Contacts of the strand formed by residues 56 - 61 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B MSE 4.0 20.8 - - + +
68B GLU* 3.3 24.2 - - - +
46C GLU* 3.1 6.8 - - - +
47C TRP* 2.7 68.8 + - + +
48C ARG* 5.4 1.8 - - - -
52C GLU* 6.3 3.4 - - + -
54C VAL* 4.7 18.4 + - + +
55C TRP* 1.3 78.6 - - - +
57C SER* 1.3 62.5 + - - +
82C TYR* 5.8 3.0 - + - -
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Residues in contact with SER 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B GLN* 2.9 29.5 + - - +
68B GLU* 3.1 29.1 + - - +
44C LYS* 3.6 27.1 + - - -
45C ALA 3.1 13.5 - - - -
46C GLU* 3.8 8.5 - - - -
47C TRP* 3.5 4.9 - - - -
55C TRP 4.2 1.3 + - - -
56C HIS* 1.3 76.7 - - - +
58C LYS* 1.3 61.3 + - - +
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Residues in contact with LYS 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B GLN* 3.9 1.8 - - - -
29B PHE 5.5 1.1 - - - -
30B ASP* 6.2 0.9 - - - +
31B GLU 6.1 1.6 - - - +
33B GLU* 4.5 14.0 + - - -
66B SER* 2.6 37.5 + - - +
67B MSE 3.7 6.5 - - - +
68B GLU 3.8 12.3 - - - +
69B GLY* 4.1 12.1 - - - +
44C LYS* 3.4 2.4 - - - -
45C ALA 2.9 31.6 + - - -
47C TRP* 3.5 9.6 - - + -
57C SER* 1.3 77.1 - - - +
59C TRP* 1.3 75.0 + - - +
60C TYR* 3.2 39.3 - - + +
72C THR 4.8 3.9 + - - +
74C VAL* 4.3 11.9 - - + +
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Residues in contact with TRP 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B ASP* 3.3 38.8 - - + +
17B GLN* 2.9 39.5 + - + +
28B GLN* 3.5 33.4 - - + +
29B PHE 4.0 8.4 + - - +
30B ASP* 3.4 15.9 - - - +
68B GLU 4.6 1.4 + - - -
42C LYS* 3.7 15.9 - - + -
43C TYR 3.4 18.6 - - - -
44C LYS* 3.6 27.2 - - + +
58C LYS* 1.3 87.4 - - - +
60C TYR* 1.3 69.7 + - - +
89C LEU* 3.7 35.2 - - + -
94C LEU* 4.0 23.8 - - + -
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Residues in contact with TYR 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B ASP* 4.0 6.3 - - - -
33B GLU* 4.1 16.6 - - + -
42C LYS* 3.3 6.2 - - - +
43C TYR* 2.7 46.2 + - + +
45C ALA* 3.6 19.4 - - + +
47C TRP* 4.5 0.3 - - - -
58C LYS* 3.2 51.3 - - + +
59C TRP* 1.3 77.5 - - - +
61C ASP* 1.3 65.7 + - - +
65C ALA* 4.9 1.8 - - + -
70C ILE 5.6 0.2 - - - -
71C VAL* 3.5 42.0 - - + -
72C THR 2.8 33.6 + - - -
73C ILE* 3.9 12.1 - - - +
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Residues in contact with ASP 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B ASP* 3.3 22.4 - - - +
32B PRO* 6.2 1.6 - - + -
41C LEU 3.8 2.8 - - - +
42C LYS* 2.8 30.2 + - - -
60C TYR* 1.3 73.0 - - - +
62C ALA* 1.3 60.9 + - - +
63C LYS* 3.2 29.5 - - - +
64C GLU* 3.3 24.9 + - + +
65C ALA* 3.0 27.8 + - - +
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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