Contacts of the strand formed by residues 181 - 187 (chain A) in PDB entry 3IFA
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 181 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174A ALA* 4.3 4.7 - - + -
175A LEU 3.7 6.3 - - - +
176A SER* 4.4 0.4 - - - -
180A GLY* 1.3 76.2 - - - +
182A ASP* 1.3 72.1 + - - +
183A LEU* 4.1 9.6 - - + -
198A LYS 4.0 0.2 - - - -
199A ASP* 3.1 8.7 + - - +
200A VAL* 2.8 55.4 + - + +
256A LEU* 4.5 2.7 - - + -
287A ILE* 3.2 52.5 - - + +
290A GLN* 3.7 11.8 + - + -
291A ALA* 3.7 11.0 - - + +
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Residues in contact with ASP 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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16A TYR* 2.7 33.6 + - - -
20A LYS* 5.5 2.3 - - - -
173A VAL 3.7 1.0 - - - +
174A ALA* 3.5 3.8 - - - -
175A LEU* 3.0 36.5 + - + +
179A GLN 5.4 2.8 - - - +
180A GLY 4.9 3.9 - - - +
181A VAL* 1.3 76.5 + - - +
183A LEU* 1.3 62.7 + - - +
184A PHE* 3.7 25.4 - - + -
195A LEU* 4.1 1.8 - - + -
197A GLU 3.4 6.5 - - - +
198A LYS* 3.4 11.3 + - - +
199A ASP* 2.8 30.0 + - - +
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Residues in contact with LEU 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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172A LEU* 4.2 10.5 - - + -
173A VAL 3.4 3.6 - - - +
174A ALA* 3.7 28.5 - - + -
181A VAL* 4.1 10.1 - - + -
182A ASP* 1.3 74.7 - - - +
184A PHE* 1.3 56.6 + - - +
195A LEU* 3.5 4.7 - - - +
196A VAL* 2.8 42.0 + - + -
197A GLU* 2.7 41.7 + - + +
200A VAL* 3.9 16.4 - - + -
253A HIS* 4.3 20.9 - - + -
256A LEU* 4.3 8.3 - - + -
257A VAL* 4.5 11.7 - - + -
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Residues in contact with PHE 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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13A LEU* 3.5 52.7 - - + -
16A TYR* 3.7 26.2 - + + -
172A LEU* 3.2 6.3 - - - +
173A VAL* 2.8 45.9 + - + +
175A LEU* 4.4 11.0 - - + -
182A ASP* 3.7 26.5 - - + -
183A LEU* 1.3 73.6 - - - +
185A MET* 1.3 62.7 + - - +
193A PHE* 3.9 18.8 - - + -
194A VAL 3.1 7.2 - - - +
195A LEU* 3.6 42.2 - - + -
196A VAL 4.3 0.2 - - - +
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Residues in contact with MET 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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170A ALA* 4.3 22.2 - - + -
171A THR 3.5 3.6 - - - +
172A LEU* 4.1 26.7 - - + -
184A PHE* 1.3 78.4 - - - +
186A LEU* 1.3 65.4 + - - +
187A ASP 3.4 2.1 + - - -
193A PHE* 3.7 3.8 - - - -
194A VAL* 2.8 41.3 + - + +
196A VAL* 3.8 32.1 - - + +
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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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42A LYS* 4.0 28.3 - - + +
45A SER* 3.9 26.7 - - - +
170A ALA* 5.4 4.2 - - - +
171A THR* 2.9 30.6 + - + +
185A MET* 1.3 73.0 - - - +
187A ASP* 1.3 67.2 + - - +
188A PRO* 3.3 21.2 - - + +
191A GLY* 4.0 3.6 - - - -
192A GLU 3.7 32.3 - - - +
193A PHE* 3.5 24.0 - - + +
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Residues in contact with ASP 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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185A MET 3.4 2.2 + - - -
186A LEU* 1.3 71.7 - - - +
188A PRO* 1.4 63.8 - - - +
189A ALA* 3.0 22.6 + - - +
190A LEU* 3.1 22.4 + - + +
191A GLY* 2.9 24.9 + - - -
192A GLU 3.0 18.6 + - - +
194A VAL* 4.3 15.2 - - + +
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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