Contacts of the strand formed by residues 168 - 175 (chain A) in PDB entry 1OWH
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 LYS 168 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A ILE* 3.2 29.3 + - + +
3A GLY* 2.9 33.3 + - - +
4A GLY 4.7 1.1 + - - -
5A GLU* 3.4 15.7 - - - +
6A PHE* 3.6 33.6 - - + +
7A THR* 3.8 3.8 - - - -
150A THR* 3.0 23.0 - - - +
151A GLY 3.1 23.3 + - - +
155A GLU* 2.8 41.8 + - + +
163A PRO* 4.3 8.5 - - + -
165A GLN 3.7 3.6 - - - +
167A LEU* 1.3 74.3 - - - +
169A MET* 1.3 60.6 + - - +
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Residues in contact with MET 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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1A ILE* 4.1 7.2 - - - +
4A GLY* 3.4 1.3 - - - -
5A GLU* 3.0 64.7 + - + +
7A THR* 3.9 17.9 - - + -
12A GLN* 4.0 18.4 - - - +
148A GLU* 3.7 19.3 - - + +
149A ILE 3.3 14.1 - - - +
150A THR* 4.4 1.6 - - + +
168A LYS* 1.3 75.6 - - - +
170A THR* 1.3 80.7 + - - +
171A VAL* 4.1 15.9 - - + -
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Residues in contact with THR 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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1A ILE* 3.8 14.1 - - + -
4A GLY* 3.4 11.7 - - - -
148A GLU* 3.4 7.4 - - - +
149A ILE* 3.1 56.6 + - + -
169A MET* 1.3 83.8 - - - +
171A VAL* 1.3 68.7 + - - +
172A VAL* 4.4 11.0 - - + -
204A THR* 2.7 35.1 + - - +
205A ASP 4.5 3.1 - - - +
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Residues in contact with VAL 171 (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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146A SER* 3.9 26.7 - - - +
147A CYS 3.4 14.1 - - - +
148A GLU* 4.3 7.4 - - + -
169A MET* 4.1 15.9 - - + -
170A THR* 1.3 87.5 + - - +
172A VAL* 1.3 69.0 + - - +
173A LYS* 6.2 0.2 - - - +
199A ASP* 5.5 0.7 - - - +
204A THR* 4.0 8.8 - - - +
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Residues in contact with VAL 172 (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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146A SER* 3.4 3.6 - - - -
147A CYS* 2.9 36.3 + - + +
149A ILE* 4.5 17.5 - - + -
170A THR* 4.4 13.0 - - + -
171A VAL* 1.3 76.5 - - - +
173A LYS* 1.3 63.6 + - - +
197A ALA* 3.8 22.2 - - + +
198A ALA* 3.8 27.1 - - - +
199A ASP* 4.1 4.7 - - - +
204A THR* 4.3 13.9 - - + +
205A ASP* 4.8 3.8 - - - +
215A LEU* 4.2 15.0 - - + -
244A TYR* 4.8 2.5 - - - +
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Residues in contact with LYS 173 (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 GLY* 3.8 22.9 - - - +
145A THR 3.4 4.3 - - - +
146A SER* 3.6 24.5 + - - +
171A VAL* 6.2 0.2 - - - +
172A VAL* 1.3 74.0 - - - +
174A LEU* 1.3 65.9 + - - +
175A ILE* 3.6 4.5 + - + +
197A ALA* 3.2 4.8 - - - -
198A ALA 3.0 34.9 + - - +
199A ASP* 5.2 0.2 - - - +
200A PRO* 4.1 27.7 - - + +
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Residues in contact with LEU 174 (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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141A PRO* 3.9 47.1 - - + +
142A GLN 4.1 1.3 - - - +
143A PHE* 3.8 5.9 - - - +
144A GLY* 2.8 30.3 + - - +
145A THR* 3.0 21.2 + - - +
147A CYS* 3.8 24.7 - - + -
173A LYS* 1.3 75.7 - - - +
175A ILE* 1.3 61.6 + - - +
195A LEU* 5.3 12.3 - - + -
196A CYS 3.6 7.0 - - - +
197A ALA* 4.0 15.5 - - + -
215A LEU* 4.1 17.5 - - + -
217A CYS* 4.4 1.1 - - - -
226A THR* 5.1 3.6 - - + -
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Residues in contact with ILE 175 (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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143A PHE* 4.2 3.1 - - - -
173A LYS* 3.7 8.1 - - + +
174A LEU* 1.3 79.6 - - - +
176A SER* 1.3 73.9 + - - +
179A GLU* 3.8 35.9 - - + +
180A CYS* 4.3 7.4 - - + +
185A TYR* 4.7 4.5 - - + -
195A LEU* 5.7 1.6 - - - +
196A CYS* 2.8 34.5 + - + +
197A ALA 4.2 0.2 - - - -
198A ALA* 3.8 24.2 - - + +
202A TRP* 5.0 3.1 - - + -
241A PRO* 3.7 27.8 - - + -
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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