Contacts of the strand formed by residues 60 - 67 (chain B) in PDB entry 2E9S
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 ARG 60 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148A LEU* 3.7 8.3 - - - -
14B PHE* 4.3 15.3 - - - -
56B TYR* 3.1 8.4 - - - -
57B LEU 2.9 38.2 + - - +
58B GLU 3.7 7.4 - - - +
59B ASP* 1.3 80.2 - - - +
61B THR* 1.3 87.4 + - - +
62B VAL* 3.5 18.2 - - + +
175B LEU* 3.5 32.1 - - + +
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Residues in contact with THR 61 (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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105A SER* 3.6 36.1 - - - +
108A ILE* 4.9 4.3 - - + -
109A ASP* 3.5 27.8 + - + +
112A ARG* 6.1 0.3 - - - +
148A LEU* 4.3 17.9 - - + -
54B THR* 3.9 12.6 - - - -
55B MET 3.3 6.5 - - - +
56B TYR* 4.9 0.7 - - - -
60B ARG* 1.3 99.6 + - - +
62B VAL* 1.3 63.2 + - - +
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Residues in contact with VAL 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B PHE* 4.1 15.3 - - + -
53B LYS 3.7 0.2 - - - +
54B THR* 3.3 2.9 - - - -
55B MET* 2.8 69.7 + - + +
57B LEU* 4.8 7.9 - - + -
60B ARG* 3.5 28.3 - - + +
61B THR* 1.3 81.6 - - - +
63B ARG* 1.3 62.9 + - - +
64B LEU* 3.6 11.8 + - + +
171B ALA* 4.6 5.4 - - + -
175B LEU* 4.1 20.2 - - + -
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Residues in contact with ARG 63 (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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109A ASP* 2.7 29.0 + - - +
110A ASP* 5.1 4.8 + - - -
113A THR* 2.9 38.4 + - - +
13B LYS* 5.9 0.2 - - - +
14B PHE* 3.3 27.3 + - + +
52B SER* 6.3 2.0 - - - -
53B LYS 3.9 4.9 - - - -
54B THR* 3.9 12.3 - - - +
60B ARG* 5.7 0.2 - - - +
62B VAL* 1.3 72.2 - - - +
64B LEU* 1.3 62.8 + - - +
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Residues in contact with LEU 64 (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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14B PHE* 3.6 27.6 - - + +
16B LEU* 4.4 13.2 - - + -
33B PHE* 4.0 25.4 - - + -
51B LEU 3.8 0.2 - - - +
52B SER* 3.2 7.3 - - - -
53B LYS 2.9 39.9 + - - +
55B MET* 3.5 30.5 - - + -
62B VAL* 4.0 19.3 - - + +
63B ARG* 1.3 73.1 - - - +
65B GLN* 1.3 60.1 + - - +
66B LEU* 4.1 12.6 + - + +
167B PHE* 4.2 14.6 - - + +
171B ALA* 4.5 7.2 - - + -
174B LEU* 5.2 0.2 - - + -
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Residues in contact with GLN 65 (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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14B PHE 2.9 13.8 + - - +
15B LYS* 3.4 33.0 + - + +
16B LEU* 2.8 27.4 + - - +
50B PHE* 3.3 39.1 - - + +
51B LEU 3.3 10.8 - - - +
52B SER* 4.5 3.1 - - - +
63B ARG 4.1 0.4 + - - -
64B LEU* 1.3 74.6 - - - +
66B LEU* 1.3 68.0 + - - +
67B TRP* 3.1 41.2 - - - +
85B ASP* 4.5 0.5 + - - +
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Residues in contact with LEU 66 (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 LEU* 3.5 18.8 - - + +
18B PHE* 4.7 2.5 - - + -
30B ILE* 3.8 34.3 - - + +
33B PHE* 4.0 17.9 - - + -
34B MET* 4.0 22.2 - - + -
49B ASP 4.1 3.3 - - - +
51B LEU* 2.7 45.6 + - + +
53B LYS* 5.6 0.7 - - + +
64B LEU* 4.2 17.5 - - + +
65B GLN* 1.3 82.0 + - - +
67B TRP* 1.3 64.3 + - - +
68B ASP 4.1 0.2 - - - -
167B PHE* 3.8 25.8 - - + -
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Residues in contact with TRP 67 (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 LYS* 4.7 8.1 - - + +
16B LEU 2.7 16.6 + - - +
17B VAL* 3.9 7.5 - - + +
18B PHE* 2.9 33.3 + - - +
30B ILE* 4.3 2.9 - - - -
49B ASP* 4.1 31.4 - - + -
50B PHE* 5.4 3.6 - + + -
65B GLN* 3.1 34.0 - - + +
66B LEU* 1.3 73.9 - - - +
68B ASP* 1.3 62.3 + - - +
69B THR* 4.9 0.2 - - - -
82B TYR* 3.8 41.5 - + + -
85B ASP* 2.9 29.2 + - + +
86B SER* 3.6 21.1 - - - -
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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