Contacts of the helix formed by residues 74 - 81 (chain A) in PDB entry 2YQM
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 ASP 74 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A GLN* 3.7 26.1 + - - +
55A THR 5.7 1.1 - - - +
56A CYS* 3.9 11.6 + - - -
59A ASN* 4.6 15.4 + - - +
72A VAL 4.3 0.2 + - - -
73A CYS* 1.3 72.8 - - - +
75A SER* 1.3 61.4 + - - +
77A HIS* 3.9 11.6 + - - +
78A THR* 2.7 47.6 + - - -
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Residues in contact with SER 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A GLN* 3.8 15.3 + - - -
48A CYS* 5.7 1.6 - - - -
52A PHE* 4.7 8.0 - - - -
73A CYS* 3.0 15.1 - - - -
74A ASP* 1.3 80.9 - - - +
76A CYS* 1.3 58.6 + - - +
79A LEU* 3.1 26.6 + - - +
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Residues in contact with CYS 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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47A ASN* 3.3 34.3 - - + +
48A CYS* 3.7 14.6 - - - -
72A VAL* 4.4 10.1 - - + -
73A CYS* 2.8 5.8 + - - +
75A SER* 1.3 82.9 - - - +
77A HIS* 1.3 57.0 + - - +
78A THR 3.5 0.2 - - - -
79A LEU* 4.2 6.7 - - - -
80A LEU* 2.8 46.9 + - + +
401A ZN 2.3 34.3 - - - -
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Residues in contact with HIS 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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59A ASN* 3.5 39.1 + - + +
60A GLU 3.7 23.8 + - - -
61A LEU* 3.8 19.5 - - + +
72A VAL* 4.2 7.9 - - + +
73A CYS 2.8 14.4 + - - +
74A ASP* 4.2 9.2 + - - -
76A CYS* 1.3 76.9 - - - +
78A THR* 1.3 64.8 + - - +
80A LEU* 3.4 5.4 + - - +
81A LEU* 2.9 55.9 + - + +
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Residues in contact with THR 78 (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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74A ASP* 2.7 37.7 + - - -
77A HIS* 1.3 79.0 + - - +
79A LEU* 1.3 57.7 + - - +
81A LEU* 3.1 13.1 + - + +
82A GLN* 2.8 40.8 + - + +
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Residues in contact with LEU 79 (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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47A ASN* 5.6 4.5 - - - +
75A SER 3.1 24.2 + - - +
76A CYS* 3.6 8.7 - - - +
77A HIS 3.2 0.4 - - - -
78A THR* 1.3 78.6 - - - +
80A LEU* 1.3 58.3 + - + +
82A GLN* 2.8 45.2 + - - +
83A ARG* 3.0 57.3 + - + +
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Residues in contact with LEU 80 (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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47A ASN* 4.1 12.3 - - - +
61A LEU* 3.3 34.3 - - + -
63A LEU* 3.9 31.0 - - + -
72A VAL* 5.5 2.7 - - + -
76A CYS* 2.8 43.6 + - + +
77A HIS 4.3 0.4 - - - +
79A LEU* 1.3 76.3 - - + +
81A LEU* 1.3 60.0 + - - +
82A GLN 3.6 0.2 + - - -
83A ARG* 3.6 33.3 + - - +
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Residues in contact with LEU 81 (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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61A LEU* 4.6 12.3 - - + -
77A HIS* 2.9 66.0 + - + +
78A THR* 3.2 13.0 - - + +
79A LEU 3.0 0.2 + - - -
80A LEU* 1.3 78.9 - - - +
82A GLN* 1.3 56.8 + - + +
83A ARG 3.4 5.0 + - - +
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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