Contacts of the helix formed by residues 126 - 131 (chain A) in PDB entry 2CLS
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 LYS 126 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A GLN* 2.6 30.5 + - - +
24A CYS 3.4 17.9 - - - +
93A ASP* 3.0 33.3 + - - +
94A ILE* 4.0 5.2 - - - +
96A ARG* 4.8 1.0 - - - +
125A CYS* 1.3 77.2 - - + +
127A THR* 1.3 64.1 + - - +
128A ASP* 3.1 6.3 - - - -
129A LEU* 3.0 32.8 + - + +
167A GLY 3.5 5.1 + - - -
168A SER* 4.5 0.2 - - - +
169A ALA 5.2 0.4 - - - +
500A GTP 3.1 73.7 + - + +
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Residues in contact with THR 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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94A ILE* 2.9 37.0 - - + -
124A GLY 4.5 0.2 - - - +
126A LYS* 1.3 75.5 - - - +
128A ASP* 1.3 62.5 + - - +
129A LEU 3.1 0.2 - - - -
130A ARG* 3.1 33.8 + - - +
166A GLU* 3.7 27.8 - - + +
167A GLY* 3.0 28.0 + - - +
168A SER* 3.6 5.7 - - - -
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Residues in contact with ASP 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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126A LYS 3.6 2.8 - - - -
127A THR* 1.3 80.6 + - - +
129A LEU* 1.3 65.8 + - - +
130A ARG 3.2 1.9 + - - -
131A THR* 3.7 15.0 + - - -
132A ASP* 3.9 7.3 + - - +
168A SER* 2.6 30.0 + - - +
170A PHE* 3.6 8.0 - - - -
171A THR* 3.8 24.7 - - + +
500A GTP 2.9 40.6 + - - -
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Residues in contact with LEU 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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94A ILE* 5.2 0.7 - - + -
95A SER* 3.5 35.9 - - - +
126A LYS* 3.0 28.3 + - + +
128A ASP* 1.3 79.3 - - - +
130A ARG* 1.3 64.2 + - - +
131A THR 3.2 1.8 - - - -
132A ASP* 3.2 37.4 + - + +
135A THR* 3.8 23.7 - - - +
146A PRO* 4.1 3.9 - - - +
500A GTP 3.6 30.5 - - - +
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Residues in contact with ARG 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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94A ILE* 3.3 20.7 - - + +
126A LYS 4.4 0.6 + - - -
127A THR* 3.1 28.1 + - - +
129A LEU* 1.3 77.6 - - - +
131A THR* 1.3 65.6 + - + +
132A ASP 3.5 0.2 - - - -
136A LEU* 3.8 21.1 - - - +
146A PRO* 4.0 19.8 - - + +
147A ILE 2.7 28.5 + - - -
148A SER* 3.6 8.2 - - - +
149A TYR* 3.6 17.2 - - - +
164A TYR* 4.2 0.2 + - - -
166A GLU* 3.0 41.4 + - - -
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Residues in contact with THR 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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127A THR 4.8 0.2 + - - -
128A ASP 3.7 9.0 + - - -
129A LEU 3.2 0.4 - - - -
130A ARG* 1.3 85.9 - - + +
132A ASP* 1.3 62.5 + - - +
133A LEU* 3.6 3.1 + - - +
136A LEU* 4.4 9.8 - - - +
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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