Contacts of the strand formed by residues 185 - 195 (chain D) in PDB entry 3Q3G
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 185 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125D ALA* 4.5 7.4 - - + -
128D THR* 3.8 26.7 - - + +
155D GLY* 3.8 30.1 - - - +
156D TYR 3.8 2.0 - - - -
157D PHE* 3.8 24.0 - - + -
181D LEU* 3.5 8.0 - - - -
182D GLN 2.7 41.9 + - - +
183D SER* 4.9 9.9 - - - -
184D ASP* 1.4 82.4 - - + +
186D TYR* 1.3 58.5 + - - +
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Residues in contact with TYR 186 (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 THR* 3.7 24.9 + - - +
155D GLY* 2.9 24.3 + - - -
156D TYR* 2.9 53.1 + + + +
157D PHE* 3.6 26.8 - + - -
158D PRO* 5.2 0.2 - - + -
159D GLU* 3.4 48.6 - - + +
179D ALA* 4.0 11.4 - - + -
180D VAL 3.4 10.5 - - - -
181D LEU* 3.6 26.1 - - + +
185D LEU* 1.3 72.0 - - - +
187D THR* 1.3 61.9 + - - +
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Residues in contact with THR 187 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184C THR* 5.5 2.9 - - + -
152D LEU* 3.8 21.1 - - + -
153D VAL 3.3 5.8 - - - +
154D LYS* 3.4 22.6 - - + +
155D GLY* 3.6 1.9 + - - -
179D ALA* 3.3 4.0 - - - -
180D VAL* 2.9 38.7 + - + +
182D GLN* 2.7 38.8 + - - +
186D TYR* 1.3 77.4 + - - +
188D LEU* 1.3 63.7 + - - +
605D EDO 3.4 17.1 + - - +
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Residues in contact with LEU 188 (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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152D LEU* 3.5 5.5 - - - +
153D VAL* 2.8 46.1 + - + +
156D TYR* 3.7 23.8 - - + +
159D GLU* 4.7 2.7 - - - +
161D VAL* 3.9 14.6 - - + +
163D VAL* 3.8 21.3 - - + -
176D THR* 3.8 23.3 - - + -
177D PHE 3.6 19.7 - - - +
178D PRO* 5.3 0.2 - - + -
179D ALA* 4.2 10.5 - - + +
187D THR* 1.3 74.9 - - - +
189D SER* 1.3 69.7 + - - +
605D EDO 3.5 11.2 - - - -
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Residues in contact with SER 189 (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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139C VAL* 4.9 2.0 - - - -
141C PHE* 3.7 17.9 - - - -
182C SER* 2.9 27.4 + - - -
135D LEU* 4.7 2.2 - - - -
151D CYS 3.2 12.1 - - - -
152D LEU* 4.3 8.5 - - - -
176D THR* 3.7 3.3 - - - +
177D PHE* 2.9 29.3 + - - -
188D LEU* 1.3 79.8 - - - +
190D SER* 1.3 60.5 + - - +
605D EDO 3.3 17.1 + - - -
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Residues in contact with SER 190 (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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141C PHE* 3.7 4.8 - - - -
150D GLY* 3.1 5.9 - - - -
151D CYS* 3.0 32.9 + - - +
163D VAL* 3.7 19.4 - - - +
165D TRP* 2.9 32.6 + - - -
174D VAL* 4.2 0.5 - - - +
175D HIS 3.7 7.2 + - - -
176D THR* 2.7 26.7 + - - -
188D LEU* 4.7 0.2 - - - +
189D SER* 1.3 73.5 - - - +
191D SER* 1.3 62.0 + - - +
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Residues in contact with SER 191 (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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141C PHE* 3.8 17.0 - - - -
143C ASN* 2.9 29.3 + - - -
148D THR* 3.8 6.4 - - - +
149D LEU 3.5 5.2 - - - -
165D TRP* 4.4 1.6 - - - -
173D GLY 4.1 1.4 + - - -
174D VAL* 3.3 8.7 - - - +
175D HIS* 3.0 46.5 + - - -
177D PHE* 3.9 7.8 - - - -
190D SER* 1.3 73.0 - - - +
192D VAL* 1.3 63.2 + - - +
193D THR* 4.5 1.7 + - - -
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Residues in contact with VAL 192 (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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147D VAL 3.7 0.9 - - - +
148D THR* 3.3 2.9 - - - +
149D LEU* 2.8 50.5 + - + +
165D TRP* 3.6 36.3 - - + -
170D LEU* 3.9 25.1 - - + -
172D SER 5.0 0.4 - - - +
173D GLY 3.4 4.0 - - - +
174D VAL* 3.4 24.2 - - + -
191D SER* 1.3 73.6 + - - +
193D THR* 1.3 67.6 + - - +
194D VAL* 4.2 8.3 - - + -
204D VAL* 3.8 12.3 - - + -
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Residues in contact with THR 193 (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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120C THR* 6.4 0.9 - - + -
143C ASN* 4.6 4.3 + - - -
144C ASN* 5.6 1.9 + - - -
146D MET* 3.6 42.1 - - + +
147D VAL 3.4 5.8 - - - +
148D THR* 2.8 28.4 + - - +
170D LEU* 5.5 0.7 - - - +
172D SER 4.3 4.9 - - - +
173D GLY* 3.0 28.7 + - - -
175D HIS* 6.1 0.3 - - - -
191D SER* 4.5 3.3 + - - -
192D VAL* 1.3 72.2 - - - +
194D VAL* 1.3 68.1 + - - +
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Residues in contact with VAL 194 (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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146D MET* 3.5 6.1 - - - -
147D VAL* 2.7 51.5 + - + +
149D LEU* 4.5 4.9 - - + -
170D LEU* 3.9 36.8 - - + -
192D VAL* 4.2 8.7 - - + +
193D THR* 1.3 78.6 - - - +
195D PRO* 1.4 79.7 - - + +
198D PRO* 4.4 6.5 - - + -
199D ARG* 3.8 17.5 - - + -
204D VAL* 4.2 14.6 - - + -
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Residues in contact with PRO 195 (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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145D SER 3.4 10.3 - - - +
146D MET* 4.0 14.1 - - + -
147D VAL* 3.7 2.1 - - - +
194D VAL* 1.4 97.8 - - + +
196D SER* 1.3 60.4 + - - +
197D SER* 3.6 10.1 - - - +
198D PRO* 3.0 40.3 - - + +
199D ARG 3.8 1.2 + - - -
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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