Contacts of the strand formed by residues 87 - 95 (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 LEU 87 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81C VAL 3.7 1.4 - - - +
82C ILE* 3.2 4.4 - - - -
83C LEU* 2.8 46.6 + - + +
86C GLU* 1.3 76.1 - - - +
88C ASN* 1.3 65.2 + - - +
89C PHE* 3.6 32.1 - - + -
110C ASN* 5.5 2.9 - - + +
111C TRP 4.1 9.9 - - - +
112C PRO* 5.1 0.4 - - + +
77D VAL* 4.5 2.0 - - + -
92D VAL 4.2 0.9 - - - +
93D GLY* 3.3 33.9 - - - +
101D ASP 4.3 4.3 - - - +
102D TYR* 3.4 21.1 - - + +
103D ASN* 3.9 19.7 - - + -
106D VAL* 4.0 11.4 - - + -
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Residues in contact with ASN 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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80C GLN* 3.0 27.0 - - - +
81C VAL 3.6 2.0 - - - -
82C ILE* 3.2 23.3 - - - +
86C GLU 3.2 17.0 - - - +
87C LEU* 1.3 77.5 - - - +
89C PHE* 1.3 64.4 + - - +
90C ALA 4.3 0.2 - - - -
110C ASN* 3.2 9.6 - - - +
111C TRP* 2.8 76.1 + - + +
112C PRO* 4.5 0.3 - - - +
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Residues in contact with PHE 89 (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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79C ALA 3.9 0.5 - - - +
80C GLN* 3.1 8.1 - - - +
81C VAL 2.9 40.6 + - - +
83C LEU* 3.9 18.8 - - + -
87C LEU* 3.6 39.0 - - + -
88C ASN* 1.3 78.6 - - - +
90C ALA* 1.3 60.6 + - - +
91C LEU* 3.9 16.7 - - + +
108C VAL* 4.5 6.3 - - + -
109C ILE 3.3 3.8 - - - -
110C ASN* 4.5 11.9 - - + -
111C TRP* 4.8 0.4 - - - -
91D LEU* 3.8 38.1 - - + -
92D VAL 4.1 5.8 - - - -
106D VAL* 3.5 27.6 - - + -
108D VAL* 3.8 18.8 - - + -
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Residues in contact with ALA 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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6C PHE* 3.7 37.4 - - + -
79C ALA 3.7 4.9 - - - -
80C GLN* 4.3 2.0 - - + +
89C PHE* 1.3 72.1 - - - +
91C LEU* 1.3 59.8 + - - +
92C VAL* 5.1 0.3 - - - +
107C VAL 3.8 1.2 - - - +
108C VAL* 3.8 2.3 - - - -
109C ILE* 2.8 57.2 + - + +
111C TRP* 3.9 12.0 - - + -
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Residues in contact with LEU 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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6C PHE* 3.7 0.6 - - - -
78C SER* 3.0 30.1 - - - -
79C ALA* 2.9 17.8 + - + +
81C VAL* 4.6 7.4 - - + -
89C PHE* 4.1 18.4 - - + -
90C ALA* 1.3 79.0 - - - +
92C VAL* 1.3 64.3 + - - +
107C VAL 3.6 1.3 - - - -
108C VAL* 4.0 20.6 - - + -
81D VAL* 3.6 31.4 - - + -
83D LEU* 4.6 5.6 - - + -
89D PHE* 3.8 42.0 - - + -
91D LEU* 4.2 18.2 - - + -
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Residues in contact with VAL 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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4C GLY* 4.3 2.7 - - - -
6C PHE* 3.6 26.7 - - + -
65C VAL* 4.1 28.5 - - + -
67C VAL* 5.2 1.6 - - + -
76C LEU* 4.3 22.2 - - + -
77C VAL 3.3 7.9 - - - +
78C SER* 4.2 3.8 - - - -
90C ALA 5.1 0.7 - - - +
91C LEU* 1.3 80.9 - - - +
93C GLY* 1.3 74.2 + - - +
105C ALA 5.5 0.7 - - - +
106C VAL* 3.4 9.2 - - - +
107C VAL* 2.9 47.3 + - + +
109C ILE* 5.8 0.4 - - + -
83D LEU* 5.2 0.4 - - - -
87D LEU* 4.6 3.4 - - - -
89D PHE* 4.3 1.1 - - - -
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Residues in contact with GLY 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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76C LEU* 3.4 4.5 - - - -
77C VAL* 2.8 38.3 + - - +
92C VAL* 1.3 78.9 - - - +
94C SER* 1.3 61.4 + - - -
102C TYR* 3.3 15.7 - - - -
105C ALA 3.8 4.7 - - - -
106C VAL* 4.7 0.7 - - - -
83D LEU* 4.9 0.4 - - - +
87D LEU* 3.4 16.0 - - - +
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Residues in contact with SER 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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26C GLN* 4.3 1.0 + - - -
67C VAL* 3.7 9.6 - - - +
74C SER* 3.9 10.9 - - - -
75C ASP 3.2 6.1 - - - -
76C LEU* 3.5 21.3 - - - -
92C VAL* 5.3 0.2 - - - -
93C GLY* 1.3 74.0 - - - -
95C GLU* 1.3 59.7 + - - +
96C ASP 4.2 0.2 - - - -
102C TYR* 3.1 24.2 + - - -
104C ASP* 3.2 14.4 + - - +
105C ALA* 2.8 39.5 + - - +
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Residues in contact with GLU 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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74C SER* 3.3 4.7 - - - -
75C ASP* 2.9 32.5 + - + +
94C SER* 1.3 73.9 - - - +
96C ASP* 1.3 59.9 + - - +
97C GLY* 2.7 39.7 + - - +
99C ASP* 3.1 8.9 - - - +
100C ASN* 3.6 21.3 - - - +
101C ASP 2.9 21.3 + - - -
102C TYR* 3.0 32.6 + - + +
104C ASP* 3.3 0.6 - - - +
116C CA 2.4 30.7 - - - -
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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