Contacts of the strand formed by residues 86 - 95 (chain B) in PDB entry 4OE5
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 ASN 86 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58B LYS* 6.0 3.4 - - - +
83B SER* 2.9 14.4 + - - +
84B PRO 3.3 0.4 - - - -
85B PHE* 1.3 93.2 - - + +
87B HIS* 1.3 52.7 + - - +
88B GLY* 3.0 11.7 + - - -
89B HIS* 2.7 47.5 + - + +
379B ASP* 6.0 0.2 - - - +
425B VAL* 3.2 17.7 - - + +
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Residues in contact with HIS 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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82B VAL* 3.7 27.6 - - + +
83B SER 3.1 8.3 + - - +
86B ASN* 1.3 68.5 - - - +
88B GLY* 1.3 65.8 + - - +
89B HIS 3.1 2.1 + - - -
90B LYS* 5.1 1.7 - - - +
423B ASP 2.9 21.2 + - - -
424B SER 3.3 21.3 - - - -
425B VAL* 3.1 23.3 + - - -
426B GLY* 3.5 14.6 - - - -
427B TYR* 3.6 46.0 - + + +
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Residues in contact with GLY 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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86B ASN* 3.0 10.9 + - - -
87B HIS* 1.3 86.5 + - - +
89B HIS* 1.3 55.1 + - - +
90B LYS* 3.4 10.9 + - - +
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Residues in contact with HIS 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B LEU* 3.3 20.2 - - + -
58B LYS* 4.6 5.2 - - + +
59B GLY* 4.0 13.8 + - - -
60B ARG 2.9 31.7 + - - -
82B VAL* 3.4 1.7 - - - -
83B SER* 3.0 34.4 + - - -
85B PHE* 6.3 0.2 - - - -
86B ASN* 2.7 30.1 + - - +
87B HIS 4.3 1.8 - - - -
88B GLY* 1.3 74.2 - - - +
90B LYS* 1.3 73.8 + - - +
91B VAL* 3.2 18.2 + - + +
149B VAL* 3.9 13.2 - - + +
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Residues in contact with LYS 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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61B MET* 3.2 36.9 - - - +
80B TYR* 4.3 21.3 - - + -
81B GLN 3.5 8.5 - - - +
82B VAL* 4.3 15.3 - - + +
87B HIS 5.1 1.3 - - - +
88B GLY 3.4 8.3 + - - +
89B HIS* 1.3 80.6 - - - +
91B VAL* 1.3 59.6 + - - +
92B ALA 3.4 1.1 - - - -
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Residues in contact with VAL 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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60B ARG 3.9 8.2 - - - +
61B MET* 3.4 4.9 - - - -
62B GLU 3.1 16.8 + - - -
81B GLN* 2.8 50.3 + - + +
82B VAL 4.4 0.9 - - - -
83B SER* 3.7 15.7 - - - +
89B HIS* 3.6 38.1 - - + +
90B LYS* 1.3 72.8 - - - +
92B ALA* 1.3 61.5 + - - +
149B VAL* 3.8 10.5 - - + +
150B GLY* 4.2 4.5 - - - -
240B LEU* 3.9 28.2 - - + +
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Residues in contact with ALA 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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61B MET* 3.7 6.3 - - - -
62B GLU 3.2 12.1 - - - +
64B ILE* 4.0 21.1 - - + -
80B TYR* 3.3 8.8 - - - -
81B GLN* 2.9 50.6 + - + +
90B LYS 3.4 1.6 - - - -
91B VAL* 1.3 84.2 + - + +
93B LYS* 1.3 61.7 + - - +
94B PHE* 4.2 0.9 - - + -
239B MET* 4.8 4.5 - - + -
240B LEU* 4.6 3.4 - - + -
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Residues in contact with LYS 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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61B MET* 3.7 22.7 - - + +
62B GLU 2.8 7.4 + - - +
63B ALA* 3.4 19.2 - - - +
64B ILE* 2.6 34.1 + - - +
74B TRP* 3.5 12.7 - - + -
78B VAL* 3.6 26.5 - - + -
79B GLN 3.4 4.3 - - - +
80B TYR* 3.6 33.7 - - + +
92B ALA* 1.3 73.5 - - - +
94B PHE* 1.3 59.8 + - - +
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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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64B ILE* 3.2 20.6 - - + +
74B TRP* 3.7 6.0 - - - -
78B VAL* 3.4 8.3 - - - +
79B GLN* 2.8 58.5 + - + +
80B TYR 4.0 14.1 - - - -
81B GLN 4.0 5.6 - - - -
92B ALA 4.7 2.7 - - - -
93B LYS* 1.3 75.0 - - - +
95B CYS* 1.3 76.4 + - - +
96B TYR* 3.8 19.7 - + - -
236B ASP* 3.6 39.3 - - + -
239B MET* 3.7 36.3 - - + -
263B PRO* 3.8 19.1 - - + -
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Residues in contact with CYS 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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64B ILE 4.1 1.2 + - - -
66B CYS* 3.7 20.8 - - - +
73B VAL 3.9 14.1 - - - -
74B TRP* 3.7 17.7 - - + -
75B THR* 3.4 46.2 - - - +
77B ASP 3.2 11.2 - - - +
78B VAL* 4.3 0.9 - - - -
79B GLN 4.3 0.9 - - - +
94B PHE* 1.3 86.7 - - - +
96B TYR* 1.3 61.1 + - - +
263B PRO* 3.7 18.5 - - - +
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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