Contacts of the strand formed by residues 69 - 76 (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 SER 69 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B PHE* 5.9 0.2 - - - -
25B THR 3.2 13.2 - - - -
26B THR* 4.2 1.1 - - - -
27B ALA* 3.7 3.8 - - - +
68B LYS* 1.3 78.3 - - - +
70B ILE* 1.3 71.1 + - - +
173B ILE* 3.7 3.6 - - - +
174B THR* 2.6 52.3 + - - +
176B ILE 2.6 18.4 + - - -
178B PHE* 3.4 28.4 - - - -
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Residues in contact with ILE 70 (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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24B PHE* 3.7 2.9 - - - +
25B THR* 2.6 44.6 + - + +
26B THR 3.6 12.3 - - - +
27B ALA* 4.5 0.7 - - - -
30B PHE* 4.1 16.4 - - + -
60B PRO* 3.7 34.3 - - + -
69B SER* 1.3 80.4 - - - +
71B VAL* 1.3 66.6 + - - +
72B ALA 3.7 0.7 + - - -
138B LEU* 4.3 7.4 - - + -
143B VAL* 3.6 31.2 - - + -
171B GLU* 3.8 17.9 - - + -
172B MET 3.6 11.7 - - - +
173B ILE* 4.3 11.4 - - + +
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Residues in contact with VAL 71 (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* 4.1 11.4 - - + -
22B ILE* 3.6 31.2 - - + -
23B GLY 3.4 8.5 - - - +
24B PHE* 3.8 23.3 - - + -
70B ILE* 1.3 74.3 - - - +
72B ALA* 1.3 61.4 + - - +
73B ILE* 3.9 7.2 + - + +
113B LEU* 5.3 0.6 - - + +
116B LEU* 5.3 2.0 - - + -
171B GLU* 3.2 6.9 - - - -
172B MET* 2.9 53.4 + - + +
174B THR* 4.5 9.2 - - + -
178B PHE* 4.1 18.8 - - + -
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Residues in contact with ALA 72 (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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22B ILE* 3.2 4.9 - - - +
23B GLY 2.7 37.5 + - - +
70B ILE 3.7 1.8 + - - -
71B VAL* 1.3 71.7 - - - +
73B ILE* 1.3 62.8 + - - +
143B VAL* 4.0 16.8 - - + -
144B ALA* 4.3 7.4 - - + -
147B ALA* 3.8 18.8 - - + -
149B ILE* 3.6 23.1 - - + +
170B ALA 3.7 7.0 - - - +
171B GLU* 4.2 1.6 - - - -
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Residues in contact with ILE 73 (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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19B VAL* 3.9 31.0 - - + -
21B LYS 3.3 4.0 - - - -
22B ILE* 4.2 10.3 - - + -
71B VAL* 3.9 5.4 + - + +
72B ALA* 1.3 79.7 - - - +
74B ALA* 1.3 61.6 + - - +
75B LEU* 4.5 2.7 - - + -
109B LEU* 4.4 11.9 - - + +
112B LYS* 4.4 13.5 - - + -
113B LEU* 3.5 31.2 - - + +
116B LEU* 3.9 22.9 - - + -
149B ILE* 4.7 2.6 - - - +
168B TYR 3.9 0.2 - - - +
169B LEU* 3.5 5.2 - - - +
170B ALA* 3.0 52.0 + - + +
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Residues in contact with ALA 74 (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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19B VAL* 4.0 0.3 - - - +
20B ASP* 3.0 24.7 + - - +
21B LYS* 2.8 25.8 + - + +
73B ILE* 1.3 76.2 - - - +
75B LEU* 1.3 64.8 + - - +
76B ALA 4.3 0.4 - - - -
149B ILE* 3.9 26.2 - - + -
160B THR* 5.4 0.7 - - + -
163B TYR* 6.4 0.2 - - + -
167B VAL* 4.2 14.1 - - + -
168B TYR 3.2 11.0 - - - +
169B LEU* 3.9 7.6 - - + -
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Residues in contact with LEU 75 (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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18B GLY 3.6 13.5 - - - +
19B VAL* 3.9 25.1 - - + -
20B ASP* 3.2 3.6 - - - +
73B ILE* 4.5 6.5 - - + -
74B ALA* 1.3 80.4 - - - +
76B ALA* 1.3 63.0 + - - +
77B TYR 3.7 0.3 + - - -
108B VAL* 4.2 15.5 - - + -
109B LEU* 4.2 23.8 - - + -
112B LYS* 4.5 10.8 - - + -
167B VAL* 4.2 3.4 - - - -
168B TYR* 2.8 39.6 + - - +
258B HIS* 3.5 27.6 - - + +
261B MET* 3.9 20.6 - - + -
505B PO4 4.3 3.6 - - - +
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Residues in contact with ALA 76 (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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20B ASP* 2.7 16.5 + - - +
75B LEU* 1.3 73.5 - - - +
77B TYR* 1.3 61.3 + - - +
78B PRO* 4.6 0.5 - - - +
163B TYR* 3.6 43.7 - - + -
166B TYR 3.4 8.5 - - - +
167B VAL* 3.9 2.8 - - - +
255B PHE* 4.1 17.7 - - + +
257B LEU* 4.7 2.6 + - + +
258B HIS* 3.2 25.6 - - - -
261B MET* 3.6 1.6 - - - +
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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