Contacts of the strand formed by residues 89 - 96 (chain C) in PDB entry 1X1O
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 GLU 89 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46C VAL* 3.8 17.8 - - + +
47C ILE 3.6 7.0 - - - -
48C LEU* 4.1 9.7 - - + +
77C LEU* 3.0 36.4 - - + +
78C VAL* 4.0 7.8 - - - +
87C GLY 3.2 4.6 + - - +
88C THR* 1.4 70.8 - - - +
90C VAL* 1.3 61.0 + - - +
91C ALA 3.4 0.4 - - - -
92C ARG* 2.9 41.5 + - - -
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Residues in contact with VAL 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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47C ILE* 3.0 25.6 + - + +
49C ALA* 4.2 18.8 - - + +
55C LEU* 3.2 46.2 - - + -
58C LEU* 3.3 17.9 - - + +
76C PRO* 3.7 1.0 - - - +
77C LEU* 2.6 27.7 + - - +
78C VAL* 3.4 14.0 + - + -
84C VAL* 4.8 7.9 - - + -
88C THR 3.0 11.4 + - - +
89C GLU* 1.3 73.0 - - - +
91C ALA* 1.3 57.0 + - + +
111C LEU* 4.7 0.7 - - + -
279C LEU* 4.7 2.0 - - + -
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Residues in contact with ALA 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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46C VAL* 3.4 5.5 - - - +
47C ILE* 2.8 38.5 + - + +
58C LEU* 4.3 5.2 - - + -
74C PHE* 3.5 33.9 - - + -
75C THR 3.2 13.9 - - - +
76C PRO* 3.7 4.5 - - + -
77C LEU* 3.8 4.9 - - - -
89C GLU 3.4 1.2 - - - -
90C VAL* 1.3 83.2 - - + +
92C ARG* 1.3 63.4 + - - +
93C VAL 4.4 0.2 - - - -
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Residues in contact with ARG 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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44C GLU* 3.3 32.3 + - + +
45C ALA 3.3 8.5 - - - +
46C VAL* 3.8 17.0 - - + +
73C ALA 3.6 1.7 - - - +
74C PHE* 4.8 1.3 - - - -
75C THR* 2.8 44.6 + - + +
77C LEU* 3.8 15.0 - - + -
89C GLU* 2.9 38.2 + - - -
91C ALA* 1.3 80.8 - - - +
93C VAL* 1.3 59.8 + - - +
94C ARG 4.3 0.2 + - - -
284C VAL* 4.8 14.8 - - - +
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Residues in contact with VAL 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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44C GLU* 3.3 4.9 - - - +
45C ALA* 2.8 54.8 + - + +
46C VAL* 5.6 0.2 - - - -
47C ILE* 5.8 4.2 - - + +
65C PHE* 4.5 18.6 - - + -
72C THR* 4.2 14.8 - - - -
73C ALA 3.1 14.1 - - - +
74C PHE* 4.4 13.2 - - + +
91C ALA 4.4 0.2 - - - -
92C ARG* 1.3 73.4 - - - +
94C ARG* 1.3 63.7 + - - +
100C ILE* 3.8 31.7 - - + +
281C LEU* 4.7 7.9 - - + -
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Residues in contact with ARG 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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42C GLU* 5.7 4.3 - - - +
43C GLY 3.6 4.5 - - - +
44C GLU* 3.2 44.3 + - + -
71C ARG 4.0 1.0 - - - +
72C THR* 3.5 2.0 - - - -
73C ALA* 2.7 50.9 + - + +
92C ARG 5.6 0.2 - - - +
93C VAL* 1.3 75.3 - - - +
95C GLY* 1.3 60.6 + - - +
100C ILE* 4.4 3.4 - - - -
285C ARG* 3.5 17.3 - - - +
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Residues in contact with GLY 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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42C GLU* 3.4 21.4 + - - -
43C GLY 2.9 27.5 + - - +
71C ARG 4.3 3.8 - - - -
72C THR* 4.7 1.6 - - - -
94C ARG* 1.3 77.4 - - - +
96C PRO* 1.3 79.3 - - - +
97C LEU* 2.9 1.0 + - - -
100C ILE* 3.8 4.4 - - - +
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Residues in contact with PRO 96 (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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39C GLU 5.3 7.6 - - - +
40C ASP 6.6 0.2 - - - -
41C LEU 4.0 2.5 - - - +
42C GLU* 3.5 16.5 - - + +
69C ASP* 3.6 19.1 - - - +
71C ARG* 3.7 55.0 - - + +
72C THR* 4.7 2.8 - - + +
95C GLY* 1.3 79.4 - - - +
97C LEU* 1.3 66.3 + - - +
98C ARG* 3.1 4.7 - - + +
99C GLY* 3.1 14.3 + - - +
100C ILE* 3.3 10.7 + - - +
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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