Contacts of the strand formed by residues 161 - 168 (chain A) in PDB entry 6TAV
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 LEU 161 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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159A ASN 4.5 5.4 - - - +
160A GLU* 1.3 88.8 - - + +
162A ILE* 1.3 61.2 + - - +
163A PRO* 3.0 17.5 - - - +
180A SER* 5.6 3.4 - - - -
181A PHE 3.6 11.2 - - - +
182A GLN* 4.2 16.6 - - + +
210A LYS* 4.5 28.6 - - + +
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Residues in contact with ILE 162 (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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129A VAL* 5.2 6.1 - - + -
148A VAL* 5.1 11.0 - - + -
160A GLU* 3.1 41.4 - - + +
161A LEU* 1.3 65.8 - - - +
163A PRO* 1.3 66.2 - - - +
164A LEU* 3.7 26.4 - - - +
165A VAL* 3.9 20.0 - - + -
178A TRP 4.8 1.2 - - - +
179A GLN 4.4 0.5 - - - -
180A SER 3.8 0.3 + - - -
181A PHE* 3.1 30.8 + - + +
183A LEU* 4.5 20.0 - - + -
207A VAL* 4.1 15.3 - - + -
208A GLN 4.0 5.2 - - - +
209A LYS* 4.3 15.5 - - + -
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Residues in contact with PRO 163 (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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161A LEU 3.0 11.8 - - - +
162A ILE* 1.3 82.9 - - - +
164A LEU* 1.4 57.3 + - + +
179A GLN* 3.4 12.3 + - - +
180A SER* 2.7 37.7 + - - +
208A GLN* 3.3 28.0 - - - +
209A LYS 3.6 11.2 - - - +
210A LYS* 3.6 23.3 - - + +
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Residues in contact with LEU 164 (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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162A ILE* 3.3 5.0 - - - +
163A PRO* 1.4 85.2 - - + +
165A VAL* 1.3 58.2 + - - +
166A TYR* 3.7 28.3 - - + -
174A ARG* 4.4 12.3 - - - +
177A GLN* 3.4 44.6 - - + +
178A TRP 3.8 2.7 - - - +
179A GLN* 4.1 16.4 - - + +
206A VAL 4.3 0.5 - - - +
208A GLN* 2.9 50.2 + - + +
214A ARG* 5.9 0.4 - - - +
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Residues in contact with VAL 165 (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 PHE* 4.3 9.6 - - + -
148A VAL* 5.5 3.8 - - + -
162A ILE* 3.9 16.6 - - + +
164A LEU* 1.3 72.4 - - - +
166A TYR* 1.3 63.6 + - - +
177A GLN* 3.4 3.6 - - - +
178A TRP* 3.0 64.0 + - + +
181A PHE* 5.6 2.2 - - + -
190A PHE* 4.9 12.3 - - + -
205A VAL* 4.1 16.4 - - + -
206A VAL 3.2 11.4 - - - +
207A VAL* 3.6 25.8 - - + -
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Residues in contact with TYR 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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164A LEU* 3.7 23.6 - - + -
165A VAL* 1.3 76.3 - - - +
167A ILE* 1.3 66.8 + - - +
168A GLN* 3.6 33.7 + - + -
174A ARG* 3.4 49.7 + - + -
176A ALA 3.3 12.8 - - - +
177A GLN* 3.9 9.9 - - + +
178A TRP* 4.5 1.8 - - - -
204A LYS 3.8 0.3 - - - +
205A VAL* 3.6 1.1 - - - -
206A VAL* 2.8 76.2 + - + +
208A GLN* 5.4 0.4 - - + -
214A ARG* 3.5 26.5 + - - -
216A GLU* 4.3 3.5 + - - -
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Residues in contact with ILE 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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144A VAL* 4.3 7.6 - - + -
146A PHE* 4.0 12.1 - - + -
166A TYR* 1.3 76.6 - - - +
168A GLN* 1.3 60.3 + - - +
174A ARG* 3.6 1.4 - - - -
175A ILE* 2.8 52.5 + - + +
176A ALA* 3.0 11.2 + - + +
178A TRP* 3.5 28.3 - - + -
192A PHE* 3.7 29.6 - - + -
203A TYR* 4.6 4.5 - - + -
204A LYS 3.5 5.4 - - - +
205A VAL* 3.9 19.1 - - + -
219A PHE* 3.9 26.2 - - + -
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Residues in contact with GLN 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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166A TYR* 3.6 33.0 + - + -
167A ILE* 1.3 74.1 - - - +
169A ASP* 1.3 66.4 + - - +
172A GLY* 3.3 37.1 - - - +
173A ASN 3.9 3.6 - - - -
174A ARG* 4.0 15.8 + - - +
203A TYR* 3.4 2.9 - - - +
204A LYS* 2.7 66.2 + - + +
206A VAL* 4.4 0.8 - - + +
216A GLU* 4.6 2.4 + - - -
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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