Contacts of the helix formed by residues 157 - 174 (chain F) in PDB entry 3HYW
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 157 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150F ALA* 3.5 33.4 - - + -
154F VAL* 3.3 36.6 - - + -
155F SER* 4.0 6.5 - - - -
156F CSS 1.3 72.8 - - - -
158F GLY* 1.3 68.7 + - - +
159F PRO* 3.3 3.8 - - - -
160F ALA* 2.9 18.8 + - + +
161F TYR* 3.3 28.3 + + + -
184F PHE* 6.0 1.6 - + - -
186F THR* 3.6 3.6 - - - -
187F SER* 3.7 5.4 - - - -
188F GLU* 3.5 30.7 - - + +
194F PHE* 3.5 26.5 - - + -
195F GLY* 3.8 17.7 - - - -
251F MET* 5.2 0.4 - - - -
308F THR* 3.5 18.6 - - + -
800F PS9 3.7 4.0 - - - -
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Residues in contact with GLY 158 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157F PHE* 1.3 74.3 - - - +
159F PRO* 1.3 62.7 - - - +
161F TYR* 3.1 12.6 + - - +
162F GLU* 2.9 29.0 + - - +
194F PHE* 4.5 0.4 - - - -
349F ALA* 5.0 1.4 - - - +
800F PS9 3.0 47.6 - - - -
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Residues in contact with PRO 159 (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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46F PRO* 4.6 0.4 - - + -
123F ILE* 3.7 6.5 - - + +
156F CSS 3.9 12.8 - - - +
157F PHE 3.3 4.7 - - - -
158F GLY* 1.3 89.2 - - - +
160F ALA* 1.3 55.0 + - - +
162F GLU* 3.6 13.7 - - - +
163F PHE* 2.9 30.5 + - - +
251F MET* 3.6 17.9 - - + -
441F FAD 3.4 53.6 - - + -
800F PS9 3.5 16.1 - - - -
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Residues in contact with ALA 160 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148F ILE* 3.6 8.2 - - + +
149F GLY 4.0 11.7 - - - +
150F ALA* 5.6 1.3 - - + -
157F PHE* 2.9 12.9 + - - +
159F PRO* 1.3 76.4 - - - +
161F TYR* 1.3 60.4 + - - +
164F ALA* 3.0 30.0 + - - +
184F PHE* 3.6 21.8 - - + -
249F MET* 4.1 4.7 - - - -
251F MET* 3.3 31.4 - - + +
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Residues in contact with TYR 161 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157F PHE* 3.3 25.5 + - + -
158F GLY* 3.1 7.5 + - - +
160F ALA* 1.3 74.7 - - - +
162F GLU* 1.3 65.0 + - + +
164F ALA* 3.4 2.9 + - - +
165F LEU* 3.1 36.3 + - + +
184F PHE* 3.5 29.7 - + - -
188F GLU* 2.5 33.3 + - - -
191F LEU* 3.4 9.8 - - + +
192F GLY 3.1 19.7 + - - -
194F PHE* 3.7 28.0 - + + -
206F VAL* 3.6 28.7 - - + -
210F PHE* 3.6 21.5 - + - -
349F ALA* 5.4 3.6 - - + -
351F PHE* 4.9 5.6 - - + -
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Residues in contact with GLU 162 (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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43F PRO 4.7 0.5 - - - +
46F PRO* 3.6 20.5 - - + +
47F HIS* 4.5 0.6 - - - -
158F GLY 2.9 15.0 + - - +
159F PRO* 3.6 14.6 - - - +
161F TYR* 1.3 76.3 - - - +
163F PHE* 1.3 57.3 + - - +
165F LEU* 3.3 1.7 + - - -
166F MET* 2.8 46.2 + - + +
348F ILE 3.5 0.2 - - - +
349F ALA* 3.7 9.9 - - + -
350F ASP* 2.8 45.3 + - - +
351F PHE* 4.6 4.0 - - - -
382F LYS* 3.1 27.7 + - - -
441F FAD 4.4 3.5 + - - -
800F PS9 4.0 13.0 - - - -
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Residues in contact with PHE 163 (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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46F PRO* 4.4 9.4 - - + +
49F ALA* 3.9 18.6 - - + -
50F MET* 3.7 23.6 - - + -
123F ILE* 3.9 20.9 - - + -
132F THR* 3.8 20.9 - - + -
136F LEU* 4.0 11.9 - - + -
148F ILE* 3.6 18.4 - - + -
159F PRO 2.9 19.2 + - - +
160F ALA 3.9 3.6 - - - +
161F TYR 3.3 0.2 - - - -
162F GLU* 1.3 77.2 - - - +
164F ALA* 1.3 56.3 + - - +
166F MET* 3.8 6.9 - - - +
167F LEU* 2.9 38.5 + - + +
247F PHE* 3.8 17.9 - + - -
249F MET* 3.6 33.2 - - + -
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Residues in contact with ALA 164 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148F ILE* 3.8 21.1 - - + -
160F ALA 3.0 18.0 + - - +
161F TYR* 3.6 5.2 - - - +
162F GLU 3.3 0.2 - - - -
163F PHE* 1.3 77.3 - - - +
165F LEU* 1.3 58.0 + - - +
168F HIS* 2.9 24.8 + - - +
182F MET* 3.3 14.7 - - + +
184F PHE* 4.1 20.2 - - + -
210F PHE* 4.8 3.8 - - + -
215F ILE* 4.5 14.6 - - + -
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Residues in contact with LEU 165 (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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161F TYR* 3.1 29.7 + - + +
162F GLU 3.9 0.4 - - - +
164F ALA* 1.3 73.2 - - - +
166F MET* 1.3 59.3 + - - +
168F HIS* 3.3 7.5 + - + +
169F TYR* 2.8 24.4 + - - +
206F VAL* 5.9 0.2 - - + -
209F LEU* 4.1 14.4 - - + -
210F PHE* 3.7 23.6 - - + -
213F ARG* 3.7 28.7 + - + +
215F ILE* 3.5 24.0 - - + -
351F PHE* 3.3 56.8 - - + +
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Residues in contact with MET 166 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46F PRO* 3.9 25.4 - - + -
47F HIS* 3.2 42.0 - - + +
50F MET* 4.0 17.7 - - + -
52F TRP* 3.6 33.6 - - + -
162F GLU* 2.8 30.0 + - + +
163F PHE* 3.8 4.5 - - - +
165F LEU* 1.3 72.6 - - - +
167F LEU* 1.3 58.4 + - - +
169F TYR* 3.2 3.6 + - - +
170F GLU* 2.9 28.2 + - - +
350F ASP* 3.3 30.7 - - + +
351F PHE 3.6 11.4 - - - -
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Residues in contact with LEU 167 (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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50F MET* 3.8 13.6 - - + +
136F LEU* 3.6 33.2 - - + -
139F LEU* 4.4 2.7 - - + -
140F TYR* 3.9 18.6 - - + +
146F VAL* 3.9 34.8 - - + -
148F ILE* 4.0 11.0 - - + -
163F PHE* 2.9 25.2 + - + +
164F ALA 3.7 4.3 - - - +
166F MET* 1.3 73.4 - - - +
168F HIS* 1.3 65.6 + - - +
170F GLU* 3.2 0.9 + - + -
171F LEU* 2.9 48.5 + - + +
182F MET* 4.1 3.8 - - + -
247F PHE* 4.3 2.7 - - + -
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Residues in contact with HIS 168 (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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367D ARG 4.9 0.9 - - - -
368D GLU 4.4 4.9 - - - -
164F ALA 2.9 15.2 + - - +
165F LEU* 3.3 13.0 - - - +
167F LEU* 1.3 75.0 - - - +
169F TYR* 1.3 65.1 + - + +
171F LEU* 3.5 2.1 + - - +
172F LYS* 3.1 55.4 + - + +
177F ARG* 3.0 33.8 + - + +
182F MET* 3.9 14.8 - - - +
213F ARG* 3.3 57.6 + - + +
215F ILE* 4.3 5.6 - - + -
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Residues in contact with TYR 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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52F TRP* 3.5 28.9 - + - -
165F LEU 2.8 16.8 + - - +
166F MET* 3.2 7.2 + - - +
168F HIS* 1.3 78.3 - - + +
170F GLU* 1.3 60.0 + - - +
172F LYS* 3.4 7.9 + - + +
173F LYS* 3.0 67.4 + - + +
351F PHE 3.7 9.6 - - - +
352F GLY* 4.0 7.2 - - - -
353F GLU* 3.9 46.4 + - + +
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Residues in contact with GLU 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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50F MET* 3.4 26.0 - - + -
52F TRP* 3.2 26.9 + - + -
140F TYR* 3.4 25.1 - - + +
166F MET 2.9 9.9 + - - +
167F LEU* 3.7 3.1 - - + +
169F TYR* 1.3 76.7 - - - +
171F LEU* 1.3 57.9 + - - +
173F LYS* 3.2 19.5 + - - +
174F ARG* 2.8 64.4 + - - +
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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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139F LEU* 4.6 5.6 - - + -
140F TYR* 3.9 20.0 - - + -
167F LEU* 2.9 40.3 + - + +
168F HIS 3.9 3.4 - - - +
170F GLU* 1.3 75.0 - - - +
172F LYS* 1.3 57.5 + - - +
174F ARG* 3.4 2.5 + - - -
175F GLY 2.9 6.1 + - - -
176F ILE* 2.9 56.6 + - + +
177F ARG* 3.3 19.0 + - + -
180F VAL* 3.7 38.8 - - + -
182F MET* 4.0 14.8 - - - -
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Residues in contact with LYS 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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368D GLU* 3.2 39.3 + - - +
369D ARG* 3.5 18.2 + - - +
431D SO4 2.7 47.9 + - - -
168F HIS* 3.1 44.2 + - + +
169F TYR* 3.6 6.7 - - + +
170F GLU 3.3 0.2 - - - -
171F LEU* 1.3 73.3 - - - +
173F LYS* 1.3 60.4 + - - +
174F ARG 3.2 0.4 - - - -
175F GLY* 2.9 17.3 + - - -
177F ARG* 3.9 9.2 - - + -
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Residues in contact with LYS 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 TYR* 3.0 50.5 + - + +
170F GLU* 3.4 21.8 - - - +
172F LYS* 1.3 77.2 - - - +
174F ARG* 1.3 60.4 + - + +
175F GLY 3.6 0.2 + - - -
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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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133F GLN* 5.9 0.2 - - - +
137F GLN* 3.9 16.6 + - - +
140F TYR* 3.3 57.2 - - - +
170F GLU* 2.8 41.3 + - - +
171F LEU* 3.8 0.4 - - - +
172F LYS 3.2 0.2 - - - -
173F LYS* 1.3 78.1 - - + +
175F GLY* 1.3 61.8 + - - +
176F ILE* 3.2 26.9 + - + +
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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
------------------------------------------------------------
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