Contacts of the strand formed by residues 137 - 142 (chain D) in PDB entry 1WOI
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 137 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128D LEU* 4.2 21.3 - - + +
131D PHE* 4.0 29.8 - - + +
134D VAL* 3.7 25.4 - - + +
135D PRO 3.1 4.1 + - - -
136D ASP* 1.3 73.1 - - - +
138D HIS* 1.3 78.3 + - - +
139D VAL* 4.8 1.1 - - + -
170D LEU* 5.4 2.2 - - + -
172D ASN* 2.7 22.0 + - - +
173D LEU* 3.6 19.8 - - + +
174D VAL 3.2 20.4 + - - -
175D HIS 3.6 5.2 + - - -
223D ASN 3.7 10.3 - - - +
225D TYR* 4.1 13.2 - - + -
268D VAL* 4.2 9.4 - - + -
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Residues in contact with HIS 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136D ASP* 2.9 29.6 + - - +
137D LEU* 1.3 81.0 - - - +
139D VAL* 1.3 62.7 + - - +
174D VAL* 3.7 14.9 - - + +
175D HIS* 3.4 33.9 + + + +
219D PRO* 3.9 15.9 - - + +
222D GLN* 3.3 39.1 + - + +
223D ASN 2.9 12.4 + - - +
224D VAL* 3.3 15.9 - - + -
225D TYR 2.9 24.1 + - - -
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Residues in contact with VAL 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128D LEU* 4.2 30.1 - - + -
137D LEU* 4.8 1.6 - - + -
138D HIS* 1.3 79.0 - - - +
140D VAL* 1.3 73.3 + - - +
141D GLN* 4.2 8.5 - - + +
163D PHE* 4.0 22.4 - - + -
173D LEU* 4.1 19.3 - - + -
175D HIS 3.0 6.7 + - - -
176D ILE* 3.4 15.2 - - + -
177D THR* 2.9 28.2 + - - +
225D TYR* 3.3 15.0 - - + +
227D SER* 4.4 5.8 - - - -
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Residues in contact with VAL 140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139D VAL* 1.3 73.9 - - - +
141D GLN* 1.3 63.0 + - - +
142D LEU* 4.1 4.4 + - + +
177D THR* 3.5 7.6 - - + +
179D VAL* 5.6 1.6 - - + -
218D LEU* 4.6 14.8 - - + -
219D PRO* 3.8 30.1 - - + -
224D VAL* 3.4 20.6 - - + -
225D TYR 3.0 6.5 + - - -
226D PHE* 3.5 31.6 - - + -
227D SER 3.0 23.4 + - - +
257D ILE* 4.7 12.1 - - + -
258D LEU* 5.0 4.1 - - + +
261D ALA* 4.4 7.0 - - + -
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Residues in contact with GLN 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121D HIS* 4.7 1.3 - - + -
139D VAL* 3.8 13.0 + - + -
140D VAL* 1.3 74.0 - - - +
142D LEU* 1.3 66.2 + - - +
143D ASP* 3.0 28.3 + - + +
145D HIS 3.5 6.3 + - - -
146D LEU 3.3 18.8 + - - +
147D ASP* 3.8 1.4 + - - -
163D PHE* 3.2 32.9 - - + -
176D ILE* 3.7 10.6 - - + +
177D THR 2.8 14.4 + - - +
178D THR* 2.8 30.8 + - + +
179D VAL* 2.8 28.6 + - - +
227D SER* 3.4 9.0 - - - +
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Residues in contact with LEU 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140D VAL* 5.1 5.2 - - + +
141D GLN* 1.3 75.7 - - - +
143D ASP* 1.3 63.9 + - - +
179D VAL* 3.5 14.1 - - + +
227D SER 2.9 10.2 + - - +
228D VAL* 4.1 23.6 - - + -
229D ASP* 2.9 31.4 + - - +
232D GLY* 4.6 1.1 - - - -
233D PHE* 4.4 8.1 - - + -
249D LEU* 4.5 9.9 - - + -
254D GLY* 4.0 16.6 - - - +
257D ILE* 4.1 35.0 - - + -
258D LEU* 3.9 36.6 - - + -
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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