Contacts of the strand formed by residues 85 - 91 (chain B) in PDB entry 5F71
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 GLY 85 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34B LYS* 3.9 6.5 - - - -
84B SER* 1.3 75.4 - - - +
86B ILE* 1.3 66.6 + - - -
87B TYR* 3.6 8.6 - - - -
105B LYS* 4.8 2.9 - - - -
106B LEU* 3.0 33.0 + - - +
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Residues in contact with ILE 86 (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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34B LYS* 3.7 3.3 - - - +
35B GLY* 2.8 25.9 + - - -
36B ALA* 4.0 28.0 - - + +
85B GLY* 1.3 77.0 - - - -
87B TYR* 1.3 69.6 + - - +
103B ASN* 3.7 29.6 - - + -
104B LEU 3.3 10.1 - - - +
105B LYS* 4.4 15.9 - - + +
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Residues in contact with TYR 87 (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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15B LEU* 3.8 18.4 - - + -
32B TRP* 3.8 25.4 - + + -
33B GLY 3.3 18.2 - - - -
34B LYS* 3.5 29.5 + - + +
35B GLY 3.8 3.1 - - - -
46B VAL* 4.9 11.0 - - + -
61B TYR* 5.2 3.0 + + - -
74B LEU* 4.7 5.4 - - + -
76B ILE* 3.8 23.7 - - + +
83B ASP* 2.8 39.9 + - - +
85B GLY 3.6 13.0 - - - -
86B ILE* 1.3 77.0 - - - +
88B CYS* 1.3 59.8 + - - +
89B CYS 4.0 0.2 + - - -
102B PHE 3.3 1.0 - - - +
103B ASN* 3.1 9.7 - - - +
104B LEU* 2.7 38.3 + - + +
106B LEU* 3.9 12.3 - - + -
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Residues in contact with CYS 88 (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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31B CYS 3.1 5.9 - - - +
32B TRP* 3.2 6.1 - - - -
33B GLY 2.8 32.1 + - - +
35B GLY 3.4 16.1 + - - +
37B CYS* 2.0 53.8 - - - +
38B PRO* 4.4 0.4 - - - -
41B GLU 4.6 1.1 - - - -
42B CYS* 3.7 29.6 - - + +
87B TYR* 1.3 72.9 - - - +
89B CYS* 1.3 59.0 + - - +
90B ARG* 4.2 11.4 - - - -
102B PHE 3.4 2.9 - - - -
103B ASN* 4.1 0.2 - - - -
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Residues in contact with CYS 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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17B CYS* 2.1 52.7 - - + -
30B VAL* 4.4 3.8 - - - -
31B CYS 3.4 2.2 - - - -
32B TRP* 3.8 30.4 - - + -
37B CYS* 4.2 0.2 - - - -
72B VAL* 4.0 4.3 - - - -
87B TYR 4.0 0.4 + - - -
88B CYS* 1.3 73.4 - - - +
90B ARG* 1.3 62.1 + - - +
91B ILE* 4.0 10.3 - - - -
100B GLU 3.6 3.5 - - - +
101B LYS* 3.6 1.0 - - - -
102B PHE* 2.8 40.5 + - + +
104B LEU* 4.1 2.7 - - + -
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Residues in contact with ARG 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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29B PRO 3.8 0.3 - - - +
30B VAL* 3.2 6.8 - - - +
31B CYS* 2.7 52.3 + - + +
37B CYS* 5.0 0.2 - - - +
38B PRO* 3.0 18.6 + - - +
39B VAL 2.7 21.6 + - - -
40B PHE* 3.2 4.0 - - - +
41B GLU* 2.4 58.9 + - - +
88B CYS* 4.2 8.7 - - - -
89B CYS* 1.3 76.8 - - - +
91B ILE* 1.3 67.0 + - - +
92B GLN* 3.9 1.2 + - + +
97B MET* 4.4 9.5 - - - +
99B ASP* 3.0 38.1 + - + +
100B GLU 3.3 9.4 - - - +
101B LYS* 3.6 26.2 - - + +
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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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17B CYS* 4.1 3.6 - - - -
19B TYR* 3.5 55.9 - - + -
28B VAL* 3.6 20.0 - - + -
29B PRO 3.8 3.8 - - - +
30B VAL* 3.9 7.4 - - + -
72B VAL* 3.9 19.3 - - + -
89B CYS* 4.0 11.7 - - - -
90B ARG* 1.3 76.8 - - - +
92B GLN* 1.3 61.4 + - - +
93B ILE* 3.4 11.8 + - + +
99B ASP* 3.5 4.6 - - - -
100B GLU* 3.0 46.8 + - + +
102B PHE* 4.5 5.2 - - + -
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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