Contacts of the strand formed by residues 183 - 190 (chain A) in PDB entry 6FY5
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 183 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177A MET 4.1 0.2 - - - -
178A GLY* 3.2 19.5 + - - -
179A PRO* 3.8 24.5 - - + -
180A GLY 3.1 15.5 + - - +
181A ASP 3.5 15.0 - - - -
182A GLY* 1.3 80.0 - - - +
184A THR* 1.3 64.1 + - - +
200A THR* 3.8 10.8 - - + -
201A GLN 3.3 3.6 - - - -
202A SER* 3.3 35.4 - - - -
203A ASP 3.7 17.5 - - - -
204A ILE* 5.1 0.4 - - - -
206A HIS* 3.4 31.2 - - + -
207A ILE* 4.1 6.3 - - + -
210A MET* 3.6 31.0 - - + -
352A LEU* 4.1 18.2 - - + -
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Residues in contact with THR 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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176A GLY* 4.0 13.8 - - - -
177A MET 3.5 22.1 + - - +
182A GLY 5.5 0.5 - - - -
183A PHE* 1.3 75.3 + - - +
185A ILE* 1.4 73.9 + - - +
186A LEU* 3.3 9.2 + - + +
200A THR* 3.4 4.4 - - - +
201A GLN* 2.7 51.4 + - - +
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Residues in contact with ILE 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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177A MET* 2.7 27.6 + - + +
178A GLY* 4.0 6.1 - - - -
179A PRO* 3.6 21.3 - - + -
184A THR* 1.4 79.8 - - - +
186A LEU* 1.3 62.9 + - - +
187A SER* 3.9 8.7 - - - +
188A SER* 3.4 26.0 - - - +
196A LYS* 5.6 5.8 - - - +
198A SER* 3.9 6.3 - - - +
199A LEU 3.7 4.9 - - - +
200A THR* 3.4 23.1 - - + +
350A TYR* 3.6 17.0 - - + -
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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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184A THR* 4.0 9.4 - - + +
185A ILE* 1.3 77.4 - - - +
187A SER* 1.3 62.1 + - - +
199A LEU* 2.8 22.2 + - + +
200A THR 4.4 2.5 - - - -
201A GLN* 3.7 41.5 - - + +
353A LEU* 5.7 0.2 - - + -
359A ILE* 3.7 47.8 - - + -
363A VAL* 6.2 0.7 - - + -
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Residues in contact with SER 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 ILE* 3.7 2.3 - - - +
186A LEU* 1.3 80.8 - - - +
188A SER* 1.4 68.5 + - - +
189A LYS* 5.3 7.1 + - - -
198A SER* 3.5 0.2 - - - -
199A LEU* 2.8 48.3 + - - +
363A VAL* 4.7 13.0 - - - +
366A MET* 4.3 4.8 - - - +
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Residues in contact with SER 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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185A ILE* 3.4 13.7 - - - +
187A SER* 1.4 78.1 + - - +
189A LYS* 1.3 70.4 + - - +
196A LYS* 3.6 19.5 - - - -
197A LEU 3.2 10.5 - - - -
198A SER* 2.8 22.0 + - - -
366A MET* 4.2 1.1 - - - -
372A LYS* 2.9 31.4 + - - +
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Residues in contact with LYS 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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187A SER* 5.3 6.6 + - - +
188A SER* 1.3 76.3 + - - +
190A SER* 1.3 61.0 + - - +
191A LEU* 4.0 1.0 + - + -
195A GLN 3.9 0.5 - - - +
196A LYS* 3.5 3.2 - - - -
197A LEU* 2.9 38.4 + - + +
366A MET* 3.6 50.3 - - + +
367A ALA* 4.5 9.4 - - - +
369A LEU* 5.2 6.7 - - + +
371A ALA* 3.6 20.6 - - + +
372A LYS* 3.5 32.7 - - + +
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Residues in contact with SER 190 (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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189A LYS* 1.3 74.3 - - - +
191A LEU* 1.3 68.9 + - - +
194A GLY* 4.2 10.6 + - - -
195A GLN 3.4 8.2 + - - -
196A LYS* 4.4 9.4 - - - +
371A ALA* 3.1 6.6 - - - -
372A LYS* 2.8 41.0 + - - +
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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