Contacts of the strand formed by residues 72 - 79 (chain B) in PDB entry 3E5X
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 GLU 72 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64B ASP* 2.4 36.1 - - + +
65B ILE 3.2 12.6 - - - +
66B ILE* 4.2 16.0 - - + +
67B PHE* 5.7 0.2 - - - -
70B GLY 3.5 5.7 + - - +
71B SER* 1.3 74.8 + - - +
73B LYS* 1.3 77.4 + - - +
95B TYR* 3.3 30.6 - - - -
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Residues in contact with LYS 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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142A ALA* 3.6 32.5 - - + +
145A ASN* 3.2 30.7 + - + +
146A THR* 3.2 31.4 - - - +
64B ASP* 3.0 8.3 - - - -
65B ILE* 2.7 40.0 + - + +
67B PHE* 4.5 2.9 - - + -
71B SER* 4.7 5.4 - - - -
72B GLU* 1.3 82.8 + - - +
74B LEU* 1.3 66.0 + - - +
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Residues in contact with LEU 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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141A VAL* 5.8 3.1 - - - +
142A ALA* 5.2 1.6 - - - +
16B PRO* 4.7 16.8 - - + -
62B LYS* 4.0 15.5 - - + +
63B LEU 3.9 0.2 - - - +
64B ASP* 3.4 17.9 + - - +
73B LYS* 1.3 78.5 - - - +
75B LEU* 1.3 76.0 + - - +
76B TYR* 3.7 26.0 - - - +
77B TYR* 3.8 24.0 - - + -
182B SER 5.2 0.2 - - - +
185B GLU* 3.7 50.8 - - + +
186B ILE* 4.7 5.6 - - + -
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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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138A ALA* 3.6 45.5 - - + +
139A ARG 5.3 0.2 - - - +
141A VAL* 5.9 1.3 - - + -
142A ALA* 4.4 2.9 - - + +
16B PRO* 3.5 13.3 - - - +
63B LEU* 2.8 27.8 + - + +
65B ILE* 3.8 29.8 - - + +
73B LYS 3.4 0.8 + - - -
74B LEU* 1.3 82.0 - - - +
76B TYR* 1.3 61.1 + - + +
92B ASN* 5.8 0.9 - - - +
94B ILE* 3.6 29.6 - - + -
137B TYR* 2.6 30.2 + - + +
504B 3C4 4.6 10.1 - - + -
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Residues in contact with TYR 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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134A VAL* 6.1 0.7 - - + -
16B PRO* 3.3 16.4 - - - +
19B PHE* 3.8 20.6 - + + -
61B ILE* 6.1 0.2 - - + -
62B LYS 3.8 0.3 - - - -
63B LEU* 2.9 47.4 + - + +
74B LEU* 3.7 13.1 - - - +
75B LEU* 1.3 83.4 - - + +
77B TYR* 1.3 72.0 + - - +
78B ALA* 3.9 18.4 - - + -
82B SER* 6.0 0.4 - - - -
83B LEU 3.7 3.3 + - - -
84B ILE* 3.4 22.4 - - + +
133B LYS* 4.4 13.9 - - + -
137B TYR* 3.5 20.2 - + - +
504B 3C4 2.5 48.5 + + - -
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Residues in contact with TYR 77 (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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16B PRO* 3.0 11.6 + - + -
17B ASP* 3.3 26.5 - - + +
18B ASN* 3.3 19.1 + - - -
19B PHE* 4.9 1.4 + - - -
60B LYS* 4.4 15.3 - - - -
61B ILE 3.4 2.9 - - - -
62B LYS* 3.4 36.2 - - + +
74B LEU* 3.8 24.7 - - + -
76B TYR* 1.3 83.5 - - - +
78B ALA* 1.3 61.2 + - - +
99B MET* 3.5 40.7 - - + +
181B LYS* 5.0 4.0 + - - -
182B SER* 4.7 12.9 + - - -
185B GLU* 3.2 18.7 + - - -
186B ILE* 6.5 0.4 - - + -
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Residues in contact with ALA 78 (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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17B ASP* 5.1 0.9 - - - -
18B ASN* 3.8 2.0 - - - -
19B PHE 6.0 0.2 - - - +
56B LEU* 3.1 11.9 - - + +
60B LYS* 3.3 7.8 - - - +
61B ILE* 2.8 44.7 + - + +
76B TYR* 3.9 19.3 - - + -
77B TYR* 1.3 77.7 - - - +
79B GLY* 1.3 57.8 + - - +
82B SER* 3.5 24.5 - - - -
84B ILE* 5.3 6.7 - - + -
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Residues in contact with GLY 79 (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 ASN* 2.9 19.8 + - - -
56B LEU* 3.5 13.4 - - - +
59B GLY 3.5 13.0 - - - -
60B LYS* 4.5 4.0 - - - -
78B ALA* 1.3 72.6 - - - +
80B GLY* 1.3 68.8 + - - -
81B ASN 3.2 0.3 + - - -
82B SER* 3.0 19.2 + - - -
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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