Contacts of the helix formed by residues 159 - 170 (chain A) in PDB entry 4OWW
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 GLY 159 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123A LEU* 3.5 6.4 - - - +
127A ASN* 5.5 0.5 + - - -
157A VAL 3.3 0.8 + - - -
158A LEU* 1.3 79.2 - - - +
160A ALA* 1.3 63.6 + - - +
161A ASP* 3.1 15.3 + - - -
162A GLY* 3.1 12.9 + - - -
163A VAL* 3.2 15.4 + - - +
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Residues in contact with ALA 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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123A LEU* 3.7 8.2 - - - +
149A VAL* 5.3 0.8 - - + +
152A LEU* 4.3 28.3 - - + +
153A VAL* 4.4 4.7 - - + -
157A VAL* 3.2 21.7 + - + +
158A LEU 3.3 0.8 + - - -
159A GLY* 1.3 79.3 - - - +
161A ASP* 1.3 56.7 - - - +
163A VAL* 3.5 6.8 + - - +
164A CYS* 3.0 31.0 + - - -
197A TRP* 3.8 17.7 - - + -
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Residues in contact with ASP 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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159A GLY* 3.6 15.6 + - - -
160A ALA* 1.3 72.6 - - - +
162A GLY* 1.3 77.3 + - - -
164A CYS* 3.3 3.7 + - - +
165A MET* 3.1 30.3 + - - +
197A TRP* 3.6 19.0 - - + -
201A SER* 3.0 28.7 + - - +
203A ILE* 4.3 6.8 - - - +
204A LEU* 3.8 22.4 - - + +
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Residues in contact with GLY 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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127A ASN* 4.3 4.9 - - - -
159A GLY* 3.1 6.9 + - - -
161A ASP* 1.3 88.3 + - - +
163A VAL* 1.3 56.2 + - - +
165A MET* 3.2 20.1 + - - +
166A THR* 2.9 32.3 + - - -
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Residues in contact with VAL 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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123A LEU* 3.7 30.5 - - + +
126A ILE* 3.6 27.1 - - + -
127A ASN* 3.5 26.4 - - - +
130A LEU* 4.0 1.9 - - + +
149A VAL* 3.7 25.8 - - + -
152A LEU* 5.3 3.4 - - + -
159A GLY 3.2 13.1 + - - +
160A ALA* 3.6 9.9 - - - +
161A ASP 3.3 0.2 - - - -
162A GLY* 1.3 73.0 - - - +
164A CYS* 1.3 60.3 + - - +
166A THR* 3.2 2.4 + - - -
167A PHE* 2.9 27.7 + - - +
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Residues in contact with CYS 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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149A VAL* 4.1 14.6 - - - -
153A VAL* 4.0 15.3 - - - -
160A ALA 3.0 19.3 + - - -
161A ASP* 3.5 9.0 - - - +
162A GLY 3.3 0.2 - - - -
163A VAL* 1.3 76.5 - - - +
165A MET* 1.3 57.3 + - - +
167A PHE* 3.2 9.0 + - - +
168A MET* 3.0 34.3 + - + +
187A VAL* 5.1 3.2 - - + +
190A ILE* 5.0 4.3 - - - -
191A LEU* 4.5 13.9 - - + -
197A TRP* 3.9 20.9 - - - -
204A LEU* 4.2 14.1 - - + -
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Residues in contact with MET 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 ASP* 3.1 25.7 + - - +
162A GLY* 3.2 18.4 + - - +
164A CYS* 1.3 72.1 - - - +
166A THR* 1.3 65.8 + - - +
168A MET* 3.4 10.3 + - + +
169A LYS* 3.3 20.8 + - - +
203A ILE* 3.8 42.6 - - + +
204A LEU* 3.7 20.9 - - + +
207A MET* 3.8 37.3 - - + +
303A CYS* 6.0 1.2 - - - +
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Residues in contact with THR 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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127A ASN* 2.9 32.3 + - - +
130A LEU* 3.6 24.9 - - + -
131A MET* 3.6 30.7 - - + -
162A GLY 2.9 11.0 + - - -
163A VAL 3.6 4.0 - - - -
165A MET* 1.3 76.3 - - - +
167A PHE* 1.3 63.4 + - - +
169A LYS* 3.4 10.6 + - - +
170A GLN* 3.1 24.8 + - - -
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Residues in contact with PHE 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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130A LEU* 3.6 27.3 - - + +
134A TYR* 4.2 10.5 - + - -
142A ARG 5.0 0.9 - - - -
145A LEU* 3.8 31.0 - - + -
146A VAL* 3.8 22.4 - - + -
149A VAL* 3.5 41.5 - - + -
163A VAL 2.9 10.9 + - - +
164A CYS* 3.2 11.6 + - - +
166A THR* 1.3 75.7 - - - +
168A MET* 1.3 63.3 + - - +
170A GLN* 3.1 20.4 + - + +
171A ILE* 3.9 2.3 + - - +
182A TRP* 6.1 0.2 - + - -
183A LEU* 3.6 31.8 - - + +
187A VAL* 4.4 15.7 - - + -
190A ILE* 6.0 2.0 - - + -
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Residues in contact with MET 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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164A CYS* 3.0 11.7 + - + +
165A MET* 3.8 22.7 - - - +
166A THR 3.3 0.4 - - - -
167A PHE* 1.3 75.6 - - - +
169A LYS* 1.3 57.4 + - - +
171A ILE* 2.9 39.4 + - + +
187A VAL* 3.6 22.7 - - + -
191A LEU* 4.0 9.4 - - + -
204A LEU* 4.1 14.4 - - + -
207A MET* 4.1 13.0 - - + +
208A ALA* 3.8 36.1 - - - +
211A THR* 4.0 16.4 - - + +
212A TYR* 3.9 18.2 - - - -
304A ARG* 3.5 10.0 + - - -
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Residues in contact with LYS 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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131A MET* 3.9 33.7 - - + -
165A MET 3.3 10.3 + - - +
166A THR* 3.4 14.1 - - - +
167A PHE 3.2 0.4 - - - -
168A MET* 1.3 77.5 - - - +
170A GLN* 1.3 61.8 + - - +
171A ILE 3.5 3.7 + - - +
302A ALA* 3.0 17.5 + - - +
303A CYS* 3.8 24.6 - - + +
304A ARG* 4.8 0.2 + - - -
305A LEU 2.7 27.1 + - - +
306A THR* 3.6 19.6 + - - +
307A PRO* 4.0 14.1 - - + -
310A GLU* 2.5 31.1 + - - -
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Residues in contact with GLN 170 (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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130A LEU* 3.1 45.1 + - + +
131A MET* 3.9 8.9 - - - -
134A TYR* 3.9 32.1 - - + +
166A THR 3.1 23.2 + - - +
167A PHE 3.5 9.9 - - - +
168A MET 3.0 1.2 - - - -
169A LYS* 1.3 77.8 - - - +
171A ILE* 1.3 63.5 + - - +
172A ALA* 3.3 5.1 + - - +
180A ASN* 4.0 3.6 - - - +
183A LEU* 3.9 17.1 - - + +
306A THR* 4.5 7.5 - - - +
307A PRO* 3.3 31.3 - - - +
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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