Contacts of the strand formed by residues 158 - 164 (chain A) in PDB entry 3OF6
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 158 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A TYR* 4.5 6.3 + - - -
126A PRO* 4.0 13.9 - - + -
153A PHE* 3.6 39.7 - - + -
156A ASP 3.5 3.3 + - - +
157A HIS* 1.3 80.2 - - - +
159A GLU* 1.3 68.3 + - - +
160A LEU 4.1 0.6 + - - -
179A PRO* 4.3 10.3 - - + -
193A LEU* 3.8 26.5 - - + +
215A VAL* 4.0 12.6 - - + -
216A GLN 3.0 7.9 - - - +
217A PHE* 3.8 12.6 - - + -
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Residues in contact with GLU 159 (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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9A ARG* 3.8 17.7 + - - -
10A TYR* 2.9 36.0 + - - +
158A VAL* 1.3 79.4 - - - +
160A LEU* 1.3 64.3 + - - +
161A SER* 3.9 4.0 + - - -
214A GLN* 3.9 1.7 + - - +
215A VAL* 3.6 1.0 - - - -
216A GLN* 2.7 43.0 + - + +
218A TYR* 3.3 26.2 + - + -
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Residues in contact with LEU 160 (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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148A CYS* 4.1 6.5 - - + +
150A ALA* 5.1 3.4 - - + -
158A VAL 4.1 1.0 + - - -
159A GLU* 1.3 72.4 - - - +
161A SER* 1.3 84.5 + - - +
162A TRP* 3.9 6.3 - - + +
173A VAL* 6.1 0.5 - - - +
175A THR* 4.3 14.3 + - + +
193A LEU* 4.1 32.7 - - + +
194A SER* 4.6 0.9 - - - -
195A SER* 3.6 40.8 - - - +
213A CYS* 3.7 21.1 - - - -
214A GLN 3.1 11.9 - - - +
215A VAL* 3.7 20.8 - - + +
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Residues in contact with SER 161 (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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159A GLU 4.5 3.1 + - - -
160A LEU* 1.3 80.6 - - - +
162A TRP* 1.3 61.9 + - - +
163A TRP* 3.1 3.3 + - - -
168A GLU* 3.3 27.6 - - - -
169A VAL 5.6 0.7 - - - -
173A VAL* 5.9 2.0 - - - -
213A CYS 3.7 0.5 - - - -
214A GLN* 2.7 69.9 + - - +
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Residues in contact with TRP 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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130A VAL* 4.5 6.7 - - + -
146A LEU* 3.8 45.5 - - + -
147A VAL 4.1 2.0 - - - -
148A CYS* 3.6 38.4 - - + -
160A LEU* 3.9 2.6 - - + +
161A SER* 1.3 73.6 - - - +
163A TRP* 1.3 67.4 + - - +
164A VAL* 6.0 0.2 - - + -
168A GLU* 3.1 8.7 - - - +
169A VAL* 3.0 47.7 + - + +
173A VAL* 3.5 29.0 - - + +
195A SER* 2.8 27.4 + - - -
196A ARG 4.1 2.4 - - - +
197A LEU* 3.8 27.9 - - + +
211A PHE* 5.3 0.4 - - + -
212A ARG 3.5 22.9 - - - -
213A CYS* 3.7 17.9 - - + -
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Residues in contact with TRP 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 SER* 3.1 19.3 + - - -
162A TRP* 1.3 91.9 + - - +
164A VAL* 1.3 62.2 + - - +
165A ASN 3.8 1.3 + - - -
166A GLY* 3.2 30.9 + - - +
167A LYS* 3.3 7.2 - - - +
168A GLU* 3.4 38.8 - - + -
210A HIS* 3.7 4.5 + - - +
212A ARG* 2.7 71.1 + - - +
214A GLN* 2.8 36.8 - - + +
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Residues in contact with VAL 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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163A TRP* 1.3 71.5 - - - +
165A ASN* 1.3 84.9 + - - +
166A GLY 3.4 0.2 - - - -
167A LYS* 2.7 22.4 + - - +
169A VAL* 3.8 24.2 - - + +
197A LEU* 3.8 29.4 - - + -
203A PHE* 3.9 29.4 - - + -
210A HIS 3.3 9.9 - - - +
211A PHE* 3.8 15.9 - - + -
212A ARG 5.5 0.2 - - - +
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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