Contacts of the helix formed by residues 123 - 129 (chain A) in PDB entry 5AJO
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 HIS 123 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A THR 3.7 2.2 + - - -
122A ARG* 1.3 77.0 - - - +
124A ASP* 1.3 71.9 + - + +
125A GLN* 3.0 54.8 + - + +
126A CYS* 2.9 22.7 + - - +
127A GLN* 4.2 2.4 + - - -
297A PRO* 3.5 28.2 - - + +
298A VAL* 3.7 21.3 - - + -
353A PRO* 5.4 1.1 + - + -
356A ARG* 4.5 5.8 - - - +
1582A SO4 3.5 32.0 + - - +
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Residues in contact with ASP 124 (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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122A ARG 3.5 4.8 + - - +
123A HIS* 1.3 80.8 + - + +
125A GLN* 1.3 62.7 + - + +
126A CYS 3.2 0.9 + - - -
127A GLN* 3.2 37.9 + - - +
128A ARG* 4.1 7.9 - - - -
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Residues in contact with GLN 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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123A HIS* 3.0 31.9 + - + +
124A ASP* 1.3 77.1 - - + +
126A CYS* 1.3 60.3 + - - +
127A GLN 3.2 1.3 + - - -
128A ARG* 3.3 41.9 + - - +
129A LYS* 4.6 1.6 + - - +
296A ASN* 4.1 7.2 - - - +
297A PRO* 4.6 11.1 - - - +
298A VAL* 3.8 27.4 - - + +
354A CYS* 4.9 0.2 - - - -
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Residues in contact with CYS 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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122A ARG* 3.8 28.3 + - + +
123A HIS* 2.9 27.8 + - - +
125A GLN* 1.3 79.1 - - - +
127A GLN* 1.3 59.9 + - - +
128A ARG 3.2 1.1 + - - -
129A LYS* 3.8 17.3 + - - +
131A TRP* 4.9 4.5 - - - -
298A VAL* 3.6 11.2 - - - -
353A PRO 4.5 1.3 - - - -
354A CYS* 2.1 60.2 - - + +
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Residues in contact with GLN 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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120A ASP* 3.3 25.3 + - - -
122A ARG* 3.6 22.4 + - - +
123A HIS 5.0 2.8 + - - -
124A ASP* 3.2 35.2 + - - +
126A CYS* 1.3 76.4 - - - +
128A ARG* 1.3 59.9 + - + +
129A LYS 3.3 9.4 + - - +
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Residues in contact with ARG 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 ASP 4.1 15.0 - - - +
125A GLN* 3.3 30.2 + - - +
126A CYS 3.2 1.6 - - - -
127A GLN* 1.3 80.6 - - + +
129A LYS* 1.3 59.2 + - - +
130A GLN* 4.2 1.2 + - - +
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Residues in contact with LYS 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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125A GLN 5.2 1.6 - - - +
126A CYS* 3.9 14.9 - - - +
127A GLN 3.3 6.8 - - - +
128A ARG* 1.3 78.5 - - - +
130A GLN* 1.3 79.6 + - - +
131A TRP* 3.5 41.5 - - + +
239A GLU* 2.6 39.6 + - - -
354A CYS* 6.5 0.4 - - - -
1600A SO4 4.7 11.7 + - - -
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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