Contacts of the strand formed by residues 167 - 174 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74B ALA* 4.2 13.2 - - + -
75B LEU 3.3 7.2 - - - +
76B ALA* 3.9 11.9 - - + +
77B TYR* 3.4 10.8 + - - -
158B ILE* 4.1 6.3 - - + +
160B THR* 4.3 21.3 - - + +
163B TYR* 3.7 28.7 - - + -
164B GLY 4.4 0.7 - - - +
165B SER 2.7 16.7 + - - +
166B TYR* 1.3 79.5 - - - +
168B TYR* 1.3 59.9 + - - +
169B LEU* 4.0 13.5 - - + -
503B B12 3.3 37.7 + - - +
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Residues in contact with TYR 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B ALA* 3.2 7.3 - - - +
75B LEU 2.8 35.3 + - - +
77B TYR* 3.4 42.6 - + + +
98B ARG 3.5 6.4 + - - -
99B ALA* 3.2 37.0 + - + -
101B TRP 4.2 10.6 + - - -
103B LYS 5.5 2.2 + - - -
105B TYR* 3.4 51.8 + + + -
109B LEU* 3.7 21.3 - - + +
167B VAL* 1.3 73.3 - - - +
169B LEU* 1.3 60.1 + - - +
261B MET* 3.9 30.0 - - + +
503B B12 3.7 9.9 - - + -
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Residues in contact with LEU 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B ILE 3.5 4.5 - - - +
74B ALA* 3.9 18.2 - - + -
109B LEU* 3.6 2.5 - - - +
133B VAL* 3.5 9.2 - - - +
140B ASP* 3.7 27.8 - - + +
141B ARG* 4.0 1.3 - - - -
144B ALA* 3.8 12.3 - - + -
149B ILE* 4.2 14.1 - - + -
158B ILE* 3.9 13.9 - - + -
167B VAL* 4.0 14.8 - - + -
168B TYR* 1.3 80.0 - - - +
170B ALA* 1.3 65.4 + - - +
171B GLU* 5.1 0.2 - - - +
503B B12 2.7 72.9 + - + +
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Residues in contact with ALA 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B ALA* 3.7 2.9 - - - +
73B ILE* 3.0 35.3 + - + +
109B LEU* 3.6 17.5 - - + -
113B LEU* 3.9 11.9 - - + -
132B MET 3.5 14.4 - - - +
133B VAL* 3.6 16.4 - - + +
140B ASP* 5.0 0.2 - - - -
169B LEU* 1.3 77.6 - - - +
171B GLU* 1.3 75.9 + - - +
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Residues in contact with GLU 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70B ILE* 3.8 3.4 - - + -
71B VAL 3.2 14.1 - - - +
113B LEU* 3.6 8.6 - - - +
130B LYS 4.2 0.5 - - - +
131B SER* 3.5 1.9 - - - -
132B MET* 3.0 46.9 + - + +
138B LEU* 3.8 28.7 - - + +
140B ASP* 2.6 45.8 - - - +
143B VAL* 3.8 25.6 - - + +
169B LEU* 5.1 0.2 - - - +
170B ALA* 1.3 93.7 + - - +
172B MET* 1.3 61.9 + - - +
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Residues in contact with MET 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B LEU* 5.1 2.2 - - + -
70B ILE* 4.1 1.8 - - - -
71B VAL* 2.9 48.5 + - + +
113B LEU* 4.1 13.0 - - + +
116B LEU* 4.0 23.3 - - + -
117B GLU* 4.0 19.7 - - - -
120B LEU* 3.7 25.6 - - + -
129B THR* 3.9 22.2 - - - -
130B LYS 3.5 4.0 - - - +
131B SER* 3.4 21.3 - - - +
171B GLU* 1.3 76.5 - - - +
173B ILE* 1.3 73.0 + - - +
174B THR* 3.5 12.5 + - + +
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Residues in contact with ILE 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B PRO* 4.0 11.0 - - + +
63B LEU* 3.9 29.8 - - + -
64B LEU* 3.7 13.9 - - + -
67B ALA* 3.5 29.2 - - + -
69B SER 3.7 9.0 - - - +
70B ILE* 4.4 12.3 - - + +
129B THR* 3.1 6.8 - - - -
130B LYS* 2.8 41.1 + - + +
132B MET* 4.2 9.2 - - + -
138B LEU* 3.9 30.3 - - + -
171B GLU* 5.7 0.4 - - + -
172B MET* 1.3 73.3 - - - +
174B THR* 1.3 63.6 + - - +
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Residues in contact with THR 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B LEU* 3.9 6.1 - - - -
67B ALA* 3.5 3.5 - - - -
68B LYS 2.8 21.1 + - - -
69B SER* 2.6 42.1 + - - +
71B VAL* 4.5 8.1 - - + -
120B LEU* 4.3 9.0 - - + -
128B ARG 3.4 9.4 - - - -
129B THR* 3.9 15.5 - - + -
172B MET* 3.5 24.7 + - + +
173B ILE* 1.3 81.0 - - - +
175B ASN* 1.3 58.9 + - - +
176B ILE* 3.1 24.3 + - + +
178B PHE* 4.2 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