Contacts of the strand formed by residues 154 - 161 (chain A) in PDB entry 1OWK
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 154 (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* 2.9 39.4 + - + +
3A GLY* 2.7 35.1 + - - +
4A GLY 4.6 1.3 - - - -
5A GLU 3.4 11.2 - - - +
6A PHE* 3.7 27.5 - - + -
7A THR* 3.7 3.1 - - - -
137A THR* 3.0 22.2 - - - +
138A GLY 3.4 18.3 + - - +
142A GLU* 3.1 41.0 + - + +
150A PRO* 4.4 6.3 - - + -
152A GLN 3.9 3.4 - - - +
153A LEU* 1.3 79.4 - - - +
155A MET* 1.3 62.8 + - - +
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Residues in contact with MET 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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1A ILE* 4.3 4.0 - - - -
4A GLY* 3.3 1.6 - - - -
5A GLU* 2.8 57.4 + - + +
7A THR* 3.4 28.7 - - + +
12A GLN* 4.8 7.6 - - - +
135A GLU* 3.6 24.5 - - + +
136A ILE 3.5 12.3 - - - +
137A THR* 4.2 7.2 - - + +
154A LYS* 1.3 77.7 - - - +
156A THR* 1.3 86.1 + - - +
157A VAL* 4.3 10.3 - - + -
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Residues in contact with THR 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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1A ILE* 3.6 18.6 - - + -
4A GLY* 3.8 8.1 - - - -
134A CYS 4.0 0.2 - - - +
135A GLU* 3.2 4.3 - - - +
136A ILE* 3.0 59.8 + - + +
155A MET* 1.3 84.4 - - - +
157A VAL* 1.3 76.2 + - - +
158A VAL* 4.8 1.6 - - + -
190A THR* 2.5 30.5 + - - +
191A ASP 4.6 3.4 - - - +
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Residues in contact with VAL 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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133A SER* 3.7 29.4 - - - +
134A CYS 3.2 15.9 - - - +
135A GLU* 4.6 5.2 - - + -
155A MET* 4.3 14.1 - - + -
156A THR* 1.3 87.1 + - - +
158A VAL* 1.3 74.0 + - - +
159A LYS* 5.6 0.4 - - + -
185A ASP* 5.3 0.9 - - - +
190A THR* 4.0 9.7 - - - +
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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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132A THR 3.6 0.3 - - - +
133A SER* 3.2 4.5 - - - -
134A CYS* 2.9 38.6 + - + +
136A ILE* 4.4 22.7 - - + -
156A THR* 4.8 2.2 - - + -
157A VAL* 1.3 79.7 - - - +
159A LYS* 1.3 65.8 + - - +
160A LEU* 4.3 0.4 + - + -
183A ALA* 3.6 24.5 - - + -
184A ALA* 3.8 25.1 - - - +
185A ASP* 4.2 5.4 - - - +
186A PRO* 6.1 0.2 - - - -
190A THR* 4.7 11.0 - - + +
191A ASP* 4.7 7.6 - - - +
201A LEU* 4.2 15.3 - - + -
230A TYR* 4.7 3.1 - - - +
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Residues in contact with LYS 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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131A GLY* 2.8 37.0 - - - +
132A THR 3.3 1.8 - - - +
133A SER* 2.9 29.6 - - - +
157A VAL* 5.6 0.9 - - + -
158A VAL* 1.3 77.9 - - - +
160A LEU* 1.3 65.8 + - - +
161A ILE* 3.4 5.4 + - + +
183A ALA* 3.3 3.9 - - - -
184A ALA 3.0 35.2 + - - +
186A PRO* 4.2 24.9 - - + +
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Residues in contact with LEU 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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128A PRO* 3.4 44.4 - - + +
129A GLN 4.0 6.7 - - - +
130A PHE* 3.5 5.1 - - - +
131A GLY* 2.6 34.3 + - - +
132A THR* 2.9 22.9 + - - +
134A CYS* 4.2 5.4 - - + -
159A LYS* 1.3 70.1 - - - +
161A ILE* 1.3 60.9 + - - +
181A LEU* 4.6 21.5 - - + -
182A CYS 3.6 12.8 - - - +
183A ALA* 4.1 12.8 - - + -
201A LEU* 4.3 17.5 - - + -
203A CYS* 4.1 11.2 - - - -
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Residues in contact with ILE 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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130A PHE* 4.2 2.2 - - - -
159A LYS* 3.8 9.9 - - + +
160A LEU* 1.3 77.2 - - - +
162A SER* 1.3 80.1 + - - +
165A GLU* 3.0 42.0 - - + +
166A CYS* 4.2 10.1 - - + +
171A TYR* 4.6 6.1 - - + +
181A LEU* 5.9 2.1 - - - +
182A CYS* 2.8 32.5 + - + +
183A ALA 4.5 0.2 - - - -
184A ALA* 3.9 19.1 - - + +
188A TRP* 5.1 3.4 - - + -
227A PRO* 3.6 31.2 - - + -
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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