Contacts of the helix formed by residues 154 - 163 (chain A) in PDB entry 4OHN
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
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Residue Dist Surf HB Arom Phob DC
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87A TRP* 4.2 0.8 - - - -
112A ARG* 4.0 1.6 - - - -
150A ALA* 5.0 0.3 - - - +
151A GLN* 2.7 48.8 + - - +
152A ALA 3.3 1.3 - - - +
153A GLY* 1.3 81.4 - - - +
155A SER* 1.3 63.8 + - - +
156A GLY* 3.4 6.6 + - - -
157A TYR* 3.0 18.2 + - - +
158A ALA* 3.3 17.3 + - - +
182A PHE* 4.4 7.0 - - - -
198A LEU 5.4 1.2 + - - -
200A ASP* 5.3 0.4 - - - -
301A HIS* 3.2 15.0 - - - -
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Residues in contact with SER 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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107A SER* 3.3 26.3 + - - -
109A THR* 4.1 14.4 - - - -
112A ARG* 3.5 25.5 - - - +
127A GLN* 3.8 7.8 + - - -
154A SER* 1.3 70.9 - - - +
156A GLY* 1.3 66.6 + - - +
158A ALA* 3.2 9.3 + - - +
159A ASP* 2.9 30.1 + - - +
227A GLU* 3.9 3.5 + - - -
301A HIS* 3.0 15.7 + - - -
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Residues in contact with GLY 156 (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 GLN* 3.4 30.1 + - - -
154A SER* 3.1 7.7 + - - -
155A SER* 1.3 83.2 + - - +
157A TYR* 1.3 56.6 + - - +
159A ASP* 3.2 8.4 + - - +
160A PHE 2.9 24.1 + - - -
198A LEU* 3.3 21.0 - - - +
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Residues in contact with TYR 157 (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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150A ALA* 4.0 23.4 - - + +
151A GLN 3.5 22.7 - - - +
152A ALA 3.9 10.5 - - - +
154A SER* 3.0 11.6 + - - +
156A GLY* 1.3 75.7 - - - +
158A ALA* 1.3 65.5 + - - +
160A PHE* 3.2 29.1 + + - +
161A GLU* 3.1 49.2 + - + +
175A GLU* 6.1 0.2 - - - -
176A ALA* 4.0 16.0 + - + -
178A GLN* 3.2 31.8 + - + -
198A LEU* 4.5 0.2 - - - +
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Residues in contact with ALA 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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111A GLU* 4.2 27.2 - - - +
154A SER 3.3 9.3 + - - +
155A SER* 3.2 12.9 + - - +
157A TYR* 1.3 82.0 - - - +
159A ASP* 1.3 64.0 + - - +
161A GLU* 3.3 6.9 + - - +
162A ALA* 3.0 24.9 + - - +
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Residues in contact with ASP 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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109A THR* 5.6 4.5 - - - +
127A GLN* 3.8 21.3 - - - +
155A SER* 2.9 22.2 + - - +
156A GLY 3.3 7.0 - - - +
158A ALA* 1.3 75.5 - - - +
160A PHE* 1.3 57.4 + - - +
162A ALA* 3.0 4.2 + - - +
163A ASN* 2.8 45.9 + - - +
224A LEU* 4.3 26.9 - - + +
225A GLU 5.6 2.1 - - - +
227A GLU* 4.2 8.0 - - - +
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Residues in contact with PHE 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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148A LEU* 3.3 30.5 - - + -
156A GLY 2.9 12.5 + - - +
157A TYR* 3.3 23.3 - + + +
159A ASP* 1.3 78.9 - - - +
161A GLU* 1.3 85.7 + - - +
163A ASN 3.9 12.1 + - - +
164A PRO* 3.9 0.2 - - - +
166A ILE* 6.5 0.2 - - - -
167A LEU* 4.0 10.5 + - + -
168A LYS* 3.4 57.7 + - + +
171A VAL* 4.2 2.5 - - + -
175A GLU* 3.7 24.2 - - - -
176A ALA* 3.9 16.6 - - + -
198A LEU* 4.0 12.8 - - + -
224A LEU* 5.8 2.5 - - - -
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Residues in contact with GLU 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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157A TYR* 3.1 45.6 + - + +
158A ALA* 3.8 8.3 - - - +
159A ASP 3.2 0.2 - - - -
160A PHE* 1.3 98.7 - - + +
162A ALA* 1.3 62.8 + - - +
163A ASN 3.6 0.2 + - - -
164A PRO* 3.6 14.0 - - - +
168A LYS* 2.6 37.3 + - - +
174A LYS 5.0 0.7 - - - +
175A GLU* 5.4 1.0 - - - -
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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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111A GLU* 5.7 3.8 - - - +
158A ALA 3.0 16.6 + - - +
159A ASP* 3.0 6.3 + - - +
161A GLU* 1.3 77.8 - - - +
163A ASN* 1.3 68.2 + - - +
164A PRO* 3.3 8.8 - - - +
165A GLU* 5.1 0.2 - - - +
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Residues in contact with ASN 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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159A ASP* 2.8 21.8 + - - +
160A PHE* 3.9 7.1 - - - +
162A ALA* 1.3 88.8 + - - +
164A PRO* 1.3 66.6 - - - +
165A GLU* 3.0 26.2 + - - +
166A ILE* 3.1 27.6 + - + +
167A LEU 4.3 0.9 + - - -
224A LEU* 4.3 13.8 - - + +
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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