Contacts of the helix formed by residues 167 - 178 (chain o) 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 167 (chain o).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5o LYS* 6.0 4.0 - - + -
57o ALA* 4.6 20.2 - - + -
166o PRO* 1.3 79.3 - - - +
168o THR* 1.3 56.7 + - - +
170o GLU* 3.9 4.5 - - - +
171o ASN* 3.1 28.9 + - - +
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Residues in contact with THR 168 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1o MET* 5.8 1.3 - - - -
2o ALA 3.8 27.4 - - - -
3o THR* 5.5 3.1 - - - -
166o PRO* 3.3 2.4 - - - +
167o MET* 1.3 77.1 - - - +
169o ALA* 1.3 64.8 + - - +
171o ASN* 3.4 7.6 + - - +
172o PHE* 3.2 22.0 + - - +
263o VAL* 5.5 0.9 - - - -
265o PHE* 4.3 19.9 - - - +
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Residues in contact with ALA 169 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160o LEU* 3.9 37.2 - - + +
166o PRO* 3.5 16.6 + - + +
167o MET 3.4 0.2 - - - -
168o THR* 1.3 77.4 - - - +
170o GLU* 1.3 57.0 + - - +
172o PHE* 3.3 6.0 + - - +
173o ARG* 2.9 29.2 + - - +
265o PHE* 4.8 9.9 - - + +
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Residues in contact with GLU 170 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166o PRO 2.9 20.1 + - - +
167o MET* 3.9 5.2 - - - +
168o THR 3.3 0.2 - - - -
169o ALA* 1.3 75.4 - - - +
171o ASN* 1.3 63.4 - - - +
173o ARG* 3.3 7.5 + - - +
174o CYS* 3.0 26.0 + - - +
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Residues in contact with ASN 171 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167o MET 3.1 17.3 + - - +
168o THR* 3.6 7.9 - - - +
170o GLU* 1.3 77.5 - - - +
172o PHE* 1.3 63.5 + - - +
174o CYS* 3.3 5.4 + - - +
175o LEU* 3.0 23.9 + - - +
213o SER* 5.0 9.2 - - - -
214o ILE* 4.9 22.3 + - + +
245o GLY 5.2 5.4 - - - +
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Residues in contact with PHE 172 (chain o).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168o THR 3.2 10.6 + - - +
169o ALA* 3.8 8.3 - - - +
171o ASN* 1.3 77.3 - - - +
173o ARG* 1.3 64.3 + - - +
175o LEU* 3.1 9.2 + - - +
176o CYS* 3.0 22.4 + - - +
265o PHE* 6.6 0.2 - - + -
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Residues in contact with ARG 173 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142o VAL* 5.5 5.8 - - - -
169o ALA 2.9 17.8 + - - +
170o GLU* 3.5 9.2 - - - +
171o ASN 3.3 0.2 - - - -
172o PHE* 1.3 74.6 - - - +
174o CYS* 1.3 61.8 + - - +
176o CYS* 3.1 17.8 + - - +
177o THR* 3.1 14.5 + - - -
299o GLU* 5.6 2.8 - - - +
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Residues in contact with CYS 174 (chain o).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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170o GLU 3.0 17.6 + - - +
171o ASN 3.7 4.3 - - - +
173o ARG* 1.3 75.4 - - - +
175o LEU* 1.3 58.5 + - - +
177o THR* 4.4 5.2 - - - +
178o HIS* 2.8 30.7 + - - -
179o GLU* 3.7 0.8 + - - -
180o LYS* 4.9 5.2 - - + -
182o PHE 4.9 0.7 - - - -
214o ILE* 4.7 16.4 - - + -
43w GLU* 3.5 16.0 - - - +
47w ARG* 4.6 16.4 - - + -
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Residues in contact with LEU 175 (chain o).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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171o ASN 3.0 16.3 + - - +
172o PHE* 3.1 8.9 + - - +
174o CYS* 1.3 78.1 - - - +
176o CYS* 1.3 58.9 + - - +
178o HIS* 4.1 1.9 + - - +
182o PHE 4.4 1.8 - - - +
183o GLY* 3.3 18.6 - - - -
184o PHE* 2.9 33.4 + - + +
185o LYS 4.8 0.5 + - - -
246o SER* 5.5 11.0 - - - -
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Residues in contact with CYS 176 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142o VAL* 4.1 15.0 - - + -
143o TYR 4.8 1.1 - - - +
172o PHE 3.0 12.5 + - - +
173o ARG 3.1 9.2 + - - +
175o LEU* 1.3 79.2 - - - +
177o THR* 1.3 60.4 + - - +
178o HIS* 5.1 0.5 - - - +
184o PHE* 5.2 2.0 - - - -
185o LYS* 5.9 1.4 + - - +
297o CYS* 3.3 35.8 - - + +
298o GLY* 3.8 24.9 - - - +
299o GLU* 5.8 0.2 - - + -
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Residues in contact with THR 177 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173o ARG 3.1 14.7 + - - -
174o CYS* 4.1 3.1 - - - -
176o CYS* 1.3 76.8 - - - +
178o HIS* 1.3 70.2 + - - +
179o GLU* 3.3 17.6 + - - +
297o CYS 5.3 0.2 - - - -
298o GLY* 4.5 8.5 - - - -
299o GLU* 5.2 11.0 - - - -
88w GLU* 5.4 1.4 - - - +
91w ILE* 3.6 14.6 - - - +
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Residues in contact with HIS 178 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174o CYS 2.8 5.8 + - - -
175o LEU 4.1 2.3 + - - +
176o CYS 3.5 3.0 - - - +
177o THR* 1.3 77.9 - - - +
179o GLU* 1.3 31.0 - - - +
181o GLY 3.0 0.2 + - - -
182o PHE 3.5 11.4 - - - +
183o GLY* 4.8 3.4 - - - +
185o LYS* 6.3 2.9 - - + -
39w LEU* 3.2 17.7 - - + +
42w ALA* 2.4 2.3 - - - +
43w GLU* 1.2 92.2 + - + +
91w ILE* 4.2 13.5 - - + +
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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