Contacts of the strand formed by residues 122 - 126 (chain C) in PDB entry 2CX9
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 122 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C PHE* 3.4 36.6 - - + -
41C TRP* 4.0 11.0 - - + -
44C VAL* 3.9 19.1 - - + -
53C PHE* 3.9 22.0 - - + -
88C THR* 4.9 3.4 - - + -
92C HIS* 3.8 4.7 - - + +
116C LEU* 4.2 1.3 - - - -
119C GLY 3.8 17.7 - - - +
121C ALA* 1.3 75.8 - - - +
123C GLY* 1.3 60.8 + - - +
161C GLN* 4.2 14.6 - - + -
164C VAL* 3.5 27.9 + - + +
165C ALA* 3.4 2.4 - - - -
166C GLY 2.7 30.5 + - - +
167C VAL 2.9 8.6 + - - -
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Residues in contact with GLY 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91C SER 5.4 0.5 - - - +
92C HIS* 3.1 17.4 + - - -
96C ALA* 3.5 23.0 - - - +
116C LEU* 4.2 6.5 - - - -
122C LEU* 1.3 76.0 - - - +
124C ALA* 1.3 60.8 + - - -
125C TRP 4.5 0.2 + - - -
161C GLN* 3.1 29.2 - - - +
165C ALA* 4.5 0.2 - - - -
167C VAL 3.1 7.9 - - - -
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Residues in contact with ALA 124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96C ALA* 4.1 4.0 - - - +
123C GLY* 1.3 74.5 - - - -
125C TRP* 1.3 60.4 + - - +
126C GLY 3.9 0.7 - - - -
159C ILE* 3.9 11.9 - - + -
160C THR 3.7 10.1 - - - +
161C GLN 3.7 21.3 - - - +
162C GLY* 4.6 0.4 - - - +
165C ALA* 3.8 9.0 - - + -
167C VAL 3.0 5.7 + - - -
168C TYR* 3.6 19.4 - - + -
169C VAL* 2.9 29.1 + - - +
218C LEU* 5.0 0.2 - - + -
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Residues in contact with TRP 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95C LEU* 3.4 58.8 + - + +
96C ALA* 3.9 2.9 - - - +
99C HIS* 3.1 14.1 + - - +
123C GLY 4.5 0.2 + - - -
124C ALA* 1.3 73.1 - - - +
126C GLY* 1.3 58.8 + - - +
127C LEU* 3.3 41.8 + - + -
128C THR* 6.0 0.7 - - - -
159C ILE* 3.3 19.5 - - - +
160C THR 4.5 1.4 + - - -
169C VAL* 3.5 14.6 - - + -
171C MET* 3.0 28.7 - - + +
241C VAL* 3.8 28.3 - - + -
244C VAL* 4.2 14.6 - - + -
245C LEU* 3.5 31.4 - - + -
369C GLU* 5.8 0.7 - - + -
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Residues in contact with GLY 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124C ALA 3.9 1.4 - - - -
125C TRP* 1.3 69.5 - - - +
127C LEU* 1.3 57.9 + - - -
156C LYS* 2.9 35.5 + - - -
159C ILE* 3.7 16.1 - - - +
169C VAL 2.7 16.0 + - - -
170C VAL* 4.5 4.2 - - - +
171C MET* 3.0 21.7 + - - +
218C LEU* 5.2 1.7 - - - +
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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