Contacts of the strand formed by residues 182 - 189 (chain A) in PDB entry 2FPO
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 182 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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157A GLU* 3.8 20.4 - - + +
158A SER 3.6 12.3 - - - +
159A GLU* 4.4 11.7 - - - +
160A VAL* 3.9 3.6 - - - -
178A VAL* 3.4 4.0 - - - +
179A ALA 3.1 29.6 + - - +
180A GLY 3.2 4.2 + - - -
181A GLN* 1.3 103.9 - - + +
183A ALA* 1.3 62.4 + - - +
184A TYR* 3.6 41.8 - - + +
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Residues in contact with ALA 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A VAL 3.8 1.7 - - - +
157A GLU* 3.7 2.9 - - - -
158A SER* 2.7 37.3 + - - +
160A VAL* 4.0 11.1 - - + +
176A GLU* 5.2 0.2 - - + -
177A LYS 3.6 4.0 - - - -
178A VAL* 4.1 14.8 - - + -
182A VAL* 1.3 73.6 - - - +
184A TYR* 1.3 61.7 + - - +
185A ARG* 3.4 42.3 + - + +
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Residues in contact with TYR 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A VAL* 3.6 35.3 - - + +
42A THR* 6.1 0.9 - - + -
46A TRP* 3.5 13.9 - - + -
155A TYR* 3.3 27.8 - - + -
156A VAL 3.9 3.4 - - - -
157A GLU* 3.7 28.5 + - + -
176A GLU* 3.3 3.1 - - - -
177A LYS* 2.7 59.5 + - + +
179A ALA* 4.0 21.4 + - + +
182A VAL* 3.6 37.7 - - + +
183A ALA* 1.3 71.6 - - - +
185A ARG* 1.3 60.3 + - - +
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Residues in contact with ARG 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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46A TRP* 4.3 3.8 - - - -
154A ILE 4.4 0.2 - - - -
155A TYR* 3.3 9.5 - - - -
156A VAL* 2.9 41.0 + - - +
158A SER* 4.4 12.9 - - - -
159A GLU 5.6 0.6 + - - -
160A VAL* 5.5 4.2 + - - +
163A GLY 3.7 17.9 + - - -
164A LEU* 3.8 19.7 - - - +
165A PRO* 3.7 17.9 - - - +
173A LEU* 3.7 15.5 - - + -
175A ARG 3.4 4.3 - - - -
176A GLU* 2.6 35.0 + - + -
178A VAL* 5.4 1.0 - - - +
183A ALA* 3.4 30.1 + - - +
184A TYR* 1.3 81.3 - - - +
186A LEU* 1.3 60.0 + - - +
187A TYR* 3.6 29.2 - - + -
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Residues in contact with LEU 186 (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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43A LEU* 4.4 4.0 - - + -
46A TRP* 4.0 30.1 - - + +
47A LEU* 4.0 26.5 - - + -
123A ILE* 6.1 1.1 - - + -
153A LEU* 3.9 33.9 - - + -
154A ILE 3.5 22.0 - - - +
155A TYR* 3.7 14.8 - - + +
173A LEU* 3.7 1.4 - - - +
174A HIS* 2.6 36.3 + - + +
175A ARG* 2.9 34.6 + - + +
185A ARG* 1.3 73.4 - - - +
187A TYR* 1.3 53.7 + - - +
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Residues in contact with TYR 187 (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 ALA 3.7 0.3 - - - +
153A LEU* 3.2 7.9 - - - +
154A ILE* 2.9 42.0 + - + +
156A VAL* 4.0 24.2 - - + -
164A LEU* 4.4 6.6 - - + +
165A PRO* 3.4 28.3 + - + +
167A VAL* 3.7 34.6 - - + +
171A TRP* 3.7 28.7 - + + -
172A SER 3.3 7.2 - - - +
173A LEU* 3.6 36.5 - - + +
174A HIS* 4.1 1.8 - - - -
185A ARG* 3.6 27.1 - - + -
186A LEU* 1.3 76.1 - - - +
188A GLN* 1.3 61.3 + - - +
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Residues in contact with GLN 188 (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 GLU* 4.1 20.9 - - - +
152A ALA 3.4 8.3 - - - +
153A LEU* 3.8 20.1 - - + +
170A ASN 3.7 1.4 - - - +
171A TRP* 3.5 2.0 - - - -
172A SER* 2.8 44.4 + - - +
174A HIS* 3.6 35.7 + - + +
187A TYR* 1.3 74.8 - - - +
189A ARG* 1.3 66.6 + - - +
190A GLU* 4.3 15.7 + - - +
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Residues in contact with ARG 189 (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 GLU* 2.8 47.9 + - - +
146A GLY* 6.4 0.2 - - - -
148A LEU* 3.7 32.6 + - + +
149A ALA 3.4 21.8 + - - -
150A ASP* 3.0 15.8 + - - +
151A GLU* 3.1 15.8 - - - -
152A ALA 2.9 15.8 + - - +
154A ILE* 3.9 15.3 - - + -
170A ASN* 3.5 10.4 - - - +
171A TRP* 3.5 16.2 - - + +
187A TYR 4.2 0.2 - - - -
188A GLN* 1.3 74.6 - - - +
190A GLU* 1.3 66.9 + - - +
191A ALA* 3.5 31.2 - - - +
192A GLN 4.5 3.2 - - - +
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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