Contacts of the strand formed by residues 68 - 75 (chain B) in PDB entry 2HEI
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 THR 68 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17B LYS 3.1 5.9 + - - -
18B ILE* 3.3 29.7 - - + +
19B CYS 3.1 25.3 + - - +
61B SER* 3.7 28.3 - - - +
62B VAL 3.5 7.4 - - - +
63B CYS* 3.8 22.0 - - - +
67B THR* 1.3 73.0 - - - +
69B VAL* 1.3 63.3 + - - +
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Residues in contact with VAL 69 (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 CYS* 3.3 4.7 - - + +
21B PHE* 3.5 35.4 - - + -
60B GLN 4.1 0.2 - - - +
61B SER* 3.1 4.0 - - - -
62B VAL* 2.8 42.9 + - + +
64B LEU* 3.7 30.3 - - + -
67B THR* 4.6 8.3 - - + +
68B THR* 1.3 75.1 - - - +
70B LYS* 1.3 61.2 + - - +
71B PHE* 4.0 15.8 + - + -
178B ALA* 3.9 29.2 - - + +
183B LYS* 5.9 1.1 - - + -
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Residues in contact with LYS 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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18B ILE* 4.1 27.1 - - + +
19B CYS 2.8 11.7 + - - +
20B GLN* 3.1 21.1 - - + +
21B PHE* 2.7 34.3 + - - +
59B THR* 3.3 33.9 - - + -
60B GLN 3.6 0.4 - - - +
61B SER* 3.4 21.3 - - - +
68B THR* 4.0 0.4 + - - -
69B VAL* 1.3 73.1 - - - +
71B PHE* 1.3 56.7 + - - +
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Residues in contact with PHE 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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21B PHE* 3.4 10.5 - - + -
23B LEU* 3.9 31.2 - - + -
40B PHE* 4.2 7.0 - + - -
58B LEU 3.6 1.2 - - - +
59B THR* 3.2 29.8 - - - +
60B GLN 2.8 21.4 + - - +
62B VAL* 4.0 15.9 - - + -
69B VAL* 4.0 10.8 - - + -
70B LYS* 1.3 76.2 - - - +
72B GLU* 1.3 58.8 + - - +
73B ILE* 3.8 20.8 + - + +
95B ALA* 4.9 0.9 - - + -
174B PHE* 3.6 39.0 - + + -
177B ILE* 4.1 4.7 - - + -
178B ALA* 3.9 20.9 - - + -
181B LEU* 3.6 24.2 - - + -
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Residues in contact with GLU 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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20B GLN* 3.7 23.4 + - + +
21B PHE 2.8 10.1 + - - +
22B LYS* 3.4 10.5 - - - +
23B LEU 2.9 26.5 + - - +
57B PHE* 3.4 46.3 - - + -
58B LEU 3.7 2.5 - - - -
59B THR* 4.2 8.2 + - + +
70B LYS 4.1 0.2 + - - -
71B PHE* 1.3 70.3 - - - +
73B ILE* 1.3 58.3 + - - +
74B TRP* 2.9 29.0 + - - +
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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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23B LEU* 3.3 9.6 - - + +
25B LEU* 3.2 34.3 - - + -
37B VAL* 3.8 20.0 - - + -
40B PHE* 3.6 35.0 - - + -
41B VAL* 4.1 15.9 - - + -
53B ILE* 4.1 3.6 - - - +
57B PHE* 3.2 6.6 - - - +
58B LEU 2.8 35.8 + - - +
60B GLN 4.9 1.1 - - - +
71B PHE* 3.8 18.4 - - + +
72B GLU* 1.3 76.2 - - - +
74B TRP* 1.3 62.7 + - - +
75B ASP 4.1 0.9 + - - -
174B PHE* 3.8 13.9 - - + -
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Residues in contact with TRP 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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22B LYS* 3.5 42.2 - - + +
23B LEU 2.8 11.8 + - - +
24B VAL* 3.5 7.1 - - + +
25B LEU* 2.9 31.4 + - - +
56B ALA 4.7 6.3 - - - +
57B PHE* 3.6 29.3 - + + -
72B GLU* 2.9 36.2 + - - +
73B ILE* 1.3 79.9 - - - +
75B ASP* 1.3 60.4 + - - +
88B MET* 4.0 36.1 - - + -
89B TYR* 3.7 37.5 - + + -
91B ARG* 5.9 3.1 - - - -
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Residues in contact with ASP 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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25B LEU* 4.5 5.5 - - - +
33B LYS* 3.5 18.6 - - - +
34B SER* 2.6 27.5 + - - -
37B VAL* 4.8 5.6 - - + -
52B THR* 4.3 0.2 - - - -
53B ILE* 3.4 46.5 + - + +
56B ALA 5.1 1.9 + - - +
73B ILE 4.1 1.8 + - - -
74B TRP* 1.3 75.1 - - - +
76B THR* 1.3 68.7 + - - +
77B ALA* 3.1 21.2 + - - +
79B GLN* 5.4 0.7 - - - +
89B TYR* 3.5 18.0 + - - -
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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