Contacts of the helix formed by residues 155 - 165 (chain A) in PDB entry 3OM0
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 155 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126A VAL* 4.3 15.3 - - + -
127A SER* 3.4 26.0 - - - +
130A VAL* 5.2 3.8 - - + -
144A LEU* 3.9 34.1 - - + -
151A CYS 2.8 16.4 + - - +
152A LEU 3.6 4.0 - - - -
154A ARG* 1.3 92.5 - - + +
156A GLU* 1.3 63.9 + - - +
157A GLU 3.2 2.7 - - - -
158A LEU* 3.0 18.1 + - + -
159A VAL* 2.9 26.9 + - + +
196A ILE* 4.8 5.2 - - + -
198A ASP* 4.2 16.2 - - + -
226A THR* 4.5 11.7 - - + -
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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
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123A ASN* 6.3 1.3 - - + -
152A LEU 3.2 13.8 + - - +
153A LEU* 3.1 23.6 + - + +
154A ARG 3.3 2.8 + - - +
155A LEU* 1.3 76.5 - - - +
157A GLU* 1.3 59.7 + - + +
159A VAL* 3.8 3.9 - - - +
160A ARG* 2.7 81.2 + - + +
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Residues in contact with GLU 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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124A GLU* 4.7 21.6 - - + +
127A SER* 3.6 21.7 + - - +
128A LEU* 3.9 29.5 - - + +
131A SER* 5.4 2.2 - - - +
154A ARG 5.1 0.2 + - - -
155A LEU 3.1 1.2 + - - -
156A GLU* 1.3 87.2 + - + +
158A LEU* 1.3 64.2 + - - +
160A ARG* 3.0 30.1 + - - +
161A GLY* 3.2 17.8 + - - -
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Residues in contact with LEU 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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127A SER* 3.7 12.4 + - - +
130A VAL* 3.5 34.5 - - + -
131A SER* 3.9 18.2 - - - +
134A LEU* 3.8 17.3 - - + -
144A LEU* 5.5 1.6 - - + -
155A LEU* 3.0 21.8 + - + +
157A GLU* 1.3 77.6 - - - +
159A VAL* 1.3 73.3 + - + +
161A GLY* 3.0 4.5 + - - -
162A PHE* 3.0 43.8 + - + -
169A LEU* 3.9 14.8 - - + -
196A ILE* 4.3 9.0 - - + -
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Residues in contact with VAL 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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144A LEU* 5.0 2.7 - - + -
152A LEU* 3.9 41.3 - - + +
155A LEU* 2.9 23.5 + - + +
156A GLU* 3.8 7.0 - - - +
158A LEU* 1.3 81.1 - - + +
160A ARG* 1.3 63.8 - - + +
162A PHE* 3.2 7.5 + - - +
163A LEU* 2.9 39.8 + - + +
169A LEU* 4.4 16.6 - - + -
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Residues in contact with ARG 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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156A GLU* 2.7 47.5 + - + +
157A GLU* 3.0 33.4 + - - +
159A VAL* 1.3 76.2 - - + +
161A GLY* 1.3 62.4 + - - +
163A LEU* 3.3 24.8 + - + +
164A ILE* 3.4 20.0 + - - +
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Residues in contact with GLY 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 GLU 3.2 10.1 + - - -
158A LEU* 3.0 9.2 + - - -
160A ARG* 1.3 75.5 - - - +
162A PHE* 1.3 62.1 + - - +
164A ILE* 3.3 13.5 + - - +
165A SER* 3.2 23.2 + - - -
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Residues in contact with PHE 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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134A LEU* 3.9 22.0 - - + -
140A PRO 3.5 25.4 - - - -
141A SER* 4.3 0.4 - - - -
142A ALA* 4.1 13.5 - - + -
158A LEU* 3.0 50.3 + - + -
159A VAL 3.7 6.1 - - - +
161A GLY* 1.3 75.3 - - - +
163A LEU* 1.3 62.2 + - + +
164A ILE 3.2 1.0 + - - -
165A SER* 3.3 14.5 + - - +
167A GLU* 3.5 29.0 - - + +
168A THR 3.6 28.9 - - - -
169A LEU* 3.8 26.2 - - + +
196A ILE* 4.8 0.9 - - + -
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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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159A VAL* 2.9 36.0 + - + +
160A ARG* 3.6 17.3 - - + +
161A GLY 3.2 0.4 - - - -
162A PHE* 1.3 77.4 - - + +
164A ILE* 1.3 63.7 + - + +
165A SER 4.8 1.1 - - - +
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Residues in contact with ILE 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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160A ARG 3.4 12.5 + - - +
161A GLY* 3.5 15.7 - - - +
163A LEU* 1.3 85.5 - - + +
165A SER* 1.3 59.6 + - - +
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Residues in contact with SER 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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161A GLY 3.2 16.6 + - - -
162A PHE* 3.3 14.4 + - - +
163A LEU 4.8 1.4 - - - +
164A ILE* 1.3 82.2 - - - +
166A LYS* 1.3 67.8 + - - +
167A GLU* 2.8 32.0 + - - +
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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