Contacts of the strand formed by residues 125 - 132 (chain D) in PDB entry 1WYK
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 VAL 125 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117D ASP* 3.7 29.6 - - + +
118D VAL 3.4 6.3 - - - +
119D LYS* 4.0 14.8 - - - -
123D GLY 4.6 1.8 - - - +
124D ASP* 1.3 72.1 - - - +
126D ILE* 1.3 60.7 + - - +
127D GLY 3.5 22.7 - - - +
128D HIS* 3.9 20.9 - - + +
212D ARG 5.2 0.7 - - - +
213D GLY* 4.4 9.3 - - - +
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Residues in contact with ILE 126 (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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118D VAL 2.8 20.4 + - - +
119D LYS 4.1 6.5 - - - -
120D ASN* 4.0 23.6 - - + +
124D ASP* 3.6 13.7 - - + +
125D VAL* 1.3 75.1 - - - +
127D GLY* 1.3 57.6 + - - +
142D VAL* 3.7 27.8 - - + +
143D LYS 3.4 30.3 - - - +
144D GLY* 3.8 8.1 - - - -
212D ARG* 6.1 2.9 - - - +
213D GLY* 3.7 17.8 + - - -
215D SER* 3.9 1.2 + - - -
264D TRP* 3.8 9.9 - - - +
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Residues in contact with GLY 127 (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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118D VAL* 3.0 25.2 + - - -
125D VAL* 3.5 8.1 - - - +
126D ILE* 1.3 80.2 - - - +
128D HIS* 1.3 72.0 + - - -
142D VAL* 4.0 8.3 - - - -
213D GLY 3.4 13.2 + - - -
215D SER* 3.5 10.8 - - - -
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Residues in contact with HIS 128 (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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115D LEU* 3.8 25.8 - - + -
116D PHE 3.3 10.5 - - - +
117D ASP* 3.7 22.1 + - - -
118D VAL* 3.7 8.0 - - - +
125D VAL* 3.9 10.2 - - + +
127D GLY* 1.3 78.9 + - - -
129D ALA* 1.3 59.6 + - - +
138D LYS* 3.7 2.3 - - - +
139D PRO* 3.5 15.0 - - - +
213D GLY 2.8 30.1 + - - -
215D SER 2.9 14.5 + - - +
216D GLY* 3.3 23.2 - - - -
217D ARG* 3.4 49.5 + - + +
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Residues in contact with ALA 129 (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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115D LEU* 3.4 6.9 - - - +
116D PHE* 2.8 37.4 + - + +
118D VAL* 3.9 2.2 - - + +
128D HIS* 1.3 74.6 - - - +
130D LEU* 1.3 61.8 + - - +
136D VAL* 4.2 8.5 - - + -
137D MET 3.2 10.8 - - - +
138D LYS* 3.9 7.4 - - + -
146D ILE* 3.9 39.0 - - + -
216D GLY 4.8 0.9 - - - -
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Residues in contact with LEU 130 (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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114D ARG 3.2 11.0 - - - +
115D LEU* 4.2 4.5 - - + -
116D PHE* 4.5 1.3 - - - -
129D ALA* 1.3 76.3 - - - +
131D ALA* 1.3 59.9 + - - +
132D MET* 3.5 32.5 - - + -
135D LYS 3.6 0.9 - - - +
136D VAL* 3.2 6.6 - - - -
137D MET* 2.8 56.1 + - + +
178D PHE* 4.2 11.4 - - + -
216D GLY 3.4 22.0 - - - +
218D PRO* 3.8 30.1 - - + -
226D VAL* 5.2 0.7 - - + -
229D ILE* 4.0 15.3 - - + -
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Residues in contact with ALA 131 (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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113D MET 4.7 0.2 - - - +
114D ARG* 2.8 21.0 + - - +
116D PHE* 4.1 10.2 - - + -
130D LEU* 1.3 69.8 - - - +
132D MET* 1.3 62.4 + - - +
135D LYS 3.4 6.1 - - - -
136D VAL* 4.5 0.4 - - - +
169D LEU* 3.8 24.9 - - + -
173D MET* 5.9 0.4 - - + -
176D GLU 3.7 21.5 - - - +
177D ALA* 3.7 1.5 - - - -
178D PHE* 2.9 29.8 + - - -
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Residues in contact with MET 132 (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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4D DIO 3.4 30.9 - - - +
130D LEU* 3.5 16.3 + - + -
131D ALA* 1.3 75.6 - - - +
133D GLU* 1.3 77.5 + - + +
134D GLY 3.4 2.0 - - - -
135D LYS* 2.8 26.9 + - - +
137D MET* 3.5 28.8 - - + +
177D ALA* 4.2 1.7 - - - +
178D PHE* 3.3 23.8 - - + +
180D TYR* 3.7 20.4 - - + +
226D VAL* 3.6 35.9 - - - -
229D ILE* 4.5 1.3 - - + -
247D TRP* 3.9 7.2 - - + -
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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