Contacts of the strand formed by residues 161 - 167 (chain A) in PDB entry 5FQU
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 PHE 161 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56A ILE* 3.4 25.6 - - + -
58A GLY 4.6 2.2 - - - -
63A ALA* 3.5 26.9 - - - -
66A GLY* 3.7 10.1 - - - -
67A GLY* 3.5 19.3 - - - -
70A ALA* 3.6 17.0 - - + -
154A PHE* 3.2 34.5 + + - +
155A ASP* 5.1 0.2 + - - -
157A LEU* 4.0 8.1 - - + -
159A ILE 3.4 2.0 + - - +
160A PRO* 1.3 76.2 - - - +
162A ARG* 1.3 88.4 + - - +
163A ALA* 3.8 21.5 - - + -
181A LEU* 3.6 32.5 - - + -
185A ILE* 4.0 7.4 - - + -
222A MSE 3.7 2.2 - - - +
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Residues in contact with ARG 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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56A ILE 3.0 9.3 + - - +
57A ALA* 3.5 2.0 - - - +
58A GLY 3.1 25.5 + - - -
154A PHE* 5.3 0.6 - - - +
155A ASP* 2.6 41.2 + - - -
161A PHE* 1.3 87.4 + - - +
163A ALA* 1.3 58.0 + - - +
164A VAL* 4.9 0.5 - - - +
175A VAL* 3.9 13.4 - - + +
176A PHE 3.4 18.6 - - - +
177A ARG* 3.4 39.8 - - - +
218A VAL* 3.6 26.2 + - + +
221A ASP* 4.4 9.7 + - - +
222A MSE 3.5 43.6 - - - +
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Residues in contact with ALA 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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58A GLY 3.5 7.0 - - - +
63A ALA* 4.4 2.9 - - + -
154A PHE* 5.2 0.6 - - + -
161A PHE* 3.8 22.2 - - + -
162A ARG* 1.3 73.8 - - - +
164A VAL* 1.3 62.3 + - - +
175A VAL* 3.5 5.0 - - - +
176A PHE* 3.0 42.5 + - + +
184A ALA* 4.2 18.4 - - + +
185A ILE 4.6 0.9 - - - +
188A SER* 4.1 17.5 - - - -
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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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58A GLY 3.1 10.2 + - - +
59A THR* 3.8 12.7 - - - +
162A ARG 4.9 1.6 - - - +
163A ALA* 1.3 81.1 - - - +
165A SER* 1.3 72.0 + - - +
173A LYS* 4.3 12.3 - - + -
174A VAL 3.6 2.5 - - - +
175A VAL* 4.4 5.2 - - + -
188A SER* 2.5 27.4 + - - -
208A GLY* 3.5 13.6 - - - +
211A VAL* 4.8 0.7 - - + -
212A ASP* 4.0 28.5 - - + +
215A PRO* 4.0 13.2 - - + -
218A VAL* 3.8 31.6 - - + -
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Residues in contact with SER 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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164A VAL* 1.3 76.3 - - - +
166A THR* 1.3 62.9 + - - +
173A LYS* 3.7 5.0 - - - -
174A VAL* 2.9 32.9 + - - -
176A PHE* 3.6 27.4 - - - -
187A ALA* 3.2 20.0 + - - +
188A SER 4.1 3.4 - - - -
205A LEU* 4.0 3.9 - - - +
206A VAL 2.6 26.4 + - - -
208A GLY* 3.6 4.9 - - - +
211A VAL* 3.8 4.7 - - - +
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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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165A SER* 1.3 73.2 - - - +
167A ASP* 1.3 73.2 + - - +
168A ILE* 3.3 6.2 + - + -
171A GLY* 4.5 6.1 - - - -
172A GLU 3.7 4.9 - - - +
205A LEU* 3.3 8.7 - - - -
206A VAL* 2.9 39.2 + - + -
207A ASP 3.1 21.3 + - - -
208A GLY* 3.5 3.1 - - - -
210A MSE 3.5 25.4 - - + +
211A VAL* 3.3 31.4 - - + +
255B LEU* 5.1 1.6 - - + -
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Residues in contact with ASP 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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166A THR* 1.3 69.3 - - - +
168A ILE* 1.3 60.2 + - - +
169A ALA* 3.5 14.0 + - - +
170A THR* 3.1 33.6 + - - +
171A GLY* 2.6 35.7 + - - -
172A GLU* 2.9 23.0 + - + +
174A VAL* 3.9 13.6 - - + +
203A ARG* 3.6 28.0 + - - +
204A LEU 3.5 19.1 + - - +
205A LEU* 4.2 3.6 - - - -
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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