Contacts of the helix formed by residues 159 - 165 (chain A) in PDB entry 2X5O
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 159 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72A PRO* 4.4 2.4 - - - +
110A THR* 4.1 2.0 - - - -
115A LYS* 4.3 3.8 - - - +
138A ASN* 4.1 19.7 + - - +
158A LEU* 1.3 77.1 - - - +
160A SER* 1.3 65.3 + - - +
161A PHE* 3.4 18.2 + - - +
162A GLN* 2.8 38.0 + - - +
163A LEU* 3.0 22.2 + - - +
198A KCX 3.4 11.2 - - - -
500A VSV 5.3 2.4 - - - -
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Residues in contact with SER 160 (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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159A SER* 1.3 72.8 - - - +
161A PHE* 1.3 72.8 + - - +
163A LEU* 3.2 8.1 + - - +
164A GLU* 3.1 26.3 + - - +
183A HIS* 4.5 0.2 - - - -
187A TYR* 2.8 31.6 + - - -
194A TYR* 3.7 23.6 - - - -
197A ALA* 3.7 14.6 - - - +
198A KCX 3.1 26.8 + - - -
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Residues in contact with PHE 161 (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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72A PRO* 3.5 27.2 - - + +
159A SER* 3.1 10.6 + - - +
160A SER* 1.3 79.3 - - - +
162A GLN* 1.3 66.9 + - - +
164A GLU* 3.2 26.0 + - - +
165A THR* 3.8 8.8 + - - +
183A HIS* 3.6 45.8 - + + -
186A ARG* 3.4 46.7 - - + +
187A TYR* 3.4 27.6 - + - -
500A VSV 3.5 31.9 - + - -
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Residues in contact with GLN 162 (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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16A THR* 6.0 1.2 - - - +
72A PRO* 4.0 22.2 - - + +
94A ASP* 3.9 12.5 + - - +
95A ILE* 3.7 38.6 - - + +
137A GLY 4.2 3.2 + - - -
138A ASN* 3.4 31.3 + - - +
157A GLU 3.8 0.3 - - - +
158A LEU* 3.3 12.8 - - + -
159A SER* 2.8 43.8 + - - +
161A PHE* 1.3 76.2 - - - +
163A LEU* 1.3 59.0 + - - +
165A THR* 3.2 16.3 + - - -
166A THR* 2.7 24.5 + - - -
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Residues in contact with LEU 163 (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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110A THR* 3.9 33.4 - - + +
158A LEU* 3.9 26.5 - - + -
159A SER 3.0 19.7 + - - +
160A SER* 3.6 4.5 - - - +
161A PHE 3.2 0.4 - - - -
162A GLN* 1.3 78.7 - - - +
164A GLU* 1.3 60.6 + - - +
166A THR* 3.1 21.9 + - + +
169A LEU* 4.5 5.6 - - + -
197A ALA 3.5 24.2 - - - +
198A KCX 4.0 10.1 - - - +
200A ARG* 2.9 24.9 + - + +
201A ILE* 3.9 28.3 - - + +
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Residues in contact with GLU 164 (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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76A LEU* 4.0 33.1 - - + +
160A SER 3.1 15.5 + - - +
161A PHE* 3.6 20.2 - - - +
162A GLN 3.2 0.6 - - - -
163A LEU* 1.3 76.2 - - - +
165A THR* 1.3 60.0 + - + +
166A THR 3.8 0.3 + - - -
187A TYR* 2.6 39.5 + - - -
197A ALA* 3.6 15.3 - - + -
200A ARG* 4.0 21.0 + - - +
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Residues in contact with THR 165 (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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70A ALA* 4.6 12.0 + - + +
71A SER 6.0 0.4 - - - +
72A PRO* 6.1 2.3 - - + +
76A LEU* 3.8 31.4 - - + -
91A ILE* 4.5 9.0 - - + +
92A VAL* 3.7 16.3 - - - +
93A GLY* 3.5 36.4 + - - -
96A GLU* 3.6 8.5 - - - +
161A PHE 3.8 8.9 + - - +
162A GLN* 3.2 13.2 + - - -
163A LEU 3.1 0.6 - - - -
164A GLU* 1.3 79.0 - - - +
166A THR* 1.3 60.2 + - - +
167A SER* 4.1 1.4 + - - -
200A ARG* 5.4 0.2 - - - -
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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