Contacts of the strand formed by residues 56 - 61 (chain B) in PDB entry 2E3V
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 HIS 56 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A MSE 3.9 23.0 - - + +
68A GLU* 3.3 22.9 + - - +
46B GLU* 3.1 6.4 - - - +
47B TRP* 2.7 68.1 + + + +
52B GLU* 3.4 35.2 + - - -
54B VAL* 3.6 12.4 + - + +
55B TRP* 1.3 76.5 - - - +
57B SER* 1.3 61.1 + - - +
82B TYR* 5.7 1.6 - + - -
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Residues in contact with SER 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A GLN* 3.0 20.8 + - - +
68A GLU* 3.0 29.0 + - - +
44B LYS* 3.6 10.4 - - - -
45B ALA 3.1 14.1 - - - -
46B GLU* 4.0 1.3 - - - -
47B TRP* 3.6 5.2 - - - -
55B TRP 4.0 0.2 + - - -
56B HIS* 1.3 76.4 - - - +
58B LYS* 1.3 61.1 + - - +
1009B BTB 2.7 46.2 + - - -
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Residues in contact with LYS 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A GLN* 4.0 1.8 - - - -
33A GLU* 4.6 6.9 + - - -
66A SER* 2.6 31.7 + - - +
67A MSE 3.7 6.5 - - - +
68A GLU 3.7 12.6 - - - +
69A GLY* 4.0 3.8 - - - +
1004A PEG 2.6 47.1 + - - -
44B LYS* 3.5 2.6 - - - -
45B ALA 2.9 29.3 + - - -
47B TRP* 3.6 13.4 - - + -
57B SER* 1.3 78.2 - - - +
59B TRP* 1.3 73.1 + - - +
60B TYR* 3.3 36.0 + - + +
72B THR 4.8 3.2 + - - +
74B VAL* 4.3 10.1 - - + +
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Residues in contact with TRP 59 (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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16A ASP* 3.3 39.3 - - + +
17A GLN* 2.9 43.1 + - + +
28A GLN* 3.5 32.3 - - + +
29A PHE 4.0 8.5 + - - +
30A ASP* 3.4 15.7 - - - +
68A GLU 4.7 0.6 + - - -
1004A PEG 4.3 1.9 + - - -
42B LYS* 3.8 24.2 - - + -
43B TYR 3.4 18.2 - - - -
44B LYS* 3.5 28.1 - - + +
58B LYS* 1.3 86.0 - - - +
60B TYR* 1.3 68.5 + - - +
89B LEU* 4.1 26.5 - - + -
94B LEU* 4.0 23.6 - - + -
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Residues in contact with TYR 60 (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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30A ASP* 3.9 5.6 - - - -
33A GLU* 4.0 16.6 - - - -
42B LYS* 3.3 7.4 - - - +
43B TYR* 2.8 40.3 + - + +
45B ALA* 3.7 19.1 - - + -
47B TRP* 4.6 0.5 - - - -
58B LYS* 3.3 49.8 - - + +
59B TRP* 1.3 78.6 - - - +
61B ASP* 1.3 66.3 + - - +
64B GLU* 5.7 4.7 - - - +
65B ALA* 4.9 2.0 - - + -
70B ILE 5.5 0.4 - - - -
71B VAL* 3.4 41.3 - - + -
72B THR 2.6 35.5 + - - -
73B ILE* 3.6 12.3 - - - +
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Residues in contact with ASP 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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30A ASP* 3.4 22.1 - - - +
31A GLU 6.3 0.2 - - - -
32A PRO* 6.2 3.6 - - + -
41B LEU 3.8 2.4 - - - +
42B LYS* 3.1 26.9 + - - -
60B TYR* 1.3 73.8 - - - +
62B ALA* 1.3 66.5 + - - +
63B LYS* 3.2 14.3 + - - +
64B GLU* 3.2 39.2 + - + +
65B ALA* 3.0 22.4 + - - +
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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