Contacts of the strand formed by residues 124 - 129 (chain A) in PDB entry 2C9Y
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 SER 124 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A ARG 3.6 1.6 + - - +
18A ALA* 3.2 7.1 - - - -
19A VAL 3.0 22.9 + - - -
122A LEU* 3.5 3.5 - - - +
123A ASP* 1.3 87.5 - - - +
125A VAL* 1.4 68.6 + - - +
126A ILE* 3.5 13.4 - - - +
206A ILE* 3.7 8.4 + - - +
208A SER* 4.7 2.1 + - - -
226A ALA 4.7 1.6 + - - -
227A PHE* 3.4 37.3 - - - -
230A ALA* 4.1 12.9 - - - +
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Residues in contact with VAL 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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19A VAL* 3.5 15.3 - - + +
21A LEU* 3.6 34.8 - - + -
122A LEU* 4.1 2.9 - - + -
124A SER* 1.4 76.3 + - - +
126A ILE* 1.3 62.5 + - - +
127A GLU 3.8 0.5 + - - -
201A TYR* 3.5 54.3 - - + -
206A ILE* 2.8 28.2 + - + +
207A HIS* 3.4 6.6 - - + -
208A SER 2.9 28.8 + - - +
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Residues in contact with ILE 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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19A VAL 2.8 10.0 + - - +
20A LEU* 3.5 14.9 - - + -
21A LEU* 2.8 35.8 + - - +
124A SER* 3.5 15.7 - - - +
125A VAL* 1.3 71.4 - - - +
127A GLU* 1.3 56.3 + - - +
128A PHE* 3.9 18.3 - - + -
208A SER* 3.5 11.2 - - - +
210A ILE* 3.8 27.8 - - + -
223A ILE* 4.0 17.3 - - + -
226A ALA* 3.5 33.0 - - + -
227A PHE* 3.6 24.9 - - + -
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Residues in contact with GLU 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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21A LEU* 3.4 11.7 - - + +
125A VAL 3.8 1.0 + - - -
126A ILE* 1.3 71.8 - - - +
128A PHE* 1.3 65.2 + - - +
129A SER* 3.1 20.5 + - - -
190A TYR* 4.4 13.9 + - - +
194A THR* 5.6 0.2 - - + -
198A ILE* 3.5 29.0 - - + +
207A HIS* 2.8 38.6 + - + +
208A SER 3.0 9.6 + - - +
209A ALA* 3.5 12.0 - - - +
210A ILE* 2.8 31.8 + - - +
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Residues in contact with PHE 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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20A LEU* 4.1 17.9 - - + -
21A LEU 2.9 23.0 + - - +
22A GLY* 4.1 3.6 - - - -
23A PRO* 3.8 18.9 - - - +
26A ALA* 3.5 31.3 - - + +
27A GLY 3.6 19.1 - - - -
28A LYS* 3.7 28.5 - - + -
31A GLN* 3.9 17.0 - - + -
126A ILE* 3.9 20.9 - - + -
127A GLU* 1.3 73.3 - - - +
129A SER* 1.3 61.6 + - - +
130A ILE 3.8 1.6 + - - -
190A TYR* 4.6 0.9 + - - -
210A ILE* 4.1 7.2 - - + -
212A ALA* 3.9 16.4 - - + -
219A VAL* 4.3 4.7 - - + -
223A ILE* 3.8 21.1 - - + -
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Residues in contact with SER 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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127A GLU* 3.1 25.1 + - - -
128A PHE* 1.3 72.3 - - - +
130A ILE* 1.3 61.2 + - - +
209A ALA* 4.4 9.4 - - - -
210A ILE 3.0 18.7 + - - +
211A ASP* 3.7 6.7 - - - +
212A ALA 2.8 23.0 + - - -
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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