Contacts of the strand formed by residues 165 - 172 (chain D) in PDB entry 6B0Z
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 165 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154D ILE 3.9 1.2 - - - +
155D THR* 3.2 3.0 - - - +
156D TYR* 2.7 49.5 + - + +
163D GLN* 3.9 31.2 - - + +
164D LYS* 1.3 79.0 - - - +
166D THR* 1.3 65.7 + - - +
167D TYR* 3.4 41.8 - - + +
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Residues in contact with THR 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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153D GLU* 3.6 37.5 - - + +
154D ILE 3.6 3.1 - - - -
155D THR* 3.0 26.8 + - - +
164D LYS* 4.3 10.1 + - - +
165D VAL* 1.3 76.9 - - - +
167D TYR* 1.3 63.6 + - - +
168D LEU 4.2 0.9 + - - +
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Residues in contact with TYR 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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142B THR* 3.7 24.9 - - + -
143B ASP 5.4 0.9 - - - -
144B PHE* 3.4 55.4 - + + +
145B VAL 5.0 1.9 + - - -
153D GLU* 3.2 4.7 - - - +
154D ILE* 2.7 54.9 + - + +
156D TYR* 5.1 1.3 - - + -
165D VAL* 3.4 39.2 - - + +
166D THR* 1.3 79.4 - - - +
168D LEU* 1.3 60.2 + - - +
169D VAL 3.5 0.2 + - - -
218D LYS* 5.1 5.1 + - - -
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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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142B THR* 3.4 16.2 + - - +
151D LYS* 3.6 34.8 - - + +
152D VAL 3.6 16.4 - - - +
153D GLU* 4.2 6.1 - - + +
166D THR* 4.2 1.6 + - - +
167D TYR* 1.3 71.8 - - - +
169D VAL* 1.3 62.4 + - - +
170D HIS* 3.8 18.4 - - - +
171D ASN* 4.0 12.8 - - + +
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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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140B ARG 4.9 1.7 - - - +
142B THR* 4.1 11.5 + - - +
154B ILE* 4.5 2.7 - - + -
181B GLY* 4.1 20.9 - - - +
182B MET 4.0 14.8 - - - +
183B TYR* 3.7 34.4 - - + -
152D VAL* 2.8 38.7 + - + +
154D ILE* 3.7 35.7 - - + +
167D TYR 3.5 0.8 + - - -
168D LEU* 1.3 76.2 - - - +
170D HIS* 1.3 61.3 + - - +
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Residues in contact with HIS 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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183B TYR* 3.3 58.3 + + + -
185B GLN* 3.7 22.6 + - + +
152D VAL* 2.9 28.7 + - - +
168D LEU* 3.7 10.5 - - - +
169D VAL* 1.3 84.0 - - - +
171D ASN* 1.3 90.1 + - - +
172D PHE* 3.7 27.4 + + + -
173D GLU 5.2 0.4 + - - -
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Residues in contact with ASN 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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159B SER* 5.2 2.3 + - - -
150D GLY* 3.6 12.7 - - - +
151D LYS* 2.8 38.0 - - - +
168D LEU* 4.0 12.6 - - + +
170D HIS* 1.3 90.5 + - - +
172D PHE* 1.3 68.5 + - - +
173D GLU* 3.2 35.5 + - - +
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Residues in contact with PHE 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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159B SER* 4.5 1.0 + - - -
183B TYR* 4.1 8.7 - - + -
184B ASN 3.6 19.5 - - - -
185B GLN* 4.1 10.5 - - + -
146D VAL* 3.8 18.4 - - + -
148D GLY 4.2 2.7 - - - +
149D PRO* 3.2 7.0 - - - +
150D GLY 2.8 43.0 + - - +
152D VAL* 3.5 26.7 - - + -
170D HIS* 3.7 33.0 - + + -
171D ASN* 1.3 70.8 - - - +
173D GLU* 1.3 58.4 + - - +
174D GLU 3.6 1.8 - - - +
175D GLY 3.6 14.4 - - - +
176D GLY 3.9 18.8 - - - -
177D GLY* 4.0 9.9 - - - -
178D VAL 3.8 19.3 - - - -
179D ALA* 5.0 0.2 - - + -
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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