Contacts of the strand formed by residues 138 - 142 (chain D) in PDB entry 1PQ3
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 CYS 138 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136D ASP 3.7 0.4 + - - -
137D LEU* 1.3 74.2 - - - +
139D VAL* 1.3 63.4 + - - +
140D VAL 4.3 0.2 + - - -
192D SER 3.3 12.8 - - - +
238D LEU* 3.7 33.4 - - + -
239D ILE* 4.4 1.6 - - - -
244D ARG* 3.8 30.3 - - - +
245D PRO 3.0 9.2 + - - -
246D ILE* 3.6 30.3 - - - -
247D HIS* 2.9 24.8 + - - +
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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
----------------------------------------------------------
127D ILE* 4.1 22.0 - - + -
137D LEU* 3.6 20.4 - - + -
138D CYS* 1.3 78.5 - - - +
140D VAL* 1.3 70.8 + - - +
141D TRP* 4.0 27.4 - - + -
188D ILE* 4.7 10.8 - - + -
192D SER 2.7 12.9 + - - +
193D ILE* 3.2 18.4 - - + -
194D VAL 2.8 26.9 + - - -
238D LEU* 3.8 4.5 - - - +
247D HIS* 3.4 18.4 - - + +
249D SER* 4.8 0.9 - - - -
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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
----------------------------------------------------------
139D VAL* 1.3 71.6 - - - +
141D TRP* 1.3 58.6 + - - +
142D VAL* 4.2 6.3 - - + -
194D VAL* 3.6 7.9 - - + +
196D ILE* 4.1 25.1 - - + -
231D MET* 5.3 1.8 - - + -
234D THR* 4.7 9.4 - - - +
235D PHE* 4.8 7.6 - - + -
238D LEU* 3.7 24.7 - - + -
246D ILE* 4.2 17.9 - - + -
247D HIS 2.9 10.1 + - - +
248D LEU* 3.5 25.8 - - + +
249D SER 3.0 23.6 + - - +
279D ILE* 5.3 0.9 - - + -
283D ILE* 4.3 12.3 - - + -
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Residues in contact with TRP 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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120D HIS* 3.2 31.3 - + - -
123D ALA* 3.6 14.8 - - + -
127D ILE* 4.0 20.9 - - + -
139D VAL* 3.9 12.5 - - + -
140D VAL* 1.3 71.0 - - - +
142D VAL* 1.3 60.1 + - - +
143D ASP* 3.3 35.2 + - + +
145D HIS 4.1 2.2 + - - -
147D ASP* 3.3 23.0 + - + -
163D PRO* 3.8 14.6 - - + -
164D VAL* 3.8 21.5 - - + -
167D LEU* 5.1 2.2 - - + -
193D ILE* 4.3 10.3 - - + -
194D VAL 2.8 11.8 + - - +
195D TYR* 3.3 32.6 - + + -
196D ILE 2.9 24.7 + - - +
249D SER* 3.5 23.1 - - - -
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Residues in contact with VAL 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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120D HIS* 5.2 0.2 - - - -
140D VAL* 4.2 10.3 - - + -
141D TRP* 1.3 71.7 - - - +
143D ASP* 1.3 62.1 + - - +
196D ILE* 3.2 16.6 - - + +
248D LEU* 4.0 17.0 - - + -
249D SER 3.0 7.4 + - - +
250D PHE* 3.6 39.5 - - + -
251D ASP* 2.9 30.1 + - - +
254D ALA* 3.6 19.1 - - + -
271D LEU* 3.7 13.0 - - + -
279D ILE* 4.2 15.7 - - + -
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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
------------------------------------------------------------
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