Contacts of the strand formed by residues 14 - 21 (chain B) in PDB entry 2ERY
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 LYS 14 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13B GLU* 1.3 76.6 - - - +
15B TYR* 1.3 75.2 + - - +
16B ARG 5.2 0.2 - - - +
63B ARG* 3.2 24.0 - - + +
65B ASP* 2.9 30.7 - - - +
87B GLU* 3.7 11.5 - - - +
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Residues in contact with TYR 15 (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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13B GLU* 3.0 43.1 + - + +
14B LYS* 1.3 83.1 - - - +
16B ARG* 1.3 60.5 + - - +
17B LEU* 3.4 22.6 + - + +
60B ARG* 4.0 1.7 + - - -
62B ALA* 3.6 23.8 - - + -
63B ARG 2.9 12.7 + - - +
64B LEU* 3.7 3.3 - - + -
65B ASP* 2.9 25.7 + - - -
87B GLU* 3.4 6.7 - - - -
172B VAL* 3.8 23.8 - - + -
175B ILE* 3.6 39.9 - - + -
176B ARG* 3.2 21.2 + - + +
179B GLN* 4.5 9.4 + - - -
180B GLU* 4.5 2.3 + - - -
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Residues in contact with ARG 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B LYS* 5.2 0.4 - - + +
15B TYR* 1.3 70.3 - - - +
17B LEU* 1.3 64.4 + - - +
18B VAL* 4.1 11.1 - - - +
50B SER* 3.3 25.1 + - - -
51B TYR 5.1 0.2 + - - -
65B ASP* 2.9 44.1 + - + +
66B ILE 3.8 7.1 - - - +
67B LEU* 3.6 18.1 - - - +
80B GLU* 3.0 41.6 + - - +
85B THR* 4.0 19.7 - - - +
86B GLY* 3.7 2.2 - - - -
87B GLU* 2.7 47.8 + - - +
88B GLY 3.5 3.8 + - - -
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Residues in contact with LEU 17 (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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15B TYR* 4.0 13.9 - - + +
16B ARG* 1.3 78.0 - - - +
18B VAL* 1.3 64.8 + - - +
64B LEU* 3.8 24.0 - - + -
65B ASP 2.9 6.7 + - - +
66B ILE* 3.4 33.6 - - + -
67B LEU* 2.8 26.2 + - - +
88B GLY 3.5 4.3 - - - +
90B LEU* 6.0 0.2 - - + -
168B PHE* 4.0 16.8 - - + +
171B LEU* 3.7 22.9 - - + -
172B VAL* 4.3 7.6 - - + -
175B ILE* 3.3 33.4 - - + -
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Residues in contact with VAL 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B ARG* 4.1 9.9 - - - +
17B LEU* 1.3 81.7 - - - +
19B VAL* 1.3 64.9 + - - +
20B VAL* 3.8 9.4 + - + -
67B LEU* 3.7 6.5 - - + +
69B THR* 3.6 26.5 - - + -
82B TYR* 3.6 29.6 - - + +
86B GLY* 3.7 29.6 - - - -
88B GLY 3.0 5.8 + - - +
89B PHE* 3.2 19.3 - - + +
90B LEU* 2.9 26.1 + - - +
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Residues in contact with VAL 19 (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 LEU 5.5 0.2 - - - -
18B VAL* 1.3 72.3 - - - +
20B VAL* 1.3 56.2 + - - +
27B LYS* 3.8 33.7 - - + +
30B LEU* 5.5 2.5 - - + -
31B THR* 3.7 18.2 - - - +
66B ILE* 3.8 21.5 - - + -
67B LEU 2.9 9.6 + - - +
68B ASP* 4.5 2.7 - - - -
69B THR* 2.8 34.0 + - - +
90B LEU* 3.8 11.0 - - + -
92B VAL* 3.8 21.5 - - + -
168B PHE* 4.0 18.6 - - + -
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Residues in contact with VAL 20 (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 VAL* 3.8 20.0 - - + -
19B VAL* 1.3 79.7 - - - +
21B GLY* 1.3 59.7 + - - +
27B LYS* 3.6 5.4 - - - -
69B THR* 3.6 13.0 - - - +
82B TYR* 4.1 15.7 - - + +
83B MET* 5.1 3.6 - - + -
89B PHE* 4.4 9.2 - - + -
90B LEU 3.0 16.4 + - - +
91B LEU* 3.7 25.4 - - + -
92B VAL* 2.9 30.1 + - - +
107B PHE* 4.0 25.6 - - + -
111B ILE* 4.6 6.3 - - + -
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Residues in contact with GLY 21 (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 VAL* 1.3 79.0 - - - +
22B GLY* 1.3 70.2 + - - +
25B VAL* 4.4 0.9 - - - -
27B LYS* 3.1 16.8 + - - +
69B THR* 4.8 0.6 + - - -
92B VAL 3.4 15.3 - - - -
104B ILE* 5.5 0.2 - - - -
107B PHE* 3.4 29.0 - - - -
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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