Contacts of the strand formed by residues 78 - 83 (chain C) in PDB entry 3EVS
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 ARG 78 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C MET* 3.8 28.5 - - + -
44C ILE 3.2 8.1 - - - +
45C GLU* 4.1 19.7 + - + +
70C ASP* 4.1 15.0 - - - +
71C THR* 4.3 16.3 + - - +
73C ILE* 3.1 37.4 - - + +
76C GLN* 4.0 23.7 + - + +
77C ARG* 1.3 76.5 - - - +
79C SER* 1.3 68.7 + - - +
80C ILE* 5.6 4.7 - - - +
97C LEU* 4.3 0.2 - - - -
98C PRO* 3.7 17.9 - - - +
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Residues in contact with SER 79 (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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43C MET* 3.2 5.2 - - - +
44C ILE* 2.8 36.0 + - - +
70C ASP* 2.9 22.7 + - - -
78C ARG* 1.3 78.4 - - - +
80C ILE* 1.3 63.3 + - - +
81C GLU* 4.9 3.8 + - - +
95C PRO* 3.7 12.5 - - - +
96C THR 3.1 32.3 + - - -
98C PRO* 4.4 3.6 - - - -
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Residues in contact with ILE 80 (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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41C PHE* 3.9 31.2 - - + -
42C THR 3.5 11.7 - - - +
43C MET* 4.1 18.2 - - + -
59C LEU* 4.2 13.0 - - + -
67C GLN* 3.2 30.7 - - + +
68C CYS 4.4 6.3 - - - +
69C ARG* 3.9 12.4 - - - +
70C ASP* 2.8 22.9 + - - +
78C ARG* 5.6 4.5 - - + -
79C SER* 1.3 76.1 + - - +
81C GLU* 1.3 78.1 + - - +
82C CYS* 4.8 0.9 - - - -
95C PRO* 4.7 0.4 - - - -
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Residues in contact with GLU 81 (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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41C PHE* 3.1 6.2 - - - +
42C THR 3.0 31.9 + - - +
68C CYS 5.3 2.7 - - - -
79C SER* 4.9 3.4 + - - +
80C ILE* 1.3 80.7 - - - +
82C CYS* 1.3 66.2 + - - +
93C LEU* 3.4 29.8 - - + +
94C HIS 4.1 12.5 + - - +
95C PRO* 3.3 28.7 - - + +
96C THR 4.6 1.4 + - - -
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Residues in contact with CYS 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C TYR* 4.0 12.6 - - + -
40C CYS 3.1 8.3 - - - +
41C PHE* 4.1 6.1 - - - -
59C LEU* 3.7 15.9 - - - -
68C CYS* 2.0 59.5 + - + +
80C ILE* 4.8 2.2 - - - -
81C GLU* 1.3 80.8 - - - +
83C CYS* 1.3 64.2 + - - +
93C LEU* 4.0 7.6 - - - +
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Residues in contact with CYS 83 (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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17C LEU* 3.9 1.0 - - - +
39C TYR* 3.7 2.6 - - - -
40C CYS* 2.9 35.8 + - - -
82C CYS* 1.3 77.4 - - - +
84C THR* 1.3 66.4 + - - +
85C GLU* 3.0 26.5 - - - +
89C CYS* 2.1 58.7 - - - -
90C ASN* 3.3 10.8 - - - -
93C LEU* 3.8 11.2 - - + -
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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