Contacts of the strand formed by residues 86 - 95 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83C SER* 2.9 14.0 + - - +
84C PRO 3.2 0.2 - - - -
85C PHE* 1.3 94.2 - - + +
87C HIS* 1.3 58.8 + - - +
88C GLY* 3.0 11.0 + - - -
89C HIS* 2.8 42.6 + - + +
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Residues in contact with HIS 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82C VAL* 3.5 39.0 - - + +
83C SER 3.3 8.5 - - - +
84C PRO* 4.5 9.2 + - + +
85C PHE 6.1 0.2 - - - -
86C ASN* 1.3 70.7 + - - +
88C GLY* 1.3 66.6 + - - +
89C HIS 3.1 1.3 + - - -
90C LYS* 3.9 4.0 - - - +
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Residues in contact with GLY 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86C ASN* 3.0 10.0 + - - -
87C HIS* 1.3 85.0 + - - +
89C HIS* 1.3 55.1 + - - +
90C LYS* 3.4 15.4 + - - +
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Residues in contact with HIS 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C LEU* 3.2 22.3 + - + -
58C LYS* 4.4 2.2 - - - -
59C GLY* 3.7 17.9 + - - -
60C ARG 2.9 29.2 + - - -
82C VAL* 3.3 1.9 - - - +
83C SER* 2.9 38.7 + - - -
85C PHE* 6.2 1.0 - - - -
86C ASN* 2.8 30.4 + - - +
87C HIS 4.3 0.7 - - - -
88C GLY* 1.3 74.4 - - - +
90C LYS* 1.3 75.0 + - - +
91C VAL* 3.4 6.5 + - + +
149C VAL* 3.8 22.0 - - + +
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Residues in contact with LYS 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60C ARG 3.5 0.3 - - - +
61C MET* 3.2 37.5 - - + +
80C TYR* 4.0 26.2 - - + -
81C GLN 3.5 5.8 - - - +
82C VAL* 3.7 23.8 - - + +
87C HIS 3.9 4.9 - - - +
88C GLY* 3.4 15.7 + - - +
89C HIS* 1.3 79.5 - - - +
91C VAL* 1.3 59.8 + - - +
92C ALA 3.4 1.1 - - - +
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Residues in contact with VAL 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60C ARG 3.8 8.0 - - - +
61C MET* 3.5 4.6 - - - -
62C GLU 3.1 16.6 + - - -
81C GLN* 2.8 48.1 + - + +
82C VAL 4.7 0.4 - - - -
83C SER* 3.8 12.6 - - - +
89C HIS* 3.8 33.2 - - + +
90C LYS* 1.3 74.8 - - - +
92C ALA* 1.3 63.7 + - + +
149C VAL* 3.9 17.9 - - + +
150C GLY* 4.4 2.5 - - - -
240C LEU* 3.6 28.2 - - + +
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Residues in contact with ALA 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61C MET* 3.7 6.0 - - - +
62C GLU 3.1 9.6 - - - +
64C ILE* 4.1 20.4 - - + -
80C TYR* 3.3 9.7 - - - +
81C GLN* 2.9 51.3 + - + +
90C LYS* 3.4 1.4 - - - +
91C VAL* 1.3 84.7 - - + +
93C LYS* 1.3 61.1 + - - +
94C PHE* 4.1 1.1 - - + -
239C MET* 4.7 5.2 - - + -
240C LEU* 4.4 3.6 - - + +
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Residues in contact with LYS 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61C MET* 3.7 25.9 - - + +
62C GLU 2.7 9.9 + - - +
63C ALA* 3.2 23.1 - - - +
64C ILE* 2.5 33.6 + - - +
74C TRP* 3.5 15.0 - - + -
78C VAL* 3.6 29.2 - - + -
79C GLN 3.5 3.1 - - - +
80C TYR* 3.6 22.7 - - + +
92C ALA* 1.3 73.7 - - - +
94C PHE* 1.3 60.4 + - - +
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Residues in contact with PHE 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64C ILE* 3.2 22.0 - - + +
74C TRP* 3.7 5.6 - - - -
78C VAL* 3.4 9.5 - - - +
79C GLN* 2.6 63.4 + - + +
80C TYR 3.9 18.6 - - - -
81C GLN 4.1 5.8 - - - -
92C ALA 4.6 2.7 - - - -
93C LYS* 1.3 74.6 - - - +
95C CYS* 1.3 78.1 + - - +
96C TYR* 3.8 19.7 - + - -
236C ASP* 3.8 38.8 - - + -
239C MET* 3.7 36.1 - - + -
263C PRO* 3.8 11.4 - - + -
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Residues in contact with CYS 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64C ILE 4.1 1.0 + - - -
66C CYS* 3.8 18.7 - - - -
73C VAL 3.8 13.7 - - - -
74C TRP* 3.8 21.5 - - + -
75C THR* 3.3 39.5 - - - +
77C ASP 3.1 15.0 - - - +
78C VAL* 4.3 0.9 - - - -
79C GLN 4.2 0.7 - - - +
94C PHE* 1.3 85.0 - - - +
96C TYR* 1.3 60.9 + - - +
263C PRO* 3.5 21.7 - - - +
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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