Contacts of the helix formed by residues 157 - 169 (chain A) in PDB entry 1ORN
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 157 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143A GLU* 5.3 0.4 - - - -
155A ASP 3.6 2.2 + - - -
156A ASP* 1.3 78.3 - - - +
158A VAL* 1.3 64.5 + - - +
159A LEU* 3.4 9.9 + - - +
160A GLU* 3.0 23.8 + - - +
161A VAL* 3.1 21.1 + - - +
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Residues in contact with VAL 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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138A VAL* 3.9 31.6 - - + +
139A ASP 5.5 1.1 - - - +
143A GLU* 3.8 28.9 + - + +
157A SER* 1.3 73.9 - - - +
159A LEU* 1.3 65.2 + - + +
161A VAL* 3.3 9.8 + - - +
162A GLU* 3.0 23.4 + - - +
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Residues in contact with LEU 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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120A ARG* 3.8 42.0 - - - +
157A SER* 3.1 8.6 + - - +
158A VAL* 1.3 84.0 - - + +
160A GLU* 1.3 58.2 + - - +
162A GLU* 3.2 7.8 + - + +
163A LYS* 2.9 57.7 + - + +
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Residues in contact with GLU 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 ASP* 3.7 19.1 - - + +
157A SER* 3.0 30.3 + - - +
159A LEU* 1.3 73.8 - - - +
161A VAL* 1.3 64.8 + - - +
163A LYS* 3.4 13.4 + - - +
164A THR* 2.9 29.8 + - - +
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Residues in contact with VAL 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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138A VAL* 4.0 17.5 - - + -
142A VAL* 4.4 2.7 - - + +
143A GLU* 4.5 9.9 - - + -
146A SER* 3.5 28.5 - - - +
147A LYS* 4.5 12.1 - - - -
152A CYS* 3.9 24.0 - - - -
156A ASP* 4.7 1.1 - - + -
157A SER 3.1 16.4 + - - +
158A VAL* 3.5 12.3 - - - +
160A GLU* 1.3 75.7 - - - +
162A GLU* 1.3 63.6 + - - +
164A THR* 3.3 7.5 + - - -
165A LEU* 3.1 33.0 + - + +
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Residues in contact with GLU 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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109A ARG* 4.3 1.0 + - - -
120A ARG* 2.8 49.8 + - - +
124A ASN* 3.1 16.6 + - - -
135A ALA* 5.8 0.3 - - - +
136A ILE* 3.3 31.6 + - + +
138A VAL* 3.8 16.2 + - + +
158A VAL 3.0 13.4 + - - +
159A LEU* 3.2 11.6 + - + +
161A VAL* 1.3 77.1 - - - +
163A LYS* 1.3 63.0 + - - +
165A LEU* 3.3 7.2 + - - +
166A MET* 3.0 40.4 + - + +
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Residues in contact with LYS 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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120A ARG* 5.6 0.2 - - - +
159A LEU* 2.9 46.7 + - + +
160A GLU* 3.9 12.1 - - - +
162A GLU* 1.3 74.2 - - - +
164A THR* 1.3 62.4 + - - +
166A MET* 3.3 20.0 + - + +
167A LYS* 3.2 48.4 + - - +
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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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7A ILE* 5.1 5.2 - - + -
151A PHE* 3.7 28.5 - - + +
152A CYS* 4.5 9.3 - - + +
156A ASP* 5.3 1.0 + - - -
160A GLU* 2.9 16.1 + - - +
161A VAL* 3.5 11.4 - - - -
163A LYS* 1.3 78.2 - - - +
165A LEU* 1.3 66.1 + - + +
167A LYS* 3.4 8.4 + - - +
168A ILE* 3.1 37.8 + - + +
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Residues in contact with LEU 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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7A ILE* 5.1 4.3 - - + -
11A LEU* 4.9 3.1 - - + -
136A ILE* 3.5 37.9 - - + -
142A VAL* 4.0 21.8 - - + -
146A SER* 4.3 1.6 - - - +
151A PHE* 3.9 30.7 - - + -
161A VAL* 3.1 24.2 + - + +
162A GLU* 3.7 3.4 - - - +
164A THR* 1.3 78.3 - - + +
166A MET* 1.3 60.0 + - - +
168A ILE* 3.2 3.9 + - + +
169A ILE* 2.9 48.5 + - + +
181A MET* 4.0 17.0 - - - -
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Residues in contact with MET 166 (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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120A ARG* 4.1 11.9 - - - +
135A ALA* 6.0 0.7 - - - -
136A ILE* 4.0 13.0 - - + -
162A GLU* 3.0 44.5 + - + +
163A LYS* 3.3 24.2 + - + +
165A LEU* 1.3 76.0 - - - +
167A LYS* 1.3 60.0 + - + +
169A ILE 3.2 17.7 - - - +
174A TRP* 3.4 54.0 - - + +
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Residues in contact with LYS 167 (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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163A LYS* 3.2 36.0 + - - +
164A THR* 3.8 7.8 - - - +
165A LEU 3.2 0.6 - - - -
166A MET* 1.3 79.6 - - + +
168A ILE* 1.3 69.3 + - + +
169A ILE 4.8 0.4 - - - -
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Residues in contact with ILE 168 (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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4A LYS* 4.1 27.4 - - + +
7A ILE* 4.2 27.8 - - + -
8A ARG* 3.7 36.9 - - + +
11A LEU* 5.2 0.4 - - + -
164A THR* 3.1 27.1 - - + +
165A LEU* 3.2 6.3 + - + +
167A LYS* 1.3 88.8 - - + +
169A ILE* 1.3 65.5 + - + +
170A PRO* 4.0 5.2 - - - +
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Residues in contact with ILE 169 (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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8A ARG* 6.4 0.2 - - + -
11A LEU* 3.4 24.0 - - + -
136A ILE* 4.6 6.5 - - + -
165A LEU* 2.9 33.1 + - + +
166A MET 3.2 8.8 - - - +
167A LYS 4.8 0.6 - - - -
168A ILE* 1.3 83.9 - - + +
170A PRO* 1.3 78.3 - - + +
171A LYS 3.3 0.7 + - - -
173A GLU* 3.7 19.5 - - + +
174A TRP* 2.7 32.3 + - + -
177A THR* 3.3 37.9 - - + +
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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