Contacts of the strand formed by residues 88 - 96 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B VAL* 4.3 4.9 - - - -
20B TYR* 3.2 20.2 - - + +
22B ASP* 3.9 11.2 - - + +
80B ILE* 3.5 7.6 - - - +
81B ASP* 2.8 38.5 + - - +
84B ARG* 3.2 47.1 + - - +
86B ALA 2.7 20.8 + - - -
87B LYS* 1.3 74.8 + - - +
89B LEU* 1.3 58.5 + - - +
90B ASN* 3.8 14.4 - - - +
200C ASP* 4.4 0.5 + - - -
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Residues in contact with LEU 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B VAL* 3.8 29.8 - - + +
12B LEU* 3.8 17.3 - - + -
13B ALA* 4.2 21.5 - - + +
18B VAL* 3.9 18.7 - - + +
20B TYR 3.0 7.4 + - - +
21B VAL* 3.3 10.3 - - + +
22B ASP 2.8 24.3 + - - -
42B PHE* 4.4 4.9 - - + -
78B ALA* 4.0 2.2 - - + -
79B ARG 3.4 32.3 - - - +
80B ILE* 3.8 12.6 - - + -
88B THR* 1.3 72.2 - - - +
90B ASN* 1.3 62.1 + - - +
91B ILE* 3.9 15.9 - - + -
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Residues in contact with ASN 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B ASP* 3.2 23.2 - - - +
24B ARG* 3.5 33.8 + - - +
77B THR 3.5 2.9 - - - +
78B ALA* 3.2 5.7 - - - -
79B ARG* 2.7 42.4 + - + +
80B ILE 4.9 0.8 + - - -
81B ASP* 3.0 43.5 + - - +
82B PRO* 5.1 1.0 - - - +
84B ARG* 4.9 0.3 + - - -
88B THR* 3.8 2.6 + - - +
89B LEU* 1.3 73.0 - - - +
91B ILE* 1.3 61.8 + - - +
92B ASN* 5.6 1.1 - - - +
244B LEU* 5.0 8.5 - - + +
247B TYR* 4.2 4.9 - - - -
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Residues in contact with ILE 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B VAL* 3.9 11.7 - - + -
21B VAL* 3.8 17.5 - - + -
22B ASP 3.0 8.7 + - - +
24B ARG* 2.9 26.2 + - - +
42B PHE* 3.4 36.6 - - + -
47B PHE* 5.6 1.1 - - + -
73B PRO* 4.2 6.1 - - + -
74B ASP 3.6 21.3 - - - +
75B PRO* 4.9 2.2 - - + -
77B THR* 3.8 4.5 - - - +
78B ALA* 4.0 14.1 - - + +
89B LEU* 3.9 8.3 - - + -
90B ASN* 1.3 80.7 - - - +
92B ASN* 1.3 77.2 + - - +
93B PHE* 3.3 20.2 - - + -
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Residues in contact with ASN 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B ARG* 3.3 24.3 - - - +
32B MET* 3.7 15.9 - - - +
74B ASP* 2.9 27.9 + - - +
77B THR* 2.8 31.6 + - + +
90B ASN* 5.6 0.5 - - - +
91B ILE* 1.3 70.0 - - - +
93B PHE* 1.3 67.9 + - - +
109B ARG* 4.0 13.4 - - - +
240B ASP* 3.1 35.0 + - - +
243B GLN* 5.6 0.8 - - - +
244B LEU* 6.4 0.2 - - - +
377B TYR* 3.8 6.7 + - - -
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Residues in contact with PHE 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B VAL* 5.6 0.7 - - + -
23B VAL* 3.7 38.6 - - + -
24B ARG 2.7 14.8 + - - +
25B PHE* 3.9 11.4 - - - +
42B PHE* 5.5 1.3 - + - -
46B VAL* 4.1 17.9 - - + -
51B LEU* 4.2 7.2 - - + -
71B LEU* 3.7 34.5 - - + -
72B LEU 3.3 7.9 - - - +
73B PRO* 3.2 39.9 - - + -
91B ILE* 3.3 37.9 - - + -
92B ASN* 1.3 79.3 - - - +
94B PHE* 1.3 61.0 + - - +
95B VAL 4.2 0.2 + - - -
107B ASP* 4.4 1.7 - - - +
109B ARG* 3.3 23.7 + - - -
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Residues in contact with PHE 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B LEU* 3.2 6.6 - - - -
72B LEU* 2.7 39.8 + - + +
73B PRO 4.6 3.4 - - - -
74B ASP* 3.4 33.2 - - + -
93B PHE* 1.3 72.8 - - - +
95B VAL* 1.3 61.4 + - - +
96B HIS* 3.5 21.9 - - + +
107B ASP* 3.3 13.0 - - - +
109B ARG* 3.5 48.7 - - + -
113B ARG* 3.2 49.6 - - + +
236B LEU* 4.4 7.6 - - + -
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Residues in contact with VAL 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B PHE* 4.2 10.8 - - + -
26B CYS 5.2 0.2 - - - +
53B PHE* 3.9 14.6 - - + -
61B PHE* 3.9 21.8 - - + -
69B MET* 3.8 14.6 - - + -
70B LEU 3.4 10.1 - - - +
71B LEU* 3.8 17.9 - - + -
94B PHE* 1.3 71.9 - - - +
96B HIS* 1.3 67.1 + - - +
103B PRO* 3.9 1.4 - - - +
104B TYR* 3.0 43.7 + - + +
107B ASP* 2.7 35.1 + - + +
110B ASN* 5.5 0.2 - - - +
113B ARG* 5.3 0.5 + - - -
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Residues in contact with HIS 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B MET* 3.5 10.8 - - - +
70B LEU* 2.8 49.7 + - + +
72B LEU* 3.5 32.4 - - + +
94B PHE* 3.5 30.0 - - + +
95B VAL* 1.3 80.6 - - - +
97B ASP* 1.3 66.2 + - - +
98B PRO 3.5 0.2 - - - -
101B LEU 2.8 26.3 + - - +
102B GLU 3.3 9.2 + - - +
103B PRO* 3.9 21.5 - - + -
104B TYR 4.1 1.3 - - - +
113B ARG* 4.0 9.0 + - - -
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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