Contacts of the helix formed by residues 154 - 164 (chain A) in PDB entry 2OX6
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 154 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A TYR* 3.5 1.2 + - - -
152A SER* 3.2 8.5 + - - -
153A GLU* 1.3 80.2 + - - +
155A ARG* 1.3 65.5 + - - +
156A GLU* 3.7 9.2 + - - +
157A SER* 2.9 27.7 + - - -
158A ARG* 3.0 30.7 + - - +
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Residues in contact with ARG 155 (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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90A TYR* 3.6 6.9 + - - -
99A TYR 4.3 0.4 + - - -
100A ASN* 2.6 34.5 + - - +
102A GLU* 2.5 34.8 + - - +
103A PHE* 3.2 31.3 - - - -
113A TYR* 3.9 15.6 + - - -
154A SER* 1.3 73.4 - - - +
156A GLU* 1.3 56.9 + - - +
158A ARG* 3.4 30.1 + - - +
159A ALA* 3.1 27.5 + - - +
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Residues in contact with GLU 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A SER* 3.1 8.5 + - - +
155A ARG* 1.3 79.4 - - - +
157A SER* 1.3 56.9 + - - +
159A ALA* 3.4 8.6 + - + +
160A LYS* 3.0 55.8 + - + +
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Residues in contact with SER 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A TYR* 3.6 17.3 - - - -
145A TYR* 4.6 2.3 - - - -
146A ARG* 4.3 0.4 - - - -
151A LEU* 3.6 27.2 - - - +
152A SER 2.8 28.6 + - - -
154A SER* 2.9 15.9 + - - -
156A GLU* 1.3 74.9 - - - +
158A ARG* 1.3 65.2 + - - +
160A LYS* 3.3 10.1 + - - +
161A TRP* 2.9 23.6 + - - +
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Residues in contact with ARG 158 (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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88A VAL* 3.9 14.7 - - + +
90A TYR* 2.8 42.7 + - - -
99A TYR* 2.8 43.9 + - - +
100A ASN* 3.4 6.9 + - - -
137A LEU* 4.4 10.8 - - + -
142A TYR* 3.4 27.8 + - + +
153A GLU* 2.6 33.3 + - - +
154A SER* 3.0 14.5 + - - +
155A ARG* 3.6 33.9 - - - +
156A GLU 3.4 0.2 - - - -
157A SER* 1.3 76.0 - - - +
159A ALA* 1.3 51.8 + - - +
161A TRP* 3.3 5.4 + - - +
162A ALA* 2.8 34.8 + - - +
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Residues in contact with ALA 159 (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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86A ALA* 5.1 3.2 - - - +
88A VAL* 4.4 5.1 - - + +
155A ARG 3.1 13.9 + - - +
156A GLU* 3.4 13.7 - - + +
157A SER 3.2 0.2 - - - -
158A ARG* 1.3 73.2 - - - +
160A LYS* 1.3 60.6 + - + +
162A ALA* 3.2 7.7 + - - +
163A ALA* 2.9 30.1 + - - +
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Residues in contact with LYS 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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145A TYR* 3.7 18.2 + - + +
151A LEU* 4.4 23.4 - - + +
156A GLU* 3.0 44.5 + - + +
157A SER* 3.5 10.5 - - - +
159A ALA* 1.3 76.5 - - + +
161A TRP* 1.3 63.7 + - - +
163A ALA* 3.5 15.4 + - - +
164A THR* 3.6 12.1 - - - +
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Residues in contact with TRP 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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88A VAL* 5.3 1.8 - - + -
135A ILE* 3.7 20.4 - - + -
136A ASN 3.5 12.6 - - - -
137A LEU* 4.0 19.5 - - + -
138A ASN* 3.5 41.5 - - + -
141A ALA* 3.9 17.9 + - + +
142A TYR* 3.7 24.2 - + + -
145A TYR* 3.6 41.3 - + + -
157A SER 2.9 13.5 + - - +
158A ARG 3.5 9.9 - - - +
160A LYS* 1.3 74.3 - - - +
162A ALA* 1.3 77.1 + - + +
164A THR* 2.5 32.1 + - - -
165A GLN* 3.6 39.9 - - + +
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Residues in contact with ALA 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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86A ALA* 3.5 27.0 - - + +
88A VAL* 3.5 24.5 - - + -
135A ILE* 4.2 11.1 - - + +
158A ARG 2.8 20.5 + - - +
159A ALA* 3.2 6.9 + - - +
161A TRP* 1.3 82.5 - - + +
163A ALA* 1.3 57.1 + - - +
165A GLN* 2.9 29.5 + - - +
166A LEU 4.0 0.5 + - - -
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Residues in contact with ALA 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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86A ALA* 4.1 9.6 - - + +
159A ALA 2.9 15.7 + - - +
160A LYS* 3.6 9.9 - - - +
161A TRP 3.1 0.4 - - - -
162A ALA* 1.3 77.3 - - - +
164A THR* 1.3 60.3 + - + +
165A GLN 3.2 1.0 + - - -
166A LEU* 3.7 24.3 + - + +
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Residues in contact with THR 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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145A TYR* 3.9 24.9 - - + +
160A LYS 3.6 15.0 - - - +
161A TRP* 2.5 23.3 + - - +
163A ALA* 1.3 77.1 - - + +
165A GLN* 1.3 74.0 + - - +
166A LEU 3.4 6.1 + - - +
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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