Contacts of the helix formed by residues 157 - 174 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150B ALA* 3.5 31.6 - - + -
154B VAL* 3.3 33.2 - - + -
155B SER* 4.2 2.7 + - - -
156B CSS 1.3 76.1 - - - -
158B GLY* 1.3 68.1 + - - +
159B PRO* 3.4 3.6 - - - -
160B ALA* 3.1 18.5 + - - +
161B TYR* 3.3 27.3 + + + -
184B PHE* 6.1 1.3 - + - -
186B THR* 3.6 1.6 - - - -
187B SER* 3.6 9.0 - - - -
188B GLU* 3.5 29.2 - - + +
194B PHE* 3.5 30.2 + - + -
195B GLY* 3.8 19.3 - - - -
251B MET* 5.1 0.2 - - - -
308B THR* 3.6 20.9 - - + -
800B PS9 3.5 3.2 - - - -
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Residues in contact with GLY 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B PHE* 1.3 77.8 - - - +
159B PRO* 1.3 61.2 - - - +
161B TYR* 3.1 12.8 + - - +
162B GLU* 2.9 33.0 + - - +
194B PHE* 4.6 6.2 - - - -
349B ALA* 4.8 1.1 - - - +
800B PS9 3.4 8.0 - - - -
802B PS9 3.9 27.3 - - - -
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Residues in contact with PRO 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B PRO* 4.5 1.3 - - + +
123B ILE* 3.8 6.5 - - + +
156B CSS 3.9 13.7 - - - +
157B PHE 3.4 4.0 - - - -
158B GLY* 1.3 90.5 - - - +
160B ALA* 1.3 51.1 + - - +
162B GLU* 3.6 13.4 - - - +
163B PHE* 2.8 35.2 + - - +
251B MET* 3.6 19.7 - - + -
441B FAD 3.3 50.9 - - + +
800B PS9 3.7 13.5 - - - -
802B PS9 5.4 1.6 - - - -
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Residues in contact with ALA 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B ILE* 3.6 9.6 - - + +
149B GLY 4.1 11.9 - - - +
150B ALA* 5.5 1.6 - - + -
157B PHE* 3.1 13.2 + - + +
159B PRO* 1.3 75.5 - - - +
161B TYR* 1.3 61.5 + - - +
163B PHE* 3.8 0.2 - - - -
164B ALA* 2.9 31.0 + - - +
184B PHE* 3.7 19.1 - - + -
249B MET* 4.0 5.8 - - + -
251B MET* 3.4 30.0 - - + +
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Residues in contact with TYR 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B PHE* 3.3 24.6 + - + -
158B GLY* 3.1 7.2 + - - +
160B ALA* 1.3 75.8 - - - +
162B GLU* 1.3 64.9 + - - +
164B ALA* 3.4 2.2 + - - +
165B LEU* 3.1 36.5 + - + +
184B PHE* 3.5 27.4 - + - -
188B GLU* 2.6 32.3 + - - -
191B LEU* 3.5 8.9 - - + +
192B GLY 3.1 20.1 + - - -
194B PHE* 3.7 28.5 - + + -
206B VAL* 3.5 30.7 - - + -
210B PHE* 3.5 21.8 - + - -
349B ALA* 5.4 4.0 - - + -
351B PHE* 5.0 4.9 - - + -
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Residues in contact with GLU 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B PRO 4.7 0.9 - - - +
46B PRO* 3.5 21.7 - - + +
47B HIS* 4.4 0.8 - - - -
158B GLY 2.9 16.3 + - - +
159B PRO* 3.6 14.3 - - - +
161B TYR* 1.3 74.2 - - - +
163B PHE* 1.3 58.4 + - - +
165B LEU* 3.2 2.1 + - - -
166B MET* 2.8 45.3 + - + +
348B ILE 3.4 0.4 - - - +
349B ALA* 3.6 12.6 - - - -
350B ASP* 2.7 48.5 + - - +
351B PHE* 4.7 3.3 - - - -
382B LYS* 3.1 25.2 + - - -
441B FAD 4.4 7.4 + - - -
802B PS9 4.5 4.2 - - - -
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Residues in contact with PHE 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B PRO* 4.3 9.9 - - + -
49B ALA* 4.0 18.8 - - + -
50B MET* 3.6 25.1 - - + -
123B ILE* 4.0 17.3 - - + -
132B THR* 3.9 13.2 - - + -
136B LEU* 3.7 22.4 - - + -
148B ILE* 3.9 8.5 - - + -
159B PRO 2.8 21.4 + - - +
160B ALA 3.9 2.7 - - - +
162B GLU* 1.3 74.3 - - - +
164B ALA* 1.3 58.3 + - - +
166B MET* 3.8 6.8 - - - +
167B LEU* 2.9 41.0 + - + +
247B PHE* 3.9 14.1 - + - -
249B MET* 3.7 40.4 - - + -
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Residues in contact with ALA 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B ILE* 3.6 24.5 - - + -
160B ALA 2.9 17.0 + - - +
161B TYR* 3.7 4.9 - - - +
163B PHE* 1.3 78.5 - - - +
165B LEU* 1.3 58.0 + - + +
167B LEU 3.5 0.2 + - - -
168B HIS* 3.1 23.2 + - - +
182B MET* 3.2 16.8 - - + +
184B PHE* 4.1 18.8 - - + -
210B PHE* 4.9 4.0 - - + -
215B ILE* 4.3 11.8 - - + +
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Residues in contact with LEU 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161B TYR* 3.1 25.0 + - + +
162B GLU 3.9 0.4 - - - +
164B ALA* 1.3 74.0 - - - +
166B MET* 1.3 60.3 + - - +
168B HIS* 3.4 7.9 + - + +
169B TYR* 3.0 23.4 + - - +
206B VAL* 6.0 0.4 - - + -
209B LEU* 3.7 24.7 - - + -
210B PHE* 3.9 15.5 - - + -
213B ARG* 3.7 35.6 + - + +
215B ILE* 4.0 18.2 - - + -
351B PHE* 3.3 53.9 - - + +
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Residues in contact with MET 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B PRO* 3.9 22.4 - - + -
47B HIS* 3.2 42.0 - - + +
50B MET* 3.9 18.8 - - + -
52B TRP* 3.6 29.2 - - + -
162B GLU* 2.8 25.5 + - + +
163B PHE* 3.8 4.3 - - - +
165B LEU* 1.3 76.7 - - - +
167B LEU* 1.3 57.9 + - - +
169B TYR* 3.3 3.9 + - - +
170B GLU* 2.9 28.1 + - - +
350B ASP* 3.4 31.9 - - + +
351B PHE 3.9 9.6 - - - -
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Residues in contact with LEU 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B MET* 3.8 13.2 - - + +
136B LEU* 3.8 27.1 - - + -
139B LEU* 4.3 7.4 - - + -
140B TYR* 3.9 18.8 - - + +
146B VAL* 4.0 27.6 - - + -
148B ILE* 4.1 3.6 - - + -
163B PHE* 2.9 37.8 + - + +
164B ALA 3.8 3.6 - - - +
166B MET* 1.3 72.5 - - - +
168B HIS* 1.3 61.0 + - - +
170B GLU 3.2 0.9 + - - -
171B LEU* 2.8 55.6 + - + +
182B MET* 4.4 3.1 - - + -
247B PHE* 4.3 2.9 - - + -
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Residues in contact with HIS 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164B ALA 3.1 14.5 + - - +
165B LEU* 3.5 12.6 - - - +
167B LEU* 1.3 76.0 - - - +
169B TYR* 1.3 66.3 + - - +
171B LEU* 3.4 1.9 + - - +
172B LYS* 3.0 56.4 + - + +
177B ARG* 3.1 36.7 + - + +
182B MET* 3.9 16.9 - - + -
213B ARG* 3.2 57.9 + - + +
215B ILE* 4.4 4.9 - - + -
367F ARG 5.1 1.1 - - - -
368F GLU 4.8 3.6 - - - -
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Residues in contact with TYR 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B TRP* 3.9 25.4 - + - -
165B LEU 3.0 14.7 + - - +
166B MET* 3.3 8.5 - - - +
168B HIS* 1.3 81.9 - - + +
170B GLU* 1.3 59.7 + - - +
172B LYS* 3.2 7.6 + - + +
173B LYS* 2.9 62.2 + - + +
351B PHE 3.8 9.6 - - - +
352B GLY* 4.2 7.0 - - - -
353B GLU* 2.8 60.6 + - + +
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Residues in contact with GLU 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B MET* 3.4 24.7 - - + -
52B TRP* 3.1 26.9 + - + -
140B TYR* 3.4 29.6 - - + +
166B MET 2.9 7.6 + - - +
167B LEU* 3.2 2.9 + - + +
169B TYR* 1.3 82.2 - - - +
171B LEU* 1.3 58.2 + - - +
173B LYS* 3.4 9.3 + - - +
174B ARG* 2.9 61.7 + - - +
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Residues in contact with LEU 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139B LEU* 4.6 5.4 - - + -
140B TYR* 3.9 20.0 - - + -
167B LEU* 2.8 43.4 + - + +
168B HIS 3.8 3.8 - - - +
170B GLU* 1.3 71.7 - - - +
172B LYS* 1.3 58.1 + - - +
174B ARG* 3.5 1.5 + - - -
175B GLY 2.9 6.2 + - - -
176B ILE* 2.8 58.2 + - + +
177B ARG* 3.9 18.6 - - - -
180B VAL* 3.6 37.9 - - + -
182B MET* 4.0 16.2 - - - -
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Residues in contact with LYS 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168B HIS* 3.0 41.2 + - + +
169B TYR* 3.2 10.7 + - + +
171B LEU* 1.3 75.1 - - - +
173B LYS* 1.3 62.2 + - - +
174B ARG 3.2 0.2 - - - -
175B GLY* 2.9 18.7 + - - -
177B ARG* 3.8 18.2 - - + -
213B ARG* 6.1 0.8 - - - +
368F GLU* 3.2 38.7 + - - +
369F ARG* 4.0 10.2 - - - +
431F SO4 2.5 45.1 + - - -
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Residues in contact with LYS 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169B TYR* 2.9 61.3 + - + +
170B GLU* 3.6 15.3 - - - +
172B LYS* 1.3 78.0 - - - +
174B ARG* 1.3 61.3 + - + +
175B GLY 3.6 0.2 + - - -
353B GLU* 4.3 8.2 + - - -
431F SO4 5.5 5.4 + - - -
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Residues in contact with ARG 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137B GLN* 3.9 16.0 + - - +
140B TYR* 3.5 60.0 - - - +
170B GLU* 2.9 42.7 + - - +
172B LYS 3.2 0.2 - - - -
173B LYS* 1.3 77.9 - - + +
175B GLY* 1.3 62.9 + - - +
176B ILE* 3.3 25.4 + - + +
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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
------------------------------------------------------------
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