Contacts of the helix formed by residues 165 - 173 (chain X) in PDB entry 6FF7
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 MET 165 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164X GLU* 1.3 80.0 - - - +
166X MET* 1.3 56.8 + - - +
169X MET* 2.8 18.1 + - - +
961v ILE* 5.4 0.8 - - + +
963v VAL* 6.1 4.3 - - + -
966v LEU* 6.6 0.2 - - + -
968v ARG* 2.7 29.2 - - + +
979v ARG* 2.8 26.4 - - + +
981v CYS 5.0 0.4 - - - +
982v GLU* 5.9 2.7 - - + -
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Residues in contact with MET 166 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164X GLU 3.2 3.0 - - - +
165X MET* 1.3 79.2 - - - +
167X LEU* 1.3 52.6 - - - +
169X MET* 2.9 17.9 + - - +
170X LEU* 2.9 10.0 + - - +
925v VAL* 5.4 7.4 - - + -
943v THR* 3.5 30.5 - - - +
944v PRO 3.8 16.8 - - - +
945v VAL* 5.3 5.4 - - + -
977v LEU* 2.0 23.0 - - + +
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Residues in contact with LEU 167 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164X GLU 3.2 2.3 + - - +
166X MET* 1.3 65.3 - - - +
168X SER* 1.3 46.6 + - - +
171X PHE 2.9 8.1 + - - -
970v TYR* 4.2 0.4 - - + -
971v ASP 2.7 20.9 - - - +
977v LEU* 1.2 93.3 + - + +
978v LEU* 1.0 169.5 + - - +
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Residues in contact with SER 168 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167X LEU* 1.3 60.3 - - - +
169X MET* 1.3 54.2 + - - +
172X ASN* 2.6 43.0 + - - +
978v LEU* 1.4 9.3 - - - +
979v ARG* 1.0 164.4 - - - +
980v LYS 4.9 0.4 - - - -
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Residues in contact with MET 169 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165X MET 2.8 14.5 + - - +
166X MET* 2.9 12.3 + - - +
168X SER* 1.3 79.3 - - - +
170X LEU* 1.4 63.3 + - - +
172X ASN* 4.3 2.9 - - - +
173X GLN* 3.7 14.2 + - - +
944v PRO 6.0 1.1 - - - +
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Residues in contact with LEU 170 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166X MET 2.9 8.2 + - - +
169X MET* 1.4 78.5 - - - +
171X PHE* 1.3 61.7 + - - +
173X GLN* 3.6 14.6 + - - +
174X PHE 4.8 0.2 + - - -
975v LYS* 5.5 4.0 - - + -
976v LYS* 3.6 29.6 - - + +
977v LEU 3.6 13.5 - - - +
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Residues in contact with PHE 171 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167X LEU 2.9 4.4 + - - -
170X LEU* 1.3 73.9 - - - +
172X ASN* 1.3 64.2 + - - +
173X GLN 3.1 3.9 + - - -
174X PHE* 3.1 21.5 + - - +
175X PRO 4.7 0.2 - - - +
177X PHE* 5.6 8.1 - - + +
192X VAL* 4.8 15.3 - - + -
203X ALA* 5.0 8.2 - - + +
973v GLY* 6.1 2.0 - - - -
976v LYS 5.6 1.3 - - - +
978v LEU* 2.8 29.2 - - + -
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Residues in contact with ASN 172 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168X SER* 2.6 33.3 + - - +
169X MET* 4.3 2.9 - - - +
171X PHE* 1.3 70.1 - - - +
173X GLN* 1.3 67.2 + - - +
174X PHE 3.1 11.3 + - - -
175X PRO* 3.4 14.0 - - - +
176X GLY* 4.4 1.3 + - - +
177X PHE* 5.3 11.7 - - + +
979v ARG 5.3 0.9 - - - +
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Residues in contact with GLN 173 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169X MET 3.7 9.0 + - - +
170X LEU* 3.6 14.9 + - - +
171X PHE 3.1 1.0 - - - -
172X ASN* 1.3 78.5 - - - +
174X PHE* 1.3 58.9 + - - +
175X PRO* 3.4 2.9 - - - +
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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