Contacts of the helix formed by residues 160 - 175 (chain B) in PDB entry 3DPH
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 PRO 160 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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158B LYS 3.5 0.4 - - - +
159B GLU* 1.3 89.9 - - + +
161B PHE* 1.3 66.9 + - - +
162B ARG* 4.1 26.5 - - + +
163B ASP* 3.1 31.7 + - - +
164B TYR* 3.2 9.0 + - - +
221B VAL 4.6 7.9 - - - +
223B GLY 2.9 25.6 - - - +
224B PRO* 3.6 5.6 - - + +
225B GLY* 3.4 28.0 - - - +
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Residues in contact with PHE 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B GLN* 3.4 20.8 - - - +
159B GLU 3.2 4.0 + - - -
160B PRO* 1.3 70.7 - - - +
162B ARG* 1.4 57.6 + - - +
164B TYR* 3.2 27.5 + + - +
165B VAL* 2.9 51.4 + - + +
190B LEU* 4.6 4.9 - - + -
194B ALA* 4.6 0.2 - - + -
198B CYS* 4.1 11.3 - - + -
202B LEU* 3.6 37.0 - - + -
214B MET* 3.8 33.9 - - + -
215B MET* 3.8 21.8 - - + -
218B CYS* 3.6 27.1 + - + +
221B VAL 5.0 2.0 + - - -
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Residues in contact with ARG 162 (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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160B PRO* 4.1 24.0 - - + +
161B PHE* 1.4 78.9 - - - +
163B ASP* 1.3 86.6 + - - +
165B VAL* 3.7 2.6 - - - +
166B ASP* 3.0 33.9 + - - +
215B MET* 3.4 33.6 - - + +
224B PRO* 4.4 10.5 + - - +
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Residues in contact with ASP 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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159B GLU* 3.8 15.2 - - + +
160B PRO* 3.1 32.1 + - - +
162B ARG* 1.3 106.7 + - - +
164B TYR* 1.3 62.8 + - - +
166B ASP* 3.3 9.1 - - - +
167B ARG* 3.1 28.3 + - + +
224B PRO 4.7 0.5 - - - +
225B GLY* 4.0 9.0 - - - -
226B HIS 4.1 7.6 + - - -
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Residues in contact with TYR 164 (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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153B ILE* 3.8 19.4 + - + -
154B ARG 3.8 7.4 - - - -
155B GLN* 3.5 47.8 - - + -
159B GLU* 3.6 11.7 + - - +
160B PRO 3.2 4.2 + - - +
161B PHE* 3.2 29.8 + + - +
163B ASP* 1.3 78.2 - - - +
165B VAL* 1.3 51.1 + - - +
167B ARG* 3.2 12.7 + - - +
168B PHE* 2.8 35.1 + + - +
190B LEU* 2.6 52.2 + - + -
193B ASN* 3.1 25.5 - - - +
194B ALA* 3.8 12.6 - - + -
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Residues in contact with VAL 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B PHE* 2.9 57.9 + - + +
162B ARG* 3.7 6.7 - - - +
164B TYR* 1.3 69.9 - - - +
166B ASP* 1.3 63.5 + - - +
168B PHE* 3.5 6.0 - - - +
169B TYR* 2.9 49.5 + - + +
190B LEU* 4.5 12.1 - - + -
211B SER* 4.8 4.5 - - - +
214B MET* 5.8 0.2 - - - -
215B MET* 3.8 26.7 - - + -
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Residues in contact with ASP 166 (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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162B ARG* 3.0 19.8 + - - +
163B ASP* 3.3 14.1 - - - +
165B VAL* 1.3 80.2 - - - +
167B ARG* 1.3 63.5 + - + +
169B TYR* 3.5 2.8 + - - +
170B LYS* 2.7 66.1 + - - +
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Residues in contact with ARG 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B ILE* 3.6 31.1 - - + +
154B ARG 2.8 33.5 + - - +
156B GLY 4.6 0.2 - - - +
159B GLU* 2.8 35.7 + - - -
163B ASP* 3.1 14.0 + - + +
164B TYR* 3.6 9.6 - - - +
166B ASP* 1.3 77.0 - - + +
168B PHE* 1.3 56.9 + - - +
170B LYS* 3.4 8.3 + - - +
171B THR* 2.6 39.1 + - - +
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Residues in contact with PHE 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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150B ILE* 3.4 36.5 - - + +
153B ILE* 3.9 22.6 - - + +
164B TYR* 2.8 22.6 + - + +
165B VAL 3.5 4.9 - - - +
166B ASP 3.3 0.2 - - - -
167B ARG* 1.3 78.3 - - - +
169B TYR* 1.3 73.1 + + + +
171B THR 3.2 0.2 + - - -
172B LEU* 2.7 38.1 + - + +
185B MET* 3.6 23.8 - - + -
186B THR* 4.1 19.7 - - - -
189B LEU* 3.8 12.6 - - + -
190B LEU* 3.5 50.7 - - + -
193B ASN* 5.5 0.2 - - - -
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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
----------------------------------------------------------
165B VAL* 2.9 46.8 + - + +
166B ASP* 4.4 2.5 - - - +
168B PHE* 1.3 80.3 - + - +
170B LYS* 1.3 57.2 + - - +
172B LEU* 3.7 18.0 - - + +
173B ARG* 2.8 32.1 + - - +
186B THR* 3.0 41.5 - - + +
190B LEU* 4.3 15.3 - - + +
211B SER* 4.1 23.4 - - - -
214B MET* 5.6 1.0 - - - +
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Residues in contact with LYS 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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166B ASP* 2.7 43.8 + - - +
167B ARG* 3.8 7.2 - - - +
169B TYR* 1.3 74.5 - - - +
171B THR* 1.3 63.1 + - - +
173B ARG* 3.8 5.7 - - - +
174B ALA* 3.2 22.2 + - - +
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Residues in contact with THR 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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148B THR* 4.4 17.4 - - + +
149B SER 3.9 5.8 - - - +
150B ILE* 3.7 36.6 - - - +
153B ILE* 3.4 20.7 - - + +
167B ARG* 2.6 22.2 + - - +
168B PHE 3.6 3.1 - - - -
170B LYS* 1.3 74.8 - - - +
172B LEU* 1.3 68.4 + - - +
174B ALA* 3.2 6.9 + - + +
175B GLU* 2.9 22.0 + - - +
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Residues in contact with LEU 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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150B ILE* 3.6 14.8 - - + +
168B PHE* 2.7 22.7 + - + +
169B TYR* 3.2 25.5 + - + +
171B THR* 1.3 77.8 - - - +
173B ARG* 1.3 62.2 + - - +
175B GLU* 2.9 16.4 + - + +
182B LYS* 2.9 47.7 + - + +
185B MET* 3.5 40.2 - - + -
186B THR* 3.5 23.6 - - - +
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Residues in contact with ARG 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 2.8 19.9 + - - +
170B LYS* 3.8 7.0 - - - +
172B LEU* 1.3 72.0 - - - +
174B ALA* 1.3 60.9 - - - +
175B GLU 3.8 1.0 - - - +
176B GLN* 5.4 0.5 - - - +
182B LYS* 3.3 18.4 + - - +
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Residues in contact with ALA 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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170B LYS 3.2 15.7 + - - +
171B THR* 3.8 6.7 - - + +
172B LEU 3.2 0.8 - - - -
173B ARG* 1.3 76.3 - - - +
175B GLU* 1.3 63.6 + - - +
176B GLN* 3.4 12.9 + - - +
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Residues in contact with GLU 175 (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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178A SER* 3.6 28.1 + - - -
181A VAL* 3.7 7.1 - - + +
148B THR 4.1 5.5 - - - +
149B SER* 3.8 8.8 + - - -
150B ILE* 3.0 44.9 + - + +
171B THR* 2.9 12.8 + - - +
172B LEU* 2.9 18.5 + - + +
173B ARG 3.8 1.0 - - - +
174B ALA* 1.3 79.3 - - - +
176B GLN* 1.3 76.1 + - - +
177B ALA* 4.6 2.0 - - + -
182B LYS* 2.8 29.9 + - - -
185B MET* 4.6 11.4 - - + -
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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
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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