Contacts of the strand formed by residues 73 - 77 (chain A) in PDB entry 4ERO
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 MET 73 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45A PHE* 3.5 31.9 - - + -
53A PHE* 4.6 8.1 - - + -
67A LEU* 3.4 26.7 - - + -
72A SER* 1.3 72.3 - - - +
74A ALA* 1.3 62.1 + - - +
75A HIS* 4.0 0.4 + - + -
84A LYS* 3.5 1.4 - - - -
85A MET* 2.7 52.2 + - + +
103A GLU* 3.8 44.2 - - + +
104A MET 3.7 7.4 - - - +
105A PRO 3.9 8.5 - - - -
106A CYS* 3.7 3.8 - - - -
111A ALA* 3.7 11.0 - - + -
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Residues in contact with ALA 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A MET* 1.3 78.1 - - - +
75A HIS* 1.3 62.6 + - - +
83A GLY 3.5 10.5 - - - +
84A LYS* 4.5 2.0 - - + +
103A GLU* 3.3 5.9 - - - +
104A MET* 2.7 36.8 + - + +
106A CYS* 3.6 24.7 - - + -
288A ILE* 3.7 25.5 - - + +
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Residues in contact with HIS 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A MET 5.6 0.2 - - - -
74A ALA* 1.3 77.1 - - - +
76A GLU* 1.3 61.7 + - - +
81A HIS* 4.0 7.0 + + - -
82A THR* 3.2 14.5 - - - +
83A GLY* 3.1 63.0 + - - +
84A LYS 4.3 0.8 + - - -
85A MET* 4.1 27.2 - - + +
91A GLN* 3.4 32.9 + - - +
101A HIS* 5.5 3.4 - - - +
102A ALA 3.3 11.7 - - - +
103A GLU* 4.4 10.8 - - + -
131A TYR* 5.0 3.0 + - - -
133A GLU* 3.4 21.3 + - - +
288A ILE* 3.8 2.6 - - - +
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Residues in contact with GLU 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A HIS* 1.3 75.7 + - - +
77A ASP* 1.3 66.2 + - - +
80A GLY* 5.5 2.1 - - - +
81A HIS 3.5 5.8 - - - -
82A THR* 3.4 21.8 - - + -
101A HIS* 3.2 4.6 - - - +
102A ALA 2.9 30.7 + - - -
131A TYR* 5.6 0.7 - - - -
284A TRP* 4.0 10.9 + - - -
285A LYS 4.5 0.5 - - - +
286A SER* 3.2 15.3 - - - -
287A LYS* 2.8 42.4 + - - +
288A ILE* 3.1 31.0 + - + +
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Residues in contact with ASP 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A GLU* 1.3 77.7 - - - +
78A PHE* 1.3 59.7 + - - +
79A CYS* 2.9 20.2 + - - +
80A GLY* 3.1 17.8 + - - -
81A HIS* 3.0 36.0 + - - +
99A ILE* 3.2 20.8 - - + +
100A LEU 3.3 13.2 - - - +
101A HIS* 3.7 7.0 - - + -
131A TYR* 3.1 35.1 + - - +
284A TRP* 3.4 17.0 + - - -
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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