Contacts of the helix formed by residues 168 - 180 (chain F) in PDB entry 4R8A
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 CYS 168 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48F PHE* 4.0 31.0 - - + -
63F LEU* 4.1 13.7 - - - -
67F VAL* 5.0 0.4 - - - -
99F TRP* 4.3 17.9 - - + +
166F LEU* 3.6 22.2 - - - -
167F ARG* 1.3 79.8 - - - +
169F MET* 1.3 62.4 + - - +
170F ALA 3.4 2.2 - - - -
171F LEU* 3.7 11.7 + - + +
172F CYS* 3.2 31.3 + - - -
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Residues in contact with MET 169 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66F MET 3.8 8.1 - - - +
67F VAL* 3.3 40.6 - - - +
69F ARG 4.3 2.2 - - - +
70F LYS 5.0 2.7 - - - +
71F GLY 3.6 23.3 - - - +
72F THR* 3.9 18.8 - - - +
166F LEU* 3.9 18.0 - - + +
167F ARG 3.6 1.6 - - - -
168F CYS* 1.3 77.0 - - - +
170F ALA* 1.3 66.2 + - - +
172F CYS* 3.2 5.5 + - - +
173F ASP* 3.0 37.4 + - - +
187F TRP* 5.6 1.3 - - - -
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Residues in contact with ALA 170 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167F ARG 5.5 0.2 + - - -
168F CYS 3.4 0.6 - - - -
169F MET* 1.3 77.2 - - - +
171F LEU* 1.3 62.8 + - - +
173F ASP* 3.3 10.0 + - - +
174F ARG* 3.2 21.8 + - - +
222F LEU* 6.0 1.4 - - - +
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Residues in contact with LEU 171 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44F GLN* 4.0 22.7 - - - +
45F GLU* 4.0 25.6 - - + +
48F PHE* 3.8 46.2 - - + -
168F CYS* 3.7 15.5 + - + +
169F MET 3.3 0.4 - - - -
170F ALA* 1.3 78.8 - - - +
172F CYS* 1.3 57.6 + - - +
174F ARG* 3.4 9.4 + - - +
175F LEU* 3.1 49.8 + - + +
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Residues in contact with CYS 172 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26F PHE* 4.6 12.6 - - + -
48F PHE* 4.4 17.5 - - - -
67F VAL* 4.0 40.2 - - + -
168F CYS* 3.2 27.6 + - - +
169F MET* 3.2 10.4 + - - +
170F ALA 3.2 0.6 - - - -
171F LEU* 1.3 78.0 - - - +
173F ASP* 1.3 60.2 + - - +
175F LEU* 3.2 11.9 + - + +
176F ARG* 2.9 28.8 + - - +
187F TRP* 4.1 9.2 - - + -
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Residues in contact with ASP 173 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169F MET* 3.0 32.7 + - - +
170F ALA* 3.3 11.1 + - - +
172F CYS* 1.3 76.4 - - - +
174F ARG* 1.3 53.3 + - - +
176F ARG* 3.0 29.0 + - - +
177F LEU* 2.7 36.3 + - - +
183F LEU* 3.4 16.8 - - + +
187F TRP* 4.8 4.0 - - - -
222F LEU* 5.3 8.5 - - + -
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Residues in contact with ARG 174 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41F LEU* 5.5 1.3 - - - -
45F GLU* 3.2 30.2 + - - -
170F ALA 3.2 10.6 + - - +
171F LEU* 3.5 11.4 - - - +
172F CYS 3.3 0.2 - - - -
173F ASP* 1.3 78.4 - - - +
175F LEU* 1.3 65.1 + - + +
177F LEU* 3.3 9.8 + - - +
178F MET* 3.0 47.8 + - + +
215F ARG* 3.4 29.4 - - - +
218F VAL* 3.4 21.4 - - + +
219F ASP* 2.4 31.7 + - - +
222F LEU* 3.5 29.7 - - + +
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Residues in contact with LEU 175 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26F PHE* 5.1 8.1 - - + -
29F VAL* 4.3 7.9 - - + +
30F LEU* 3.6 31.4 - - + -
33F ILE* 3.7 25.3 - - + +
41F LEU* 4.3 23.3 - - + -
45F GLU* 5.7 0.2 - - + -
48F PHE* 4.4 9.4 - - + -
49F ILE* 4.8 5.2 - - + -
171F LEU* 3.1 40.1 + - + +
172F CYS* 3.3 14.4 - - - +
174F ARG* 1.3 81.4 - - + +
176F ARG* 1.3 61.9 + - - +
178F MET* 3.3 8.0 + - - +
179F TYR* 3.1 20.3 + - - +
187F TRP* 6.1 0.9 - - + -
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Residues in contact with ARG 176 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29F VAL* 5.2 3.8 - - - +
172F CYS 2.9 14.8 + - - +
173F ASP* 3.0 26.7 + - - +
175F LEU* 1.3 74.2 - - - +
177F LEU* 1.3 64.9 + - - +
179F TYR* 3.1 14.5 + - - +
180F PHE* 3.3 35.9 + - + +
182F ASN 3.8 1.2 - - - +
183F LEU* 2.7 49.3 + - - +
185F GLN 2.9 18.7 + - - -
186F ASP* 3.8 16.0 - - - +
187F TRP* 3.4 44.6 - - + +
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Residues in contact with LEU 177 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173F ASP 2.7 20.6 + - - +
174F ARG* 3.3 4.7 + - - +
176F ARG* 1.3 72.4 - - - +
178F MET* 1.3 55.8 + - - +
180F PHE 2.6 16.4 - - - +
182F ASN* 3.3 31.1 + - - +
183F LEU* 3.8 9.6 - - + +
212F PHE* 3.3 21.5 - - + -
218F VAL* 4.0 19.7 - - + +
221F TYR* 3.5 37.9 - - + -
222F LEU* 3.6 36.8 - - + -
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Residues in contact with MET 178 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33F ILE* 3.6 22.4 - - + -
37F TYR* 3.2 48.5 + - + -
40F LEU* 3.7 28.5 - - + +
41F LEU* 4.6 16.6 - - + -
174F ARG* 3.0 53.3 + - + +
175F LEU* 3.6 2.0 - - - +
176F ARG 3.1 0.2 - - - -
177F LEU* 1.3 78.9 - - - +
179F TYR* 1.3 65.5 + - - +
180F PHE 4.1 0.7 - - - +
181F GLY* 5.4 0.2 - - - -
211F GLY* 5.0 3.1 - - - -
212F PHE* 4.5 5.5 - - + -
215F ARG* 5.0 0.2 - - + -
218F VAL* 3.8 28.5 - - + -
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Residues in contact with TYR 179 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28F ALA* 4.9 1.2 - - - +
29F VAL* 3.9 32.1 - - + -
32F TRP* 3.5 51.1 + + + -
33F ILE* 3.9 4.5 - - + +
37F TYR* 4.2 1.9 + - - -
175F LEU 3.1 13.2 + - - +
176F ARG* 3.1 8.7 + - - +
178F MET* 1.3 79.7 - - - +
180F PHE* 1.3 103.5 + + + +
181F GLY 3.7 0.3 + - - -
190F PHE* 3.5 33.7 - + - -
411F PHE* 4.1 5.7 - - - +
412F HIS* 3.3 23.1 - - + +
413F PRO* 3.5 24.6 - - + +
414F PHE* 3.9 6.6 - + - -
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Residues in contact with PHE 180 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29F VAL* 6.0 1.1 - - + -
176F ARG* 3.3 30.6 + - + +
177F LEU 2.6 30.8 - - - +
178F MET 4.4 0.4 - - - -
179F TYR* 1.3 104.6 - + + +
181F GLY* 1.3 52.4 + - - +
182F ASN* 2.8 16.7 + - - +
185F GLN* 3.7 45.8 - - + +
186F ASP 3.4 28.0 - - - -
187F TRP* 5.2 3.1 - + - -
189F GLU* 4.0 11.4 - - + -
190F PHE* 4.3 11.9 - + - -
412F HIS* 3.6 15.7 - + - -
414F PHE* 3.8 16.8 - + - -
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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