Contacts of the helix formed by residues 114 - 120 (chain A) in PDB entry 2D7I
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 ASN 114 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A MET* 4.0 1.7 - - - +
102A GLU 2.8 22.5 - - - +
107A ALA* 3.3 19.8 - - - +
108A TYR* 3.2 19.9 + - - +
113A PHE* 1.3 69.6 - - - +
115A ILE* 1.3 57.3 + - - +
116A TYR* 2.8 22.0 - - - +
117A VAL* 2.9 26.2 - - + +
118A SER* 3.0 21.5 + - - -
271A HIS 2.8 22.4 + - - +
272A ASP 3.6 11.2 - - - +
274A PHE* 3.4 12.2 - - + -
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Residues in contact with ILE 115 (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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106A GLN 5.1 1.3 - - - +
107A ALA 3.0 16.6 + - - +
110A GLU* 4.8 15.0 - - + +
111A ASN* 3.7 29.8 - - - +
113A PHE* 3.0 11.9 + - + -
114A ASN* 1.3 70.1 - - - +
116A TYR* 1.3 87.5 - - + +
118A SER* 3.8 7.6 - - - +
119A ASP* 3.0 41.4 + - - +
157A GLY* 4.4 9.0 - - - -
158A TRP 4.9 1.3 - - - +
159A SER* 3.5 25.4 - - - +
160A SER* 4.3 7.0 - - - +
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Residues in contact with TYR 116 (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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101A ALA 3.7 19.3 - - - -
102A GLU* 4.1 15.3 - - + +
104A VAL* 3.4 20.1 - - + +
106A GLN* 3.5 22.4 - - - +
107A ALA* 3.5 25.6 - - + -
114A ASN* 2.8 10.1 - - - +
115A ILE* 1.3 94.1 - - + +
117A VAL* 1.3 61.9 + - - +
119A ASP* 3.6 8.2 + - - +
120A LYS* 3.2 29.6 + - - +
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Residues in contact with VAL 117 (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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96A TYR* 3.4 35.7 - - + -
98A MET* 4.0 6.1 - - - -
102A GLU* 3.8 21.1 - - + -
114A ASN* 2.9 35.6 - - + +
116A TYR* 1.3 74.4 - - - +
118A SER* 1.3 66.3 + - - +
120A LYS* 3.0 15.9 + - - +
121A ILE* 3.3 20.9 + - + +
272A ASP 3.3 17.3 - - - +
273A ASP 4.3 1.1 - - - -
274A PHE* 4.2 8.1 - - + -
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Residues in contact with SER 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A ASN 3.0 12.1 + - - -
115A ILE* 3.6 13.6 - - - +
116A TYR 3.4 0.2 - - - -
117A VAL* 1.3 76.9 - - - +
119A ASP* 1.3 62.4 + - - +
121A ILE* 3.1 18.0 + - - +
159A SER* 2.7 20.7 + - - -
160A SER* 3.5 7.9 + - - -
163A ARG* 2.5 41.3 + - - +
274A PHE* 3.5 25.2 - - - -
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Residues in contact with ASP 119 (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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115A ILE* 3.0 35.5 + - - +
116A TYR* 3.8 9.5 - - - +
117A VAL 3.2 0.2 - - - -
118A SER* 1.3 75.7 - - - +
120A LYS* 1.3 63.3 + - + +
121A ILE 3.2 4.9 + - - +
158A TRP* 5.6 1.7 - - - +
159A SER* 2.7 37.6 + - - -
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Residues in contact with LYS 120 (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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89A ASN* 4.4 9.0 + - - +
96A TYR* 3.6 35.5 + - + +
102A GLU* 2.9 29.1 + - - +
116A TYR* 3.2 18.9 + - - +
117A VAL* 3.0 8.8 + - - +
119A ASP* 1.3 78.3 - - + +
121A ILE* 1.3 59.0 + - - +
122A SER 4.3 0.2 + - - -
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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