Contacts of the strand formed by residues 174 - 184 (chain D) in PDB entry 1CT8
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 174 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117D THR* 3.8 33.2 - - + +
144D GLY* 3.9 21.5 - - - +
145D TYR 3.6 12.8 - - - +
146D PHE* 3.9 4.3 - - + -
170D LEU* 3.5 2.1 - - - +
171D GLN* 2.6 61.3 + - - +
173D ASP* 1.3 99.7 - - - +
175D TYR* 1.3 56.8 + - - +
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Residues in contact with TYR 175 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110D THR* 5.6 4.7 - - - +
144D GLY 2.8 22.5 + - - -
145D TYR* 2.9 51.3 + + + +
146D PHE* 3.9 27.7 - + - -
147D PRO* 5.1 0.2 - - + -
148D GLU* 3.4 42.2 - - + +
168D ALA* 4.0 13.9 - - + -
169D VAL 3.3 7.0 - - - +
170D LEU* 3.6 47.1 - - + +
171D GLN* 3.1 6.1 - - - -
174D LEU* 1.3 71.0 - - - +
176D THR* 1.3 58.9 + - - +
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Residues in contact with THR 176 (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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160C LEU* 4.1 28.3 - - + +
178C THR* 5.6 4.9 - - + +
141D LEU* 3.7 28.5 - - + -
142D VAL 3.3 7.6 - - - +
143D LYS* 3.7 15.8 - - + +
144D GLY 3.5 7.4 + - - -
145D TYR* 4.4 0.7 - - - -
167D PRO 4.3 1.0 - - - +
168D ALA* 3.3 1.0 - - - -
169D VAL* 2.9 32.6 + - - +
171D GLN* 2.7 23.8 + - - +
175D TYR* 1.3 73.4 + - - +
177D LEU* 1.3 65.6 + - - +
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Residues in contact with LEU 177 (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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160C LEU* 6.3 0.2 - - - -
141D LEU* 3.6 4.3 - - - +
142D VAL* 2.8 44.4 + - + +
145D TYR* 3.9 15.0 - - + +
148D GLU* 5.2 1.3 - - - +
150D VAL* 3.8 23.1 - - + +
152D VAL* 3.8 26.7 - - + -
165D THR* 4.2 11.2 - - + -
166D PHE* 3.2 25.4 - - - +
167D PRO* 4.8 2.0 - - + -
168D ALA* 3.9 11.4 - - + +
176D THR* 1.3 78.3 - - - +
178D SER* 1.3 71.8 + - - +
179D SER 4.8 0.2 - - - +
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Residues in contact with SER 178 (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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133C VAL* 4.9 6.2 - - - +
135C PHE* 3.7 13.1 - - - -
176C SER* 3.2 29.6 + - - -
178C THR* 4.9 2.9 + - - -
124D LEU* 5.2 0.4 - - - -
140D CYS 3.2 13.2 - - - -
141D LEU* 4.3 13.9 - - - -
165D THR* 3.7 0.5 - - - -
166D PHE* 2.8 32.5 + - - +
177D LEU* 1.3 82.3 - - - +
179D SER* 1.3 64.2 + - - +
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Residues in contact with SER 179 (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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135C PHE* 3.5 6.7 - - - -
139D GLY* 3.2 3.8 - - - -
140D CYS* 3.0 31.5 + - - -
142D VAL* 6.3 0.2 - - - -
152D VAL* 3.9 23.0 - - - +
154D TRP* 3.0 29.3 + - - -
163D VAL* 3.9 1.9 - - - +
164D HIS 3.2 7.8 + - - -
165D THR* 3.0 25.5 + - - -
166D PHE* 4.4 0.2 - - - -
177D LEU* 5.1 0.2 - - - -
178D SER* 1.3 76.2 - - - +
180D SER* 1.3 61.0 + - - +
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Residues in contact with SER 180 (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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135C PHE* 3.4 35.2 - - - -
137C ASN* 3.6 13.0 + - - -
137D THR* 4.0 7.6 - - - -
138D LEU 3.4 7.0 - - - -
139D GLY* 4.3 0.2 - - - -
154D TRP* 4.3 2.5 - - - -
162D GLY 4.1 1.3 + - - -
163D VAL* 3.2 7.1 - - - +
164D HIS* 2.8 52.0 + - - +
166D PHE* 3.9 3.5 - - - -
179D SER* 1.3 73.2 - - - +
181D VAL* 1.3 62.7 + - - +
182D THR* 5.6 0.6 + - - -
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Residues in contact with VAL 181 (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 VAL 3.7 1.0 - - - +
137D THR* 3.3 2.4 - - - -
138D LEU* 2.9 51.1 + - + +
154D TRP* 3.7 39.5 - - + +
159D LEU* 3.7 25.8 - - + -
161D SER 4.1 6.7 - - - +
162D GLY 3.4 2.5 - - - -
163D VAL* 3.6 24.2 - - + -
180D SER* 1.3 75.9 - - - +
182D THR* 1.3 63.8 + - - +
183D VAL* 4.3 4.3 - - + -
193D VAL* 4.2 5.4 - - + -
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Residues in contact with THR 182 (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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137C ASN* 4.6 8.0 + - - -
135D MET* 3.7 45.3 - - + +
136D VAL 3.3 8.3 - - - +
137D THR* 3.2 22.5 + - - +
161D SER 4.1 11.8 - - - +
162D GLY* 3.2 20.9 + - - -
164D HIS* 5.7 0.9 + - - -
180D SER* 5.6 0.5 + - - -
181D VAL* 1.3 73.8 - - - +
183D VAL* 1.3 67.5 + - - +
184D PRO* 4.8 0.2 - - - +
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Residues in contact with VAL 183 (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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135D MET* 3.4 7.4 - - - -
136D VAL* 2.8 54.2 + - + +
138D LEU* 3.9 15.9 - - + -
159D LEU* 3.8 39.3 - - + -
181D VAL* 4.3 7.6 - - + -
182D THR* 1.3 80.4 - - - +
184D PRO* 1.3 79.3 - - + +
187D THR* 4.1 19.5 - - + +
188D TRP* 4.2 5.2 - - + -
193D VAL* 4.9 1.8 - - + -
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Residues in contact with PRO 184 (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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134D SER* 3.2 13.2 - - - +
135D MET* 3.8 13.4 - - + -
136D VAL* 4.4 0.4 - - - -
182D THR 4.8 0.4 - - - +
183D VAL* 1.3 90.3 - - + +
185D SER* 1.3 53.1 + - - +
186D SER* 2.7 17.8 + - - +
187D THR* 2.7 46.6 + - - +
188D TRP 3.7 2.1 + - - -
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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