Contacts of the strand formed by residues 165 - 172 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154A ILE 4.0 0.5 - - - +
155A THR* 3.2 5.2 - - - -
156A TYR* 2.9 48.8 + - + +
158A PRO* 6.2 0.2 - - + -
163A GLN* 4.1 18.8 - - + +
164A LYS* 1.3 77.7 - - - +
166A THR* 1.3 65.4 + - - +
167A TYR* 3.4 43.7 - - + +
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Residues in contact with THR 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A GLU* 3.6 35.7 - - + +
154A ILE 3.8 2.2 - - - -
155A THR* 3.5 26.0 - - + +
164A LYS* 4.2 15.7 + - - +
165A VAL* 1.3 75.1 - - - +
167A TYR* 1.3 64.1 + - - +
168A LEU 4.1 0.9 + - - -
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Residues in contact with TYR 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A GLU* 3.3 6.5 - - - +
154A ILE* 2.8 58.1 + - + +
155A THR* 5.1 0.2 - - - -
156A TYR* 5.0 2.2 - - + -
165A VAL* 3.4 40.5 - - + +
166A THR* 1.3 74.5 - - - +
168A LEU* 1.3 60.8 + - - +
142C THR* 3.7 21.8 - - + -
143C ASP 5.1 1.3 - - - -
144C PHE* 3.4 59.4 - + + +
145C VAL 4.9 2.9 + - - -
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Residues in contact with LEU 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A LYS* 4.4 19.7 - - + -
152A VAL 3.7 14.8 - - - +
153A GLU* 4.2 15.9 - - + +
166A THR 4.1 1.8 + - - -
167A TYR* 1.3 71.8 - - - +
169A VAL* 1.3 61.5 + - - +
170A HIS* 3.8 20.9 - - - +
171A ASN* 4.0 14.8 - - + +
142C THR* 3.2 18.7 + - - +
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Residues in contact with VAL 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A VAL* 2.9 35.7 + - + +
154A ILE* 3.8 35.9 - - + +
167A TYR 3.5 0.4 + - - -
168A LEU* 1.3 77.1 - - - +
170A HIS* 1.3 61.6 + - - +
179A ALA* 5.1 0.2 - - + -
140C ARG 6.0 0.2 - - - -
141C ALA* 6.3 0.2 - - - -
142C THR* 4.0 10.5 + - - +
154C ILE* 4.4 2.5 - - + -
181C GLY* 4.0 25.4 - - - +
182C MET 3.9 26.2 - - - +
183C TYR* 3.7 20.3 - - + -
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Residues in contact with HIS 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A LYS* 3.8 0.2 - - - -
152A VAL* 2.9 28.0 + - - +
168A LEU* 3.7 10.4 - - - -
169A VAL* 1.3 84.6 + - + +
171A ASN* 1.3 88.2 + - - +
172A PHE* 3.7 24.5 + + + -
183C TYR* 3.2 54.5 + + + -
185C GLN* 3.3 26.7 + - - -
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Residues in contact with ASN 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A GLY* 3.7 10.1 - - - +
151A LYS* 3.5 33.3 - - + +
168A LEU* 4.0 15.0 - - + +
170A HIS* 1.3 89.7 + - - +
172A PHE* 1.3 67.0 + - - +
173A GLU* 3.3 34.7 + - + +
159C SER* 6.0 0.5 - - - -
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Residues in contact with PHE 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A VAL* 3.8 18.2 - - + -
148A GLY 4.1 1.6 - - - +
149A PRO* 3.1 7.2 - - + +
150A GLY 2.9 48.8 + - - +
152A VAL* 3.6 25.4 - - + -
170A HIS* 3.8 23.1 - + + -
171A ASN* 1.3 74.0 - - - +
173A GLU* 1.3 59.7 + - - +
175A GLY 3.7 13.2 - - - +
176A GLY 3.8 27.8 - - - -
177A GLY* 4.1 0.9 - - - -
178A VAL 3.7 21.1 - - - -
159C SER* 5.5 0.5 - - - -
183C TYR* 4.1 12.8 - + + -
184C ASN 3.7 17.0 - - - -
185C GLN* 3.8 23.1 - - + +
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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