Contacts of the helix formed by residues 70 - 75 (chain A) in PDB entry 2C56
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 SER 70 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67A ASP* 2.9 14.5 + - - -
68A VAL 3.5 0.6 + - - -
69A PHE* 1.3 78.5 - - - +
71A TRP* 1.3 59.1 + - - +
73A ARG* 3.0 48.3 + - - +
74A TYR* 3.1 35.3 - - - -
97A HIS 2.8 23.8 + - - -
98A GLY* 3.3 12.6 - - - -
99A LEU* 4.0 0.3 + - - +
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Residues in contact with TRP 71 (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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32A TRP* 3.9 27.6 + + - -
36A MET* 4.0 14.6 - - + -
68A VAL 3.3 21.9 + - - -
69A PHE* 3.5 26.7 - + - +
70A SER* 1.3 81.1 + - - +
72A THR* 1.3 78.4 + - + +
73A ARG 3.2 0.2 - - - -
74A TYR* 4.1 7.3 + - - +
75A CYS* 4.0 12.0 + - - +
98A GLY 3.3 18.8 - - - +
99A LEU* 3.9 21.8 - - + -
144A LEU* 4.0 32.1 - - + +
145A LEU 4.5 3.8 - - - +
146A LEU* 3.4 34.9 - - + +
150A LEU* 4.2 12.2 - - + +
168A PHE* 5.0 3.1 - + - -
169A VAL* 5.5 2.5 - - + -
172A VAL* 4.3 17.9 - - + -
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Residues in contact with THR 72 (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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28A ILE* 3.6 10.4 - - + -
29A ASP* 3.2 33.5 + - - +
32A TRP* 3.1 37.2 + - + +
36A MET* 3.7 22.2 - - - -
69A PHE* 2.8 25.6 + - + +
71A TRP* 1.3 104.7 - - + +
73A ARG* 1.3 59.9 + - - +
75A CYS 3.3 5.7 - - - +
76A THR* 5.2 0.3 - - - -
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Residues in contact with ARG 73 (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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26A PHE 3.6 8.1 + - - -
27A LEU* 2.8 44.6 + - - +
29A ASP* 4.1 17.8 - - + +
66A GLU* 2.9 30.3 + - - +
67A ASP* 4.0 7.9 + - - -
69A PHE 4.0 8.5 + - - -
70A SER* 3.0 32.8 + - - +
72A THR* 1.3 87.2 - - - +
74A TYR* 1.3 67.3 + - + +
75A CYS* 3.3 4.1 + - - +
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Residues in contact with TYR 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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70A SER* 3.1 38.2 - - - -
71A TRP* 4.1 5.3 + - - +
73A ARG* 1.3 79.1 - - + +
75A CYS* 1.3 61.8 + - - +
79A GLU* 4.9 0.3 - - - +
97A HIS* 3.3 18.7 - - - -
99A LEU* 3.7 25.1 - - + -
136A GLU* 2.8 44.9 + - + -
139A ALA* 3.3 36.3 - - + +
140A ARG* 3.4 34.8 - - + +
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Residues in contact with CYS 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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32A TRP* 2.9 22.7 + - - -
71A TRP 4.0 5.7 + - - +
72A THR 3.3 8.8 - - - +
73A ARG 3.3 1.5 - - - -
74A TYR* 1.3 81.4 - - - +
76A THR* 1.3 71.7 + - - +
79A GLU* 3.5 20.9 - - + +
80A VAL* 4.1 14.8 - - - -
139A ALA* 3.4 19.5 - - - +
140A ARG 4.1 6.3 - - - +
142A GLY* 3.8 17.5 - - - +
143A VAL 5.5 2.7 - - - -
144A LEU* 5.6 4.0 - - - -
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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