Contacts of the helix formed by residues 124 - 129 (chain A) in PDB entry 1N78
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 GLY 124 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103A TYR* 3.5 10.8 - - - -
122A TYR* 3.2 27.1 + - - -
123A ASP* 1.3 78.6 + - - +
125A ARG* 1.3 63.1 + - - +
126A ALA 3.2 3.4 - - - -
127A ARG* 3.1 27.8 + - - +
128A ASN* 4.6 1.6 + - - -
175A ASP* 4.2 9.0 - - - -
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Residues in contact with ARG 125 (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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107A GLU* 3.3 20.9 - - - +
111A GLU* 3.0 24.9 + - - +
115A ILE* 3.6 29.9 - - - +
119A LYS* 2.8 20.8 - - - +
122A TYR* 3.5 3.1 + - + +
123A ASP* 2.7 36.8 + - - +
124A GLY* 1.3 76.3 - - - +
126A ALA* 1.3 61.0 + - - +
127A ARG 3.0 5.4 + - - -
128A ASN* 3.1 31.2 + - - +
129A ILE* 5.0 0.9 - - - +
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Residues in contact with ALA 126 (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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103A TYR* 3.6 14.6 - - + +
104A ARG 3.7 5.1 - - - +
105A ALA* 3.6 28.0 - - + -
107A GLU* 3.7 6.1 - - - +
122A TYR* 3.0 22.5 + - - +
124A GLY 3.2 0.8 - - - -
125A ARG* 1.3 72.1 - - - +
127A ARG* 1.3 59.9 + - - +
128A ASN 3.0 6.1 - - - -
129A ILE* 3.2 35.5 + - + +
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Residues in contact with ARG 127 (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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103A TYR* 3.2 34.5 - - + -
124A GLY* 3.1 19.6 + - - +
125A ARG 3.0 1.6 + - - -
126A ALA* 1.3 77.3 - - - +
128A ASN* 1.3 63.3 + - - +
129A ILE 3.2 7.1 + - - +
149A LYS* 2.9 42.3 + - - +
150A VAL 3.3 29.5 + - - +
151A PRO* 5.3 0.6 - - - +
152A ARG* 3.4 29.9 + - - +
175A ASP* 2.9 30.1 + - - -
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Residues in contact with ASN 128 (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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124A GLY 4.9 1.8 + - - -
125A ARG* 3.1 24.3 + - - +
126A ALA 3.0 1.2 - - - -
127A ARG* 1.3 82.1 - - - +
129A ILE* 1.3 62.6 + - - +
130A PRO* 3.6 7.3 - - - +
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Residues in contact with ILE 129 (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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104A ARG 4.5 1.1 - - - +
106A PHE* 4.0 22.2 - - + +
125A ARG 5.0 0.7 - - - +
126A ALA* 3.2 34.7 + - + +
127A ARG 4.0 6.1 - - - +
128A ASN* 1.3 78.9 - - - +
130A PRO* 1.3 83.7 - - + +
131A PRO* 3.2 7.4 - - - +
133A GLU* 3.9 14.8 - - + +
134A ALA* 3.9 24.5 - - + +
137A ARG* 3.9 20.6 - - - +
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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