Contacts of the strand formed by residues 165 - 172 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154B ILE 4.1 0.2 - - - +
155B THR* 3.2 5.4 - - - -
156B TYR* 2.9 49.1 + - + +
163B GLN* 3.9 11.0 - - + +
164B LYS* 1.3 76.8 - - - +
166B THR* 1.3 66.8 + - - +
167B TYR* 3.6 38.4 - - + +
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Residues in contact with THR 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153B GLU* 3.6 33.2 - - + +
154B ILE 3.8 2.0 - - - -
155B THR* 3.6 22.9 - - + +
164B LYS* 4.2 12.4 + - - +
165B VAL* 1.3 79.8 - - - +
167B TYR* 1.3 70.9 + - - +
168B LEU 4.3 0.6 + - - +
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Residues in contact with TYR 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153B GLU* 3.2 4.4 - - - +
154B ILE* 2.8 60.1 + - + +
156B TYR* 5.0 2.6 - - + -
165B VAL* 3.6 38.7 - - + +
166B THR* 1.3 81.2 - - - +
168B LEU* 1.3 60.3 + - - +
169B VAL 3.4 0.2 + - - -
142D THR* 3.7 21.3 - - + -
143D ASP 5.3 0.9 - - - -
144D PHE* 3.5 57.4 - + + +
145D VAL 4.9 2.9 + - - -
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Residues in contact with LEU 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151B LYS* 3.6 31.2 - - + +
152B VAL 3.5 17.7 - - - +
153B GLU* 4.4 5.8 - - + +
166B THR* 4.3 0.8 - - - +
167B TYR* 1.3 70.9 - - - +
169B VAL* 1.3 61.5 + - - +
170B HIS* 3.5 21.8 - - - +
171B ASN* 4.2 19.7 - - + +
142D THR* 3.1 17.7 + - - +
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Residues in contact with VAL 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152B VAL* 2.9 35.4 + - + +
153B GLU 4.2 0.2 - - - -
154B ILE* 3.7 33.7 - - + +
167B TYR 3.4 0.4 + - - -
168B LEU* 1.3 76.3 - - - +
170B HIS* 1.3 60.1 + - - +
141D ALA* 6.1 0.6 - - - -
142D THR* 3.8 11.7 + - - +
154D ILE* 4.6 2.9 - - + -
181D GLY* 3.9 35.2 - - - +
182D MET 3.9 17.5 - - - +
183D TYR* 3.5 23.0 - - + -
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Residues in contact with HIS 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151B LYS* 3.7 0.3 - - - -
152B VAL* 2.9 29.6 + - + +
168B LEU* 3.5 11.3 - - - +
169B VAL* 1.3 84.1 + - + +
171B ASN* 1.3 76.6 + - + +
172B PHE* 3.5 34.8 + + + -
183D TYR* 3.4 54.1 + + + -
185D GLN* 2.5 33.5 + - - -
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Residues in contact with ASN 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150B GLY 3.7 14.8 + - - -
151B LYS* 3.1 33.4 + - - +
168B LEU* 4.2 14.8 - - + +
170B HIS* 1.3 90.2 + - + +
172B PHE* 1.3 66.2 + - - +
173B GLU* 3.0 26.0 + - + +
159D SER* 5.9 0.4 + - - -
185D GLN* 4.5 0.2 - - - +
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Residues in contact with PHE 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146B VAL* 4.0 25.1 - - + -
148B GLY 4.1 1.1 - - - +
149B PRO* 3.2 7.1 - - + +
150B GLY 2.7 43.4 + - - +
152B VAL* 4.0 12.8 - - + -
170B HIS* 3.5 35.4 - + + -
171B ASN* 1.3 69.6 + - - +
173B GLU* 1.3 60.5 + - - +
174B GLU 3.5 2.2 - - - +
175B GLY 3.8 12.3 - - - +
176B GLY* 3.5 37.5 - - - -
177B GLY* 3.9 4.7 - - - -
178B VAL 3.9 20.9 - - - -
179B ALA* 5.1 0.2 - - + -
159D SER* 4.3 1.6 + - - -
183D TYR* 4.3 7.4 - + + -
184D ASN 4.0 2.9 - - - -
185D GLN* 3.9 21.1 - - + -
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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