Contacts of the helix formed by residues 80 - 85 (chain C) in PDB entry 3I54
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 GLU 80 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47C LEU* 3.8 11.9 - - + -
77C MET* 3.7 32.7 - - + +
78C PHE* 3.2 5.5 - - - -
79C GLY* 1.3 77.4 + - - +
81C LEU* 1.3 86.5 + - + +
82C SER 3.3 0.2 - - - -
83C ILE* 3.0 3.5 + - - +
84C PHE* 2.9 51.3 + - + -
127C LEU* 3.8 7.2 - - + +
130C ARG* 3.0 27.1 + - - -
301C CMP 2.2 28.5 + - - -
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Residues in contact with LEU 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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80C GLU* 1.3 89.5 - - + +
82C SER* 1.3 54.1 + - - +
84C PHE* 3.4 1.9 + - + -
85C ASP* 2.7 40.8 + - - +
90C THR* 3.9 22.9 - - + +
127C LEU* 3.2 36.1 - - + -
301C CMP 3.2 41.0 + - + +
128D ALA* 3.9 26.6 - - + +
131D LEU* 4.3 23.6 - - + -
132D ARG* 4.5 4.7 - - - +
135D ASN* 4.9 0.4 - - - +
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Residues in contact with SER 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C GLY 2.9 19.6 + - - +
81C LEU* 1.3 77.4 - - - +
83C ILE* 1.3 57.2 + - - +
85C ASP 3.5 9.0 - - - -
86C PRO* 3.2 12.3 - - - +
87C GLY 3.4 22.6 + - - +
88C PRO 4.0 7.6 - - - -
89C ARG* 3.0 20.1 + - - -
106C ARG* 2.9 20.1 + - - -
301C CMP 3.0 11.0 + - - -
132D ARG* 3.7 10.1 - - - +
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Residues in contact with ILE 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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44C GLY 3.2 26.2 - - - +
45C ASP 3.5 16.6 - - - +
46C ARG 3.7 15.7 - - - -
47C LEU* 3.9 25.8 - - + +
79C GLY 3.8 7.4 - - - +
80C GLU 3.0 11.1 + - - +
82C SER* 1.3 76.6 - - - +
84C PHE* 1.3 62.9 + - - +
86C PRO* 3.6 4.2 - - - +
104C MET 4.8 0.7 - - - +
105C ASP 4.9 0.2 - - - +
106C ARG* 3.2 50.0 + - + +
109C LEU* 3.4 30.8 - - + +
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Residues in contact with PHE 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C LEU* 4.5 0.9 - - + -
77C MET* 4.5 2.2 - - + -
80C GLU* 2.9 48.7 + - + +
81C LEU* 4.0 4.5 - - - +
83C ILE* 1.3 76.2 - - + +
85C ASP* 1.3 58.3 + - - +
86C PRO* 3.5 5.7 - - - +
109C LEU* 3.3 39.3 - - + -
123C LEU* 3.7 33.7 - - + -
127C LEU* 3.7 32.1 - - + -
121D GLU* 4.8 4.5 - - - +
124D LEU* 4.0 37.0 - - + +
125D ARG* 3.7 22.7 + - - +
128D ALA* 4.2 2.5 - - + -
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Residues in contact with ASP 85 (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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81C LEU 2.7 21.9 + - - +
82C SER* 3.5 1.9 - - - -
84C PHE* 1.3 75.1 - - - +
86C PRO* 1.3 71.3 - - - +
87C GLY 3.1 2.9 + - - -
125D ARG* 3.5 6.3 + - - +
128D ALA* 3.6 14.4 - - + -
129D ARG* 2.9 61.2 + - - +
132D ARG* 2.4 37.6 + - - +
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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