Contacts of the helix formed by residues 127 - 132 (chain A) in PDB entry 1XAH
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 LEU 127 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125A THR* 3.3 4.6 - - - +
126A ILE* 1.3 77.2 - - - +
128A ALA* 1.3 57.8 + - - +
129A HIS* 3.1 6.2 + - - -
130A ASP* 3.4 11.0 + - - +
131A SER* 3.5 7.1 + - - +
171A GLN 5.5 0.4 + - - +
174A SER* 3.4 34.1 - - - +
175A GLY* 3.5 15.0 - - - +
178A GLU* 3.7 25.1 - - + -
256A HIS* 3.9 20.2 - - + -
257A GLY* 4.0 1.8 - - - +
400A NAD 3.7 61.5 - - + +
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Residues in contact with ALA 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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99A GLY 4.4 9.4 - - - -
100A GLY 5.0 0.4 - - - +
123A PRO* 3.4 27.0 - - + +
124A THR 4.3 0.4 - - - +
125A THR* 3.1 31.0 + - - +
126A ILE 3.0 1.6 - - - -
127A LEU* 1.3 73.9 - - - +
129A HIS* 1.3 62.1 + - - +
130A ASP 3.0 2.0 - - - -
131A SER* 3.2 16.4 - - - +
132A SER* 2.9 29.3 + - - +
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Residues in contact with HIS 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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126A ILE 2.8 25.6 + - - +
127A LEU 4.2 0.6 - - - -
128A ALA* 1.3 79.2 - - - +
130A ASP* 1.3 73.0 + - + +
132A SER* 4.5 0.7 - - - -
133A VAL* 3.6 22.0 - - - +
159A TYR* 3.4 30.5 + - + +
175A GLY 4.8 0.2 - - - -
178A GLU* 3.7 29.4 - - + -
179A VAL* 3.7 24.1 - - + +
182A HIS* 3.1 21.5 + + - -
214A ILE* 3.7 33.9 - - + -
217A GLY* 4.0 3.6 - - - -
218A ILE* 3.7 24.0 - - + +
221A LYS* 5.3 0.9 - - - +
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Residues in contact with ASP 130 (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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127A LEU 3.6 8.5 - - - +
128A ALA 3.0 0.2 - - - -
129A HIS* 1.3 100.8 + - + +
131A SER* 1.3 59.3 + - - +
133A VAL 3.0 12.0 + - - +
178A GLU* 3.4 20.9 - - + +
181A LYS* 3.9 5.5 + - - -
182A HIS* 3.9 15.6 + - + -
221A LYS* 2.7 63.3 + - - +
238A LEU* 5.3 0.9 - - - +
400A NAD 3.3 24.3 - - - -
600A ZN 3.6 2.3 - - - -
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Residues in contact with SER 131 (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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100A GLY* 3.3 23.4 - - - -
104A ASP* 4.6 4.0 - - - +
121A GLN* 4.2 6.0 + - - -
127A LEU 3.5 3.1 + - - -
128A ALA* 3.2 22.7 - - - +
130A ASP* 1.3 75.5 - - - +
132A SER* 1.3 58.7 + - - +
133A VAL 3.1 9.8 + - - +
135A GLY 5.4 1.9 + - - -
136A LYS 4.4 4.7 + - - +
400A NAD 3.6 54.4 + - - +
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Residues in contact with SER 132 (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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121A GLN* 3.6 31.5 + - - +
123A PRO* 3.7 18.8 - - - +
128A ALA* 2.9 22.8 + - - -
129A HIS* 4.3 1.9 + - - -
131A SER* 1.3 78.6 + - - +
133A VAL* 1.3 64.1 + - - +
134A GLY 4.2 0.5 + - - -
135A GLY 5.1 1.5 + - - -
154A PRO* 4.3 6.8 - - - +
157A VAL* 3.4 41.7 - - - +
159A TYR* 5.5 1.0 - - - -
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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