Contacts of the strand formed by residues 134 - 140 (chain C) in PDB entry 5A0Q
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 134 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74C CYS* 5.0 2.2 - - + -
75C SER 3.2 4.7 - - - +
76C VAL* 3.1 53.2 - - + -
86C LEU* 3.9 14.6 - - + -
90C LEU* 4.2 13.5 - - + -
114C LEU* 3.4 32.8 - - + -
118C LYS* 4.5 3.8 - - - +
132C VAL* 4.0 7.9 - - + +
133C SER* 1.3 78.1 - - - +
135C LEU* 1.3 67.5 + - - +
136C TYR* 3.9 9.9 - - + +
149C GLN* 3.3 9.9 - - - +
150C SER* 2.8 38.7 + - - -
164C ILE* 5.5 1.3 - - - -
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Residues in contact with LEU 135 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C CYS* 4.2 4.7 - - - -
35C LEU* 4.2 2.0 - - - -
36C GLY* 3.7 19.5 - - - +
45C LEU* 3.6 28.0 - - + -
74C CYS* 3.2 10.4 - - - +
75C SER* 3.0 35.2 + - - -
134C LEU* 1.3 82.0 - - - +
136C TYR* 1.3 66.0 + - - +
137C ILE* 4.0 1.6 - - + +
147C LEU* 4.2 8.1 - - + -
148C TYR 3.0 8.1 - - - +
149C GLN* 3.7 18.6 - - + -
162C THR* 3.4 29.4 - - + +
164C ILE* 4.1 25.8 - - + -
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Residues in contact with TYR 136 (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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68C LEU* 4.2 16.6 - - + -
73C ALA 3.5 5.6 - - - +
74C CYS* 4.3 2.0 - - + -
90C LEU* 3.9 27.4 - - + -
107C CYS* 4.4 15.0 - - - -
110C LEU* 5.3 1.8 - - + -
111C VAL* 2.9 53.6 + - + +
114C LEU* 3.3 31.0 - - - +
115C CYS* 4.4 0.3 - - - -
134C LEU* 3.9 6.9 - - + +
135C LEU* 1.3 80.0 - - - +
137C ILE* 1.3 62.2 + - - +
146C GLN 3.7 0.5 - - - +
147C LEU* 2.8 8.9 - - - +
148C TYR* 2.5 52.0 + - + +
150C SER* 3.8 27.7 + - - -
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Residues in contact with ILE 137 (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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43C VAL* 3.7 29.4 - - + +
44C LEU 3.9 10.1 - - - +
45C LEU* 3.8 27.4 - - + -
65C ILE* 4.3 3.1 - - + -
72C MET* 3.6 1.0 - - - -
73C ALA* 2.9 55.8 + - + +
74C CYS* 5.0 0.4 - - - +
75C SER 6.2 0.2 - - - +
107C CYS* 4.1 4.4 - - - -
135C LEU* 4.0 1.7 - - + -
136C TYR* 1.3 77.9 - - - +
138C GLY* 1.3 57.7 + - - +
146C GLN 3.7 3.8 - - - -
147C LEU* 4.0 11.7 - - + -
214C ALA* 3.8 25.4 - - + +
216C LEU* 3.9 18.4 - - + -
225C ILE* 5.3 1.1 - - + -
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Residues in contact with GLY 138 (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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43C VAL* 3.8 0.8 - - - +
71C ASP 3.5 7.4 - - - -
72C MET* 3.9 0.2 - - - -
107C CYS* 3.9 13.9 - - - -
137C ILE* 1.3 75.1 - - - +
139C TRP* 1.3 60.8 + - - -
140C ASP 4.0 1.3 - - - -
145C PHE* 3.3 9.9 - - - -
146C GLN* 2.9 31.9 + - - +
216C LEU* 3.2 16.6 - - - +
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Residues in contact with TRP 139 (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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71C ASP* 3.1 43.9 + - - +
72C MET* 4.4 2.8 - - - +
138C GLY* 1.3 73.5 - - - -
140C ASP* 1.3 64.7 + - - +
141C LYS* 3.5 20.5 + - + -
144C GLY* 2.9 22.3 - - - -
145C PHE* 2.8 60.3 - + + -
218C ARG* 2.9 51.6 - - - +
223C THR* 3.5 12.8 - - + -
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Residues in contact with ASP 140 (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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72C MET* 4.1 10.4 - - - +
106C PRO* 3.7 18.6 - - + +
107C CYS* 3.4 24.9 + - - +
108C GLU* 4.5 2.4 + - - +
138C GLY 4.0 1.2 - - - -
139C TRP* 1.3 79.0 - - - +
141C LYS* 1.3 62.8 + - - +
142C HIS* 4.0 4.0 - - - +
143C TYR* 3.0 36.4 + - - +
144C GLY* 3.0 20.8 + - - +
146C GLN* 2.7 35.7 + - - +
73K TYR* 4.2 3.8 + - - -
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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