Contacts of the strand formed by residues 165 - 172 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154C ILE 4.2 0.2 - - - +
155C THR* 3.2 5.1 - - - -
156C TYR* 2.8 50.1 + - + +
158C PRO* 5.8 0.2 - - + -
163C GLN* 4.0 10.5 - - + +
164C LYS* 1.3 77.0 - - - +
166C THR* 1.3 65.7 + - - +
167C TYR* 3.7 34.2 - - + +
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Residues in contact with THR 166 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153C GLU* 3.6 37.0 - - + +
154C ILE 3.8 2.2 - - - -
155C THR* 3.5 20.3 - - + +
164C LYS* 4.0 13.4 + - - +
165C VAL* 1.3 77.9 - - - +
167C TYR* 1.3 68.8 + - - +
168C LEU 4.3 1.0 + - - +
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Residues in contact with TYR 167 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A THR* 4.0 20.6 - - + -
143A ASP 5.1 1.1 - - - -
144A PHE* 3.4 61.5 - + + +
145A VAL 4.6 3.8 + - - -
153C GLU* 3.5 3.5 - - - +
154C ILE* 2.8 56.4 + - + +
156C TYR* 5.1 1.6 - - + -
165C VAL* 3.7 34.7 - - + +
166C THR* 1.3 80.1 - - - +
168C LEU* 1.3 61.9 + - - +
218C LYS* 6.4 1.1 - - - -
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Residues in contact with LEU 168 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A THR* 3.3 20.4 + - - +
151C LYS* 3.8 26.7 - - + -
152C VAL 3.5 13.0 - - - +
153C GLU* 4.4 5.2 - - + +
166C THR* 4.2 2.0 + - - +
167C TYR* 1.3 71.9 - - - +
169C VAL* 1.3 67.1 + - - +
170C HIS* 3.6 17.5 - - - +
171C ASN* 3.5 26.5 - - - +
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Residues in contact with VAL 169 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A THR* 4.1 10.6 + - - +
154A ILE* 4.5 2.2 - - + -
181A GLY* 4.0 30.7 - - - +
182A MET 4.1 4.7 - - - +
183A TYR* 3.7 37.6 - - + -
152C VAL* 3.0 33.2 + - + +
154C ILE* 3.8 36.8 - - + +
168C LEU* 1.3 78.0 - - - +
170C HIS* 1.3 65.2 + - + +
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Residues in contact with HIS 170 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A TYR* 3.4 53.6 + + + -
185A GLN* 3.1 30.6 + - - +
151C LYS* 3.7 1.2 - - - -
152C VAL* 2.9 29.0 + - + +
168C LEU* 3.6 10.1 - - - +
169C VAL* 1.3 84.2 + - + +
171C ASN* 1.3 80.5 + - - +
172C PHE* 3.7 32.3 + + + -
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Residues in contact with ASN 171 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A GLN* 4.5 0.2 - - - +
150C GLY 3.9 3.5 - - - -
151C LYS* 3.3 39.6 - - - +
168C LEU* 3.5 26.2 - - - +
170C HIS* 1.3 89.7 + - - +
172C PHE* 1.3 59.5 + - - +
173C GLU* 3.2 22.4 + - + +
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Residues in contact with PHE 172 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A SER* 4.6 1.0 + - - -
183A TYR* 4.1 8.1 - - + -
184A ASN 3.7 19.1 - - - -
185A GLN* 4.0 15.3 - - + +
146C VAL* 3.8 23.8 - - + -
148C GLY 4.1 1.6 - - - +
149C PRO* 3.2 7.6 - - + +
150C GLY* 2.8 50.1 + - - +
152C VAL* 3.7 24.9 - - + -
170C HIS* 3.7 35.2 - + + -
171C ASN* 1.3 69.8 - - - +
173C GLU* 1.3 59.3 + - - +
174C GLU 3.6 0.7 - - - -
175C GLY 3.8 13.0 - - - +
176C GLY* 3.7 29.2 - - - -
177C GLY* 4.1 1.3 - - - -
178C VAL 3.9 13.2 - - - -
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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