
88E THR* 1.3 72.9 - - - +
90E ASN* 1.3 57.5 + - - +
91E ILE* 3.8 17.5 - - + -
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Residues in contact with ASN 90 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22E ASP* 3.2 23.2 - - - +
24E ARG* 3.5 33.7 + - - +
77E THR 3.5 3.3 - - - +
78E ALA* 3.2 5.4 - - - -
79E ARG* 2.7 44.0 + - + +
80E ILE 4.9 0.4 + - - -
81E ASP* 3.0 44.0 + - - +
82E PRO* 5.2 0.8 - - - +
84E ARG* 4.9 0.2 + - - -
88E THR* 3.9 2.3 + - - +
89E LEU* 1.3 72.9 - - - +
91E ILE* 1.3 59.6 + - - +
92E ASN* 5.6 0.9 - - - +
244E LEU* 5.0 8.6 - - + +
247E TYR* 4.1 5.5 - - - -
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Residues in contact with ILE 91 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9E VAL* 3.8 7.0 - - + -
21E VAL* 3.8 13.5 - - + -
22E ASP 3.0 9.5 + - - +
24E ARG* 2.8 27.7 + - - +
42E PHE* 3.5 34.8 - - + -
47E PHE* 5.6 1.1 - - + -
73E PRO* 4.3 6.1 - - + -
74E ASP 3.8 21.8 - - - +
75E PRO* 4.9 2.0 - - + -
77E THR* 3.8 3.8 - - - +
78E ALA* 3.9 15.7 - - + +
89E LEU* 3.8 17.9 - - + -
90E ASN* 1.3 80.4 - - - +
92E ASN* 1.3 76.8 + - - +
93E PHE* 3.3 19.3 - - + -
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Residues in contact with ASN 92 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24E ARG* 3.3 22.7 - - - +
32E MET* 3.8 16.3 - - - +
74E ASP* 2.8 28.1 + - - +
77E THR* 2.8 31.5 + - + +
90E ASN* 5.6 1.0 - - - +
91E ILE* 1.3 74.4 - - - +
93E PHE* 1.3 62.2 + - - +
109E ARG* 4.0 15.0 - - - +
240E ASP* 3.0 34.4 + - - +
243E GLN* 5.6 1.4 - - - +
377E TYR* 3.8 7.1 + - - -
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Residues in contact with PHE 93 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21E VAL* 5.5 1.3 - - + -
23E VAL* 3.5 40.4 - - + -
24E ARG 2.6 14.0 + - - +
25E PHE* 3.8 11.6 - - - +
42E PHE* 5.5 1.8 - + - -
46E VAL* 4.1 18.2 - - + -
51E LEU* 4.1 7.0 - - + -
71E LEU* 3.6 33.2 - - + -
72E LEU 3.4 7.9 - - - +
73E PRO* 3.3 40.2 - - + -
74E ASP 4.4 0.2 - - - +
91E ILE* 3.3 35.9 - - + -
92E ASN* 1.3 79.2 - - - +
94E PHE* 1.3 60.6 + - - +
95E VAL 4.2 0.3 + - - -
107E ASP* 4.5 1.4 - - - +
109E ARG* 3.3 23.7 + - - -
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Residues in contact with PHE 94 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71E LEU* 3.2 6.6 - - - -
72E LEU* 2.8 37.6 + - + +
73E PRO 4.7 3.6 - - - -
74E ASP* 3.4 34.1 - - + -
93E PHE* 1.3 73.6 - - - +
95E VAL* 1.3 61.8 + - - +
96E HIS* 3.5 21.3 - - + +
107E ASP* 3.4 12.3 - - - +
109E ARG* 3.4 47.3 - - + -
113E ARG* 3.2 49.8 - - + +
236E LEU* 4.4 7.4 - - + -
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Residues in contact with VAL 95 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25E PHE* 4.1 11.7 - - + -
26E CYS 5.2 0.2 - - - +
53E PHE* 4.0 15.9 - - + -
61E PHE* 3.9 21.5 - - + -
69E MET* 3.8 14.4 - - + -
70E LEU 3.4 9.0 - - - +
71E LEU* 3.7 17.3 - - + -
94E PHE* 1.3 73.3 - - - +
96E HIS* 1.3 68.3 + - - +
103E PRO* 3.8 1.4 - - - +
104E TYR* 2.9 43.0 + - + +
107E ASP* 2.7 35.5 + - + +
113E ARG* 5.3 0.5 + - - -
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Residues in contact with HIS 96 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69E MET* 3.6 10.5 - - - +
70E LEU* 2.7 50.7 + - + +
72E LEU* 3.6 31.8 - - + +
94E PHE* 3.5 30.5 - - + +
95E VAL* 1.3 82.5 - - - +
97E ASP* 1.3 65.8 + - - +
98E PRO 3.5 0.3 - - - -
101E LEU 2.9 25.6 + - - +
102E GLU 3.3 4.7 - - - +
103E PRO* 3.5 25.8 - - + -
104E TYR 4.1 0.9 - - - +
113E ARG* 3.9 9.6 + - - -
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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