Contacts of the strand formed by residues 162 - 172 (chain D) in PDB entry 3LBF
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 162 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141D PRO* 4.0 2.5 - - - +
142D PHE 3.5 7.6 - - - +
145D ILE* 3.6 26.0 - - + +
158D LEU 3.5 14.1 + - - +
159D MET* 3.0 15.8 + - - +
160D THR 3.8 0.5 - - - +
161D GLN* 1.3 79.3 - - - +
163D ASP* 1.3 65.6 + - - +
166D GLY* 3.9 11.0 - - - +
167D ILE 3.8 29.2 - - - +
168D LEU* 3.9 22.4 - - + +
182D VAL* 4.2 7.6 - - + +
184D ARG* 2.8 35.9 + - + +
189D PHE* 4.2 16.2 - - + -
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Residues in contact with ASP 163 (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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78D ARG* 5.3 4.9 + - - +
141D PRO* 3.6 32.2 - - + +
142D PHE 2.9 20.4 + - - +
143D ASP* 4.3 12.8 - - - +
162D LEU* 1.3 76.7 - - - +
164D GLU* 1.3 73.7 + - - +
165D GLY 3.1 0.3 + - - -
166D GLY* 2.7 25.4 + - - -
184D ARG* 3.6 8.7 - - - -
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Residues in contact with GLU 164 (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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143D ASP* 4.9 4.3 - - - +
163D ASP* 1.3 90.0 + - - +
165D GLY* 1.3 66.4 + - - +
166D GLY 3.4 0.5 + - - -
183D ARG* 4.4 3.5 + - - -
184D ARG* 4.4 5.9 + - - +
185D ARG* 3.6 9.9 + - - +
186D GLY* 2.5 49.5 + - - +
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Residues in contact with GLY 165 (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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143D ASP* 4.6 1.2 - - - +
164D GLU* 1.3 75.7 + - - +
166D GLY* 1.3 66.8 + - - +
167D ILE* 3.7 12.1 + - - +
183D ARG* 3.7 20.4 + - - +
184D ARG 3.0 21.1 + - - -
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Residues in contact with GLY 166 (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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142D PHE 4.1 2.9 - - - -
143D ASP* 3.4 17.9 - - - -
162D LEU* 3.9 15.7 - - - -
163D ASP 2.7 24.2 + - - -
164D GLU 3.2 1.4 + - - -
165D GLY* 1.3 74.7 - - - +
167D ILE* 1.3 59.4 + - - +
182D VAL 3.8 0.3 - - - +
183D ARG* 3.4 4.9 - - - -
184D ARG* 3.0 25.0 + - - +
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Residues in contact with ILE 167 (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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70D LEU 3.7 15.9 - - - +
71D LEU* 4.0 22.0 - - - +
72D GLU* 3.8 24.9 - - + +
143D ASP 3.0 11.0 + - - +
144D ALA* 3.4 4.5 - - - -
145D ILE 3.0 23.7 + - - +
162D LEU* 3.8 2.9 - - - +
165D GLY 3.9 9.9 - - - +
166D GLY* 1.3 78.0 - - - +
168D LEU* 1.3 61.3 + - - +
169D VAL* 4.0 10.1 - - + -
181D ARG* 3.4 36.3 - - - +
182D VAL 3.3 4.7 - - - +
183D ARG* 4.0 14.4 - - + -
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Residues in contact with LEU 168 (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 ILE* 3.3 31.2 - - + +
147D VAL* 3.9 17.7 - - + -
154D ILE* 3.9 28.3 - - + -
158D LEU* 4.0 24.2 - - + +
159D MET* 4.4 3.8 - - + -
162D LEU* 3.9 19.2 - - + +
167D ILE* 1.3 73.8 - - - +
169D VAL* 1.3 71.5 + - - +
170D LEU* 3.9 15.3 - - + -
180D LYS 3.8 0.7 - - - +
181D ARG* 3.4 3.5 - - - -
182D VAL* 2.7 48.5 + - + +
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Residues in contact with VAL 169 (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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67D MET* 4.0 27.8 - - + +
70D LEU* 3.7 29.4 - - + -
71D LEU* 3.7 25.4 - - + -
145D ILE 2.9 9.3 + - - +
146D ILE* 3.4 4.1 - - + +
147D VAL* 3.0 26.2 + - - +
167D ILE* 4.0 10.5 - - + -
168D LEU* 1.3 79.2 - - - +
170D LEU* 1.3 63.4 + - - +
179D LEU* 3.8 21.1 - - + -
180D LYS 3.4 6.5 - - - +
181D ARG* 4.4 5.6 - - - -
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Residues in contact with LEU 170 (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* 3.5 26.7 - - + -
151D PRO* 3.8 24.5 - - + -
154D ILE* 4.3 11.7 - - + -
155D PRO* 3.8 17.3 - - + -
158D LEU* 5.3 0.2 - - + -
168D LEU* 3.9 25.1 - - + -
169D VAL* 1.3 74.7 - - - +
171D PRO* 1.3 67.5 - - + +
172D VAL* 3.5 25.1 - - + -
179D LEU* 3.8 6.3 - - - -
180D LYS* 2.8 41.6 + - + +
182D VAL* 4.5 4.0 - - + -
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Residues in contact with PRO 171 (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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67D MET* 4.3 7.0 - - + -
147D VAL 3.2 18.8 - - - +
149D ALA 3.7 13.7 - - - +
150D ALA* 3.2 24.1 - - + -
151D PRO* 3.3 9.0 - - - +
170D LEU* 1.3 84.7 - - + +
172D VAL* 1.3 60.4 + - - +
177D GLN* 4.4 1.1 - - - +
178D TYR 3.4 7.4 - - - +
179D LEU* 3.9 4.7 - - + -
197D VAL* 3.7 12.8 - - + -
199D PHE* 3.5 46.0 - - + -
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Residues in contact with VAL 172 (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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156C THR* 4.1 15.0 - - + +
151D PRO 3.4 7.2 - - - +
152D PRO 3.6 20.2 - - - +
153D GLU* 4.3 6.3 - - - +
154D ILE* 3.8 18.2 - - + +
170D LEU* 3.5 33.0 - - + +
171D PRO* 1.3 76.8 - - - +
173D GLY* 1.3 61.0 + - - +
176D HIS 4.1 1.0 - - - +
177D GLN* 3.3 3.6 - - - -
178D TYR* 2.9 35.3 + - - +
180D LYS* 4.1 17.7 - - + -
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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
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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