Contacts of the helix formed by residues 123 - 131 (chain A) in PDB entry 1XSC
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 123 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27A ASN* 5.1 10.5 - - - -
29A ILE 3.7 20.4 - - - -
30A GLU* 4.0 3.3 - - - +
31A PHE* 3.5 6.0 - - - -
122A LEU* 1.3 74.1 - - - +
124A LEU* 1.3 53.6 + - - -
125A GLU* 3.5 4.2 - - - +
126A GLU* 4.2 4.5 - - - +
127A ALA* 2.7 37.4 + - - +
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Residues in contact with LEU 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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27A ASN* 5.4 3.2 - - - +
29A ILE 4.9 0.4 + - - -
31A PHE* 3.9 12.7 - - + -
123A GLY* 1.3 70.7 - - - -
125A GLU* 1.3 59.9 + - - +
128A CYS* 2.8 58.9 + - - +
140A LEU* 3.4 33.7 - - + +
141A GLN* 3.3 38.8 - - + +
144A HIS* 4.2 19.2 - - + -
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Residues in contact with GLU 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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27A ASN* 4.0 21.4 + - - +
123A GLY* 5.1 2.5 - - - +
124A LEU* 1.3 82.6 - - - +
126A GLU* 1.3 94.9 + - + +
128A CYS* 3.5 5.8 - - - +
129A GLN* 2.8 26.5 + - - +
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Residues in contact with GLU 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 LEU* 3.1 37.9 - - + -
123A GLY 4.0 3.7 + - - +
124A LEU 3.3 0.2 - - - -
125A GLU* 1.3 108.7 - - + +
127A ALA* 1.3 59.5 + - - +
128A CYS 2.8 3.8 - - - -
129A GLN* 2.6 55.2 + - + +
130A LEU* 2.8 9.4 + - - +
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Residues in contact with ALA 127 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A PHE* 3.9 10.8 - - + -
33A LEU* 3.4 28.3 - - + +
122A LEU* 3.8 3.4 - - - +
123A GLY 2.7 24.7 + - - +
124A LEU* 3.9 2.5 - - - +
126A GLU* 1.3 76.7 - - - +
128A CYS* 1.3 56.1 + - - +
131A ALA* 2.9 31.0 + - - +
140A LEU* 3.6 26.5 - - + +
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Residues in contact with CYS 128 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124A LEU* 2.8 39.4 + - - +
125A GLU* 3.5 5.8 - - - +
127A ALA* 1.3 78.9 - - - +
129A GLN* 1.3 64.2 + - - +
130A LEU 3.3 0.4 - - - -
131A ALA* 3.4 6.6 - - - +
132A GLN* 3.5 1.0 + - - -
137A LYS* 3.2 73.5 - - + +
140A LEU* 4.5 1.1 - - - -
141A GLN* 4.4 4.7 - - - -
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Residues in contact with GLN 129 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122A LEU* 5.8 0.2 - - - -
125A GLU 2.8 13.7 + - - +
126A GLU* 2.6 53.7 + - + +
128A CYS* 1.3 73.5 - - - +
130A LEU* 1.3 83.3 + - + +
132A GLN* 3.3 24.1 + - - +
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Residues in contact with LEU 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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33A LEU* 4.3 2.0 - - + -
42A HIS* 4.8 0.9 - - - +
43A TRP* 3.0 64.3 + - + +
120A ARG* 4.2 10.8 - - - +
122A LEU* 3.1 50.9 - - + -
126A GLU 2.8 14.0 + - - +
127A ALA 4.4 1.8 - - - +
129A GLN* 1.3 92.6 - - + +
131A ALA* 1.3 56.7 + - - +
132A GLN* 2.4 32.8 + - - +
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Residues in contact with ALA 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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33A LEU* 4.6 3.1 - - + -
43A TRP 3.5 23.7 + - - +
127A ALA 2.9 23.3 + - - +
128A CYS 3.4 4.5 - - - -
130A LEU* 1.3 73.1 - - - +
132A GLN* 1.3 53.0 + - - +
133A PHE* 2.6 26.5 + - - +
136A MET* 3.5 22.4 - - + -
137A LYS* 2.8 14.2 - - - +
140A LEU* 3.9 8.5 - - + -
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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