Contacts of the strand formed by residues 75 - 83 (chain C) in PDB entry 1OXC
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 ASP 75 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A ALA* 2.7 25.7 + - - +
73C PRO 4.0 0.6 + - - -
74C SER* 1.3 71.6 - - - +
76C LEU* 1.3 64.4 + - - +
94C SER* 3.2 4.9 - - - -
95C GLU* 2.9 37.4 + - + +
102C TYR* 2.6 37.1 + - + +
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Residues in contact with LEU 76 (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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1A ALA* 4.5 3.5 + - - +
3C GLN* 3.5 40.2 - - + +
4C GLY* 4.3 4.5 - - - -
64C GLN* 6.3 0.4 - - - +
65C VAL 3.3 27.1 - - - +
66C GLN* 4.5 5.4 - - + -
67C VAL* 4.0 19.3 - - + +
74C SER 3.8 13.5 - - - +
75C ASP* 1.3 82.3 + - - +
77C VAL* 1.3 70.5 + - - +
92C VAL* 4.3 9.0 - - + -
93C GLY 3.4 5.6 - - - +
94C SER* 3.5 26.2 - - - -
102C TYR* 4.6 0.2 - - - -
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Residues in contact with VAL 77 (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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1A ALA* 3.1 35.9 - - + -
3A GLN* 5.3 2.7 - - - +
3C GLN* 3.3 9.0 - - - +
76C LEU* 1.3 76.3 - - - +
78C SER* 1.3 65.4 + - - +
92C VAL* 3.3 2.8 - - - +
93C GLY* 2.8 51.7 + - - +
102C TYR* 3.6 18.2 - - + -
83D LEU* 4.1 25.3 - - + +
84D THR* 4.0 11.9 - - + +
87D LEU* 4.1 5.8 - - + -
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Residues in contact with SER 78 (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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83B LEU* 4.9 5.4 - - - +
84B THR* 5.0 4.0 + - - -
3C GLN* 2.9 27.1 + - - +
4C GLY* 2.8 32.0 + - - -
5C VAL 4.8 0.3 + - - -
6C PHE* 3.8 14.3 - - - -
77C VAL* 1.3 75.9 - - - +
79C ALA* 1.3 66.8 + - - +
91C LEU 3.0 16.2 - - - -
92C VAL* 4.2 2.5 - - - -
83D LEU* 3.8 11.2 - - - +
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Residues in contact with ALA 79 (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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79A ALA* 4.9 0.9 - - + -
81B VAL* 4.6 9.0 - - + -
82B ILE 3.6 13.2 - - - +
83B LEU* 4.2 14.1 - - + +
84B THR 5.7 0.7 - - - +
6C PHE* 3.8 7.0 - - - -
78C SER* 1.3 79.4 - - - +
80C GLN* 1.3 61.6 + - - +
81C VAL* 5.2 1.8 - - + -
89C PHE 3.9 0.2 - - - +
90C ALA* 3.7 1.2 - - - -
91C LEU* 2.9 34.3 + - + +
81D VAL* 5.0 5.4 - - + -
83D LEU* 3.7 22.1 - - + +
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Residues in contact with GLN 80 (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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80B GLN 3.9 0.2 - - - +
81B VAL* 3.2 7.4 - - - +
82B ILE* 2.8 61.1 + - + +
85B ASN* 4.5 9.9 - - - +
6C PHE* 4.6 14.6 - - + +
7C THR 4.4 10.0 + - - +
79C ALA* 1.3 75.5 - - - +
81C VAL* 1.3 66.1 + - - +
82C ILE* 3.7 12.5 - - + +
88C ASN* 3.0 29.1 - - - +
89C PHE 3.1 18.2 - - - +
90C ALA* 4.5 1.8 - - + -
111C TRP* 3.6 22.3 - - + -
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Residues in contact with VAL 81 (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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81A VAL* 5.5 5.8 - - + -
79B ALA* 4.8 5.6 - - + -
80B GLN 3.3 9.4 - - - +
81B VAL* 4.4 10.1 - - + -
79C ALA* 5.2 1.6 - - + -
80C GLN* 1.3 79.8 - - - +
82C ILE* 1.3 67.7 + - - +
83C LEU* 3.9 24.2 - - + -
87C LEU 3.7 1.0 - - - +
88C ASN* 3.6 1.7 - - - -
89C PHE* 2.9 36.4 + - + +
91C LEU* 4.6 5.2 - - + -
79D ALA* 4.9 4.7 - - + -
81D VAL* 4.2 35.2 - - + -
91D LEU* 4.1 19.1 - - + -
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Residues in contact with ILE 82 (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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79B ALA* 3.7 6.9 - - - +
80B GLN* 2.9 67.5 + - + +
82B ILE* 4.5 4.3 - - + -
80C GLN* 3.7 13.9 - - + +
81C VAL* 1.3 77.2 - - - +
83C LEU* 1.3 67.0 + - - +
84C THR 4.2 0.2 + - - -
85C ASN* 3.9 14.2 + - - +
86C GLU 3.8 20.4 - - - +
87C LEU 3.2 9.2 - - - +
88C ASN* 3.2 32.1 - - - +
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Residues in contact with LEU 83 (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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78B SER 5.0 2.0 - - - +
79B ALA* 4.3 9.4 - - + +
81C VAL* 3.9 13.0 - - + -
82C ILE* 1.3 77.2 - - - +
84C THR* 1.3 74.6 + - - +
85C ASN 2.9 4.0 + - - -
86C GLU 2.9 10.9 + - - -
87C LEU* 2.8 22.5 + - + +
89C PHE* 3.9 27.6 - - + -
77D VAL* 3.5 29.4 - - + +
78D SER* 3.9 27.4 - - - +
79D ALA* 3.7 25.8 - - + -
91D LEU* 4.2 10.5 - - + +
93D GLY 4.6 0.2 - - - +
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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