Contacts of the helix formed by residues 77 - 81 (chain N) in PDB entry 2IAN
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 GLN 77 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43G ASP* 3.1 25.5 + - - +
44G VAL* 4.0 24.2 - - + +
14N GLU* 4.9 11.9 + - - +
15N GLY* 5.4 1.6 - - - +
57N ARG* 3.6 14.3 + - - +
75N SER* 2.8 22.3 + - - +
76N SER* 1.3 77.3 + - - +
78N THR* 1.3 63.3 + - - +
79N THR* 3.1 17.5 - - - +
80N ASP* 2.7 34.5 + - - +
106N ILE* 3.3 14.3 - - - +
166N LYS* 5.3 11.8 - - - +
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Residues in contact with THR 78 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14N GLU* 4.4 4.5 - - - +
77N GLN* 1.3 74.0 - - - +
79N THR* 1.3 64.5 + - - +
81N SER* 2.8 30.5 + - - -
106N ILE* 3.2 27.4 - - + +
107N ASN 4.1 2.7 - - - +
108N PRO* 3.9 27.4 - - + -
157N VAL* 4.3 16.5 - - + +
166N LYS* 4.0 26.7 - - + -
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Residues in contact with THR 79 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48G ARG* 5.3 12.0 + - - +
35N HIS* 4.4 5.2 + - - -
37N ASN* 5.8 0.3 - - - +
38N PRO* 5.2 4.5 - - - +
57N ARG* 5.2 1.2 + - - -
77N GLN* 3.7 15.8 - - - +
78N THR* 1.3 78.0 + - - +
80N ASP* 1.3 58.4 + - - -
81N SER 3.0 18.7 + - - +
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Residues in contact with ASP 80 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35N HIS* 3.2 3.2 - - - -
57N ARG* 2.4 49.6 + - - -
58N LEU* 6.0 1.8 - - - +
73N ILE* 3.6 11.1 - - + +
76N SER* 3.3 5.9 - - - -
77N GLN* 2.7 24.9 + - - +
79N THR* 1.3 74.4 + - - +
81N SER* 1.3 65.1 + - - +
84N TYR* 2.6 40.6 + - - +
104N LEU* 3.3 13.1 - - + +
106N ILE* 4.5 1.3 - - + -
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Residues in contact with SER 81 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35N HIS* 3.1 12.8 + - - -
38N PRO* 3.7 20.1 - - - +
77N GLN 4.0 0.2 + - - -
78N THR 2.8 22.0 + - - -
79N THR 3.0 6.3 - - - +
80N ASP* 1.3 81.4 - - - +
82N GLY* 1.3 58.3 + - - +
104N LEU* 3.5 15.7 - - - +
105N THR* 3.8 3.7 - - - +
106N ILE* 3.1 27.4 + - - +
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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