Contacts of the strand formed by residues 167 - 174 (chain C) in PDB entry 5D0A
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 VAL 167 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20C ASP* 6.1 0.2 - - + -
74C ALA* 4.1 13.9 - - + -
75C LEU 3.2 7.2 - - - +
76C ALA* 3.9 11.0 - - + +
77C TYR* 3.5 9.5 + - - -
157C MET* 5.5 0.2 - - - +
158C ILE* 4.1 8.3 - - + +
160C THR* 4.3 18.4 - - + +
163C TYR* 3.6 31.9 - - + -
164C GLY 4.4 1.6 - - - +
165C SER 2.8 11.6 + - - +
166C TYR* 1.3 80.6 - - - +
168C TYR* 1.3 60.9 + - - +
169C LEU* 4.0 14.6 - - + -
503C B12 3.4 36.6 + - - +
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Residues in contact with TYR 168 (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 ALA* 3.1 7.4 - - - -
75C LEU 2.7 35.7 + - - +
77C TYR* 3.5 39.7 - + + +
98C ARG 3.5 6.1 + - - -
99C ALA* 3.2 40.2 + - + -
101C TRP 4.1 10.6 + - - -
103C LYS 5.5 2.0 + - - -
105C TYR* 3.4 50.9 + + + -
109C LEU* 3.7 20.6 - - + +
167C VAL* 1.3 73.1 - - - +
169C LEU* 1.3 60.9 + - - +
261C MET* 3.7 30.7 - - + +
503C B12 3.7 9.0 - - + -
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Residues in contact with LEU 169 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C ILE 3.5 4.5 - - - +
74C ALA* 3.9 18.4 - - + -
109C LEU* 3.6 2.1 - - - +
133C VAL* 3.5 9.2 - - - +
140C ASP* 3.7 36.4 - - + +
141C ARG* 3.9 7.0 - - - -
144C ALA* 3.7 22.7 - - + -
149C ILE* 4.3 5.2 - - + -
158C ILE* 4.0 6.1 - - + -
167C VAL* 4.0 13.7 - - + -
168C TYR* 1.3 79.6 - - - +
170C ALA* 1.3 65.4 + - - +
503C B12 2.7 69.0 + - + +
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Residues in contact with ALA 170 (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 ALA* 3.5 2.8 - - - +
73C ILE* 2.8 40.3 + - + +
109C LEU* 3.5 18.8 - - + -
113C LEU* 4.0 10.5 - - + -
132C MET 3.6 14.1 - - - +
133C VAL* 3.7 11.4 - - + +
140C ASP* 5.0 0.4 - - - -
169C LEU* 1.3 78.8 - - - +
171C GLU* 1.3 75.6 + - - +
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Residues in contact with GLU 171 (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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70C ILE* 3.7 14.6 - - + -
71C VAL 3.1 13.5 - - - +
72C ALA* 4.1 0.4 - - - -
73C ILE 4.6 0.4 - - - +
113C LEU* 4.0 8.3 - - - +
130C LYS 4.2 0.3 - - - +
131C SER* 3.6 1.2 - - - -
132C MET* 3.1 48.5 + - + +
138C LEU* 3.7 31.0 - - + +
140C ASP* 2.6 46.5 - - - +
143C VAL* 3.9 13.4 - - + +
169C LEU* 5.1 0.3 - - - +
170C ALA* 1.3 94.2 + - - +
172C MET* 1.3 63.2 + - - +
173C ILE* 5.5 0.7 - - + +
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Residues in contact with MET 172 (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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10C LEU* 5.2 2.9 - - + -
70C ILE* 3.4 2.5 - - - -
71C VAL* 2.7 58.5 + - + +
113C LEU* 4.2 11.4 - - + +
116C LEU* 4.2 17.9 - - + -
117C GLU* 4.0 21.8 - - - -
120C LEU* 3.6 23.3 - - + -
129C THR* 4.0 22.0 - - - -
130C LYS 3.5 4.7 - - - +
131C SER* 3.3 21.5 - - - +
171C GLU* 1.3 75.4 - - - +
173C ILE* 1.3 70.9 + - - +
174C THR* 3.7 10.9 + - + +
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Residues in contact with ILE 173 (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 PRO* 4.0 12.1 - - + +
63C LEU* 4.0 38.6 - - + -
64C LEU* 3.5 14.9 - - + +
67C ALA* 3.5 29.8 - - + -
69C SER 3.6 10.1 - - - +
70C ILE* 4.3 11.7 - - + +
129C THR* 3.2 6.6 - - - -
130C LYS* 2.8 40.4 + - + +
132C MET* 4.3 7.9 - - + -
138C LEU* 4.0 22.9 - - + -
171C GLU* 5.6 0.9 - - + -
172C MET* 1.3 73.7 - - - +
174C THR* 1.3 63.9 + - - +
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Residues in contact with THR 174 (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 LEU* 3.8 6.1 - - - -
67C ALA* 3.5 1.6 - - - -
68C LYS 2.8 21.2 + - - -
69C SER* 2.8 37.4 + - - +
71C VAL* 4.3 9.4 - - + -
120C LEU* 4.1 13.2 - - + -
128C ARG 3.4 9.4 - - - -
129C THR* 4.1 4.0 - - + -
172C MET* 3.9 30.7 - - + +
173C ILE* 1.3 80.9 - - - +
175C ASN* 1.3 60.8 + - - +
176C ILE* 2.9 25.7 + - + +
178C PHE* 4.1 0.5 - - - -
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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