Contacts of the strand formed by residues 134 - 144 (chain D) in PDB entry 3U0T
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 THR 134 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114C SER* 6.1 1.6 - - - +
116C PHE* 3.9 22.7 - - + -
133D SER* 1.3 81.4 + - - +
135D ALA* 1.3 60.2 + - - +
182D THR* 3.0 28.6 + - - +
183D VAL 3.9 4.7 - - - -
184D PRO* 5.1 0.4 - - - -
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Residues in contact with ALA 135 (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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116C PHE* 4.7 3.7 - - - -
125D PRO* 5.7 6.3 - - + -
133D SER 4.0 3.0 + - - -
134D THR* 1.3 75.3 + - - +
136D ALA* 1.3 65.3 + - - +
182D THR* 3.4 9.4 - - - +
183D VAL* 2.9 45.2 + - + +
185D SER* 4.8 12.8 - - - +
213D ARG 6.0 4.5 - - - +
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Residues in contact with ALA 136 (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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116C PHE* 4.1 37.7 - - + -
118C PHE* 3.7 15.1 - - + -
135C LEU* 4.5 9.2 - - + -
125D PRO* 3.7 22.3 - - - +
135D ALA* 1.3 80.3 - - - +
137D LEU* 1.3 66.9 + - - +
181D VAL 3.3 10.1 - - - +
182D THR* 4.8 4.9 - - - +
183D VAL 4.9 0.2 - - - +
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Residues in contact with LEU 137 (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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118C PHE* 4.4 4.9 - - - -
123D LEU* 3.2 15.3 - - - +
124D ALA* 4.9 3.6 - - - -
125D PRO* 5.0 2.5 - - + -
135D ALA* 6.5 0.2 - - + -
136D ALA* 1.3 75.5 - - - +
138D GLY* 1.3 60.2 + - - +
153D TRP* 4.1 14.4 - - + -
180D VAL* 3.5 4.4 - - - +
181D VAL* 2.9 55.8 + - + +
183D VAL* 4.5 11.0 - - + -
194D TYR* 3.8 32.3 - - + -
211D VAL* 4.2 15.7 - - + +
212D GLU 4.4 6.1 - - - +
213D ARG 4.2 24.7 - - - +
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Residues in contact with GLY 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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122D PRO* 3.5 4.9 - - - +
123D LEU* 2.6 45.8 + - - +
137D LEU* 1.3 80.0 - - - +
139D CYS* 1.3 61.5 + - - -
153D TRP* 3.7 11.2 - - - -
179D SER 3.2 11.2 - - - -
180D VAL* 4.1 0.9 - - - -
211D VAL* 3.6 9.2 - - - +
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Residues in contact with CYS 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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120D VAL* 3.9 14.6 - - + -
121D PHE 3.4 2.9 - - - -
123D LEU* 3.6 7.0 - - - +
138D GLY* 1.3 78.8 - - - -
140D LEU* 1.3 59.7 + - - +
141D VAL* 3.9 8.5 + - + +
151D VAL* 5.6 0.2 - - + -
153D TRP* 4.0 4.3 - - + -
178D SER* 3.3 5.5 - - - -
179D SER* 2.8 39.0 + - - +
196D CYS* 2.1 52.3 - - + -
209D LYS* 4.2 3.8 - - - -
211D VAL* 4.1 13.2 - - - -
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Residues in contact with LEU 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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124C GLN* 4.5 5.8 - - - +
131C SER* 3.7 32.3 - - - +
133C VAL* 4.4 21.8 - - + -
178C THR* 4.9 8.5 - - + +
119D SER 3.4 2.4 - - - +
120D VAL* 3.2 5.3 - - - -
121D PHE* 2.7 54.5 + - + +
123D LEU* 4.1 14.3 - - + +
139D CYS* 1.3 71.9 - - - +
141D VAL* 1.3 58.9 + - - +
142D LYS* 3.7 16.9 + - + -
176D SER* 3.9 17.3 - - - +
177D LEU 3.8 15.0 - - - +
178D SER* 4.6 6.1 - - - -
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Residues in contact with VAL 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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118D PRO* 3.6 26.9 - - + -
119D SER 3.6 3.1 - - - -
120D VAL* 4.3 8.3 - - + +
139D CYS* 4.6 9.4 - - + +
140D LEU* 1.3 73.0 - - - +
142D LYS* 1.3 59.0 + - - +
144D TYR* 3.6 14.6 - - + -
149D VAL* 4.3 6.7 - - + -
151D VAL* 4.5 5.6 - - + -
176D SER* 3.5 4.7 - - - -
177D LEU* 2.9 51.6 + - + +
179D SER 5.7 0.4 - - - +
198D VAL* 3.9 38.8 - - + -
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Residues in contact with LYS 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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124C GLN* 3.2 21.5 - - - +
129C THR* 4.5 14.5 + - - +
131C SER* 3.0 24.9 - - - +
178C THR* 6.1 0.4 - - - -
180C THR* 5.4 3.2 - - - +
118D PRO* 3.5 2.3 - - - +
119D SER* 2.8 39.6 + - - +
121D PHE* 4.3 20.9 - - + -
140D LEU* 4.5 11.7 - - + -
141D VAL* 1.3 73.9 - - - +
143D ASP* 1.3 98.0 + - - +
144D TYR* 3.6 2.0 - - - -
170D GLN* 3.5 16.2 + - - -
176D SER* 3.7 17.3 - - - +
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Residues in contact with ASP 143 (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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116D LYS* 3.0 38.1 + - - +
117D GLY 3.6 3.6 - - - +
119D SER* 5.4 2.1 - - - +
142D LYS* 1.3 99.5 + - - +
144D TYR* 1.3 60.3 + - - +
170D GLN* 3.0 22.9 + - - -
172D SER* 4.6 1.9 + - - -
174D LEU* 3.8 26.1 - - + +
175D TYR 3.0 12.7 + - - -
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Residues in contact with TYR 144 (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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116D LYS 3.2 11.7 - - - +
118D PRO* 3.8 21.8 - - + -
141D VAL* 3.6 37.7 - - + -
143D ASP* 1.3 80.8 - - - +
145D PHE* 1.3 66.6 + - - +
146D PRO 3.7 17.0 - - - -
147D GLU* 2.8 33.3 + - - -
149D VAL* 3.8 15.6 - - + +
167D ALA* 3.2 15.6 - - - +
174D LEU* 3.7 2.2 - - - -
175D TYR* 2.9 53.9 + - + -
176D SER* 4.0 2.5 - - - -
177D LEU* 3.8 12.2 - - - +
200D HIS* 3.7 10.5 - + - +
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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