Contacts of the strand formed by residues 177 - 185 (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 GLY 177 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145A VAL* 3.6 6.9 - - - +
146A VAL* 2.7 37.8 + - - +
172A PHE* 4.1 2.0 - - - -
176A GLY* 1.3 74.8 - - - -
178A VAL* 1.3 66.1 + - - +
184C ASN 3.3 10.8 - - - -
186C ASP* 3.3 22.3 + - - +
189C ILE* 5.7 0.4 - - - -
222C ARG* 4.5 0.5 - - - -
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Residues in contact with VAL 178 (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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144A PHE 3.4 13.0 - - - +
145A VAL* 4.4 2.9 - - - -
146A VAL* 4.0 5.1 - - - +
172A PHE* 3.7 3.1 - - - -
177A GLY* 1.3 79.3 - - - +
179A ALA* 1.3 63.5 - - - +
183C TYR* 3.2 5.5 - - - +
184C ASN* 2.8 53.7 + - + +
189C ILE* 4.7 7.4 - - + -
218C LYS 3.6 14.1 - - - +
219C TYR* 3.8 31.0 - - + +
222C ARG* 3.6 30.1 - - + -
223C PHE* 4.7 0.4 - - + -
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Residues in contact with ALA 179 (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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143A ASP* 3.3 3.6 - - - +
144A PHE* 3.0 57.7 + - + +
146A VAL* 4.2 5.6 - - + +
152A VAL* 3.9 20.0 - - + -
178A VAL* 1.3 77.2 - - - +
180A MET* 1.3 62.5 + - - +
154C ILE* 4.8 0.7 - - + -
182C MET 3.1 13.9 - - - +
183C TYR* 4.2 4.0 - - + -
219C TYR* 3.8 4.4 - - - -
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Residues in contact with MET 180 (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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141A ALA* 4.1 9.4 - - + -
142A THR 3.2 11.9 - - - +
143A ASP* 3.6 8.3 - - + -
144A PHE* 4.8 0.2 - - - -
179A ALA* 1.3 77.4 - - - +
181A GLY* 1.3 58.1 + - - +
182A MET* 3.7 31.1 - - + +
154C ILE* 3.6 8.9 - - - +
180C MET 3.9 0.2 - - - +
181C GLY* 3.1 4.9 - - - -
182C MET* 2.9 56.5 + - + +
216C LEU* 3.7 36.3 - - + -
219C TYR* 3.6 34.8 - - + -
270C LYS* 5.8 0.9 - - - -
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Residues in contact with GLY 181 (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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141A ALA* 3.5 2.4 - - - +
142A THR* 2.9 34.5 + - - +
154A ILE* 4.6 1.1 - - - -
180A MET* 1.3 75.8 - - - +
182A MET* 1.3 60.3 + - - -
154C ILE* 3.9 13.0 - - - +
169C VAL* 4.0 24.3 - - - +
180C MET 3.2 8.7 - - - -
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Residues in contact with MET 182 (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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141A ALA* 4.3 18.6 - - + +
180A MET* 3.7 24.5 - - + +
181A GLY* 1.3 76.1 - - - +
183A TYR* 1.3 65.2 + - - +
219A TYR* 4.2 5.4 - - - +
169C VAL* 4.1 4.0 - - - +
179C ALA* 3.1 4.7 - - - +
180C MET* 2.9 69.4 + - + +
182C MET* 4.1 20.2 - - + +
216C LEU* 5.8 0.9 - - + -
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Residues in contact with TYR 183 (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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141A ALA* 4.6 16.8 - - - +
182A MET* 1.3 79.6 - - - +
184A ASN* 1.3 74.4 + - - +
185A GLN* 4.5 6.5 - - + -
219A TYR* 3.2 13.4 + - - -
169C VAL* 3.7 31.9 - - + -
170C HIS* 3.4 53.2 + + + -
172C PHE* 4.1 9.0 - + + -
178C VAL 3.2 12.6 - - - +
179C ALA* 4.2 3.1 - - + -
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Residues in contact with ASN 184 (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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133A HIS* 2.8 31.8 + - - -
183A TYR* 1.3 79.6 + - - +
185A GLN* 1.3 61.9 + - - +
188A SER* 3.5 10.6 + - - -
189A ILE* 4.2 11.4 - - + -
219A TYR* 2.9 29.9 + - - -
223A PHE* 3.9 13.4 - - + -
270A LYS* 5.1 1.6 - - - +
172C PHE* 3.7 3.0 - - - -
177C GLY* 3.3 3.8 - - - -
178C VAL* 2.9 46.1 + - + +
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Residues in contact with GLN 185 (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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183A TYR* 4.3 7.4 - - + -
184A ASN* 1.3 75.1 + - - +
186A ASP* 1.3 67.3 + - - +
187A LYS* 3.2 12.5 - - + +
188A SER* 3.1 22.5 + - - +
189A ILE* 3.2 12.8 + - - +
170C HIS* 3.1 36.4 + - + +
171C ASN 4.5 0.2 - - - +
172C PHE* 4.0 24.6 - - + -
173C GLU 4.4 3.1 + - - -
174C GLU* 4.3 16.5 + - - +
176C GLY 3.8 5.8 - - - +
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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