Contacts of the helix formed by residues 125 - 128 (chain A) in PDB entry 4LQL
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 125 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A TYR* 5.3 4.8 - - - -
81A HIS 3.5 1.0 + - - -
82A THR* 3.1 46.1 - - - +
83A PHE* 3.9 10.5 - - - +
121A MET* 3.3 25.6 - - + +
122A ASN* 3.5 37.5 + - - +
123A LEU 3.9 2.7 - - - +
124A HIS* 1.3 72.2 - - - +
126A SER* 1.3 61.5 + - - +
127A ALA 3.2 3.1 - - - -
128A HIS* 3.1 51.0 + - + -
129A GLY 3.6 0.9 + - - -
333C TYR 4.0 9.0 - - - -
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Residues in contact with SER 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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79A TRP* 3.9 3.8 - - - -
80A MET 3.2 25.8 - - - -
81A HIS* 3.9 8.9 + - - -
82A THR 3.7 7.3 + - - -
104A ALA* 5.9 0.3 - - - +
105A THR 3.3 21.6 + - - -
106A GLN* 3.4 22.2 - - - +
124A HIS* 3.3 2.5 + - - -
125A GLN* 1.3 70.9 - - - +
127A ALA* 1.3 58.8 + - - +
128A HIS 2.9 11.2 + - - -
129A GLY 3.7 1.8 - - - +
130A ASP* 3.1 27.1 + - - +
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Residues in contact with ALA 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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106A GLN* 4.4 1.4 - - - +
125A GLN 3.2 0.8 - - - -
126A SER* 1.3 80.0 + - - +
128A HIS* 1.3 56.3 + - - +
131A ARG* 3.4 22.9 + - - -
332C ASP* 3.4 24.6 - - - +
333C TYR 4.6 1.6 - - - -
334C THR* 3.9 31.0 - - - +
335C LEU* 4.2 13.5 - - + -
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Residues in contact with HIS 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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83A PHE* 4.4 14.7 - + + +
121A MET* 3.4 29.6 - - + +
125A GLN* 3.1 35.2 + - + -
126A SER 2.9 0.4 - - - -
127A ALA* 1.3 80.1 - - - +
129A GLY* 1.3 58.2 + - - +
130A ASP 3.7 0.9 - - - -
131A ARG* 4.0 7.9 - - - -
132A GLU* 3.9 3.5 + - - +
331C GLU* 3.4 23.6 + - - -
332C ASP* 2.4 34.1 + - + +
333C TYR* 4.0 2.4 + - - -
446C HIS* 3.3 52.1 + + + +
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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