Contacts of the helix formed by residues 162 - 175 (chain B) in PDB entry 1DBQ
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 ALA 162 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160B ASP* 3.3 17.9 + - - +
161B ASN* 1.3 72.4 - - - +
163B PHE* 1.3 63.4 - - - +
165B GLY* 2.8 13.9 + - - -
166B GLY 2.8 14.6 + - - -
195B GLY* 4.7 4.0 - - - -
196B ARG* 3.5 31.9 - - + +
274B TYR* 3.3 17.4 + - + +
292B GLN* 4.3 7.1 - - - +
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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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161B ASN* 3.2 1.5 - - - +
162B ALA* 1.3 81.7 - - - +
164B GLU* 1.3 66.9 + - + +
167B TYR* 3.1 25.5 + + + +
195B GLY* 3.7 18.2 - - - +
198B ALA* 3.7 15.0 - - + -
199B GLY* 3.3 31.8 - - - -
202B LYS* 4.1 30.5 - - + -
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Residues in contact with GLU 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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161B ASN* 2.8 43.6 + - + +
163B PHE* 1.3 85.0 - - + +
165B GLY* 1.3 61.3 + - - +
167B TYR* 3.3 10.1 - - + +
168B MET* 3.1 45.9 + - + +
322B HIS* 3.2 31.9 + - - +
323B PRO* 3.4 4.4 - - + +
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Residues in contact with GLY 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 ASN 2.7 11.5 + - - -
162B ALA 2.8 7.1 + - - -
164B GLU* 1.3 75.7 - - - +
166B GLY* 1.3 64.1 + - - -
168B MET* 3.2 5.4 - - - +
169B ALA 3.2 16.1 + - - -
274B TYR* 3.2 25.6 - - - -
290B ILE* 3.9 8.9 - - - +
323B PRO* 3.9 14.1 - - - -
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Residues in contact with GLY 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 ALA 2.8 13.3 + - - -
165B GLY* 1.3 71.8 - - - -
167B TYR* 1.3 61.4 - - - +
169B ALA* 3.2 8.3 + - - +
170B GLY 3.0 19.9 + - - -
196B ARG* 3.4 24.9 - - - -
200B PHE* 3.6 18.1 - - - +
244B PHE* 4.6 4.5 - - - -
274B TYR* 3.7 7.2 - - - -
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Residues in contact with TYR 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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163B PHE* 3.1 22.8 + + + +
164B GLU* 3.3 15.3 - - + +
165B GLY 3.1 0.4 - - - -
166B GLY* 1.3 77.1 - - - +
168B MET* 1.3 68.2 + - + +
170B GLY* 3.3 1.4 + - - -
171B ARG* 2.9 51.0 + - + +
199B GLY* 3.5 21.5 - - - +
200B PHE* 4.7 0.4 - - - +
202B LYS* 4.3 11.9 - - + -
203B ALA* 3.6 22.0 - - + +
206B GLU* 2.3 35.4 + - - -
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Residues in contact with MET 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 GLU* 3.1 43.1 + - + +
165B GLY 3.2 10.8 - - - +
167B TYR* 1.3 84.0 - - + +
169B ALA* 1.3 62.8 + - - +
171B ARG* 3.3 6.7 + - - +
172B TYR* 2.9 23.6 + - - +
290B ILE* 4.4 8.3 - - + -
323B PRO* 3.6 33.4 - - + +
324B ARG* 4.1 14.4 - - - -
325B LEU* 4.1 16.3 - - + +
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Residues in contact with ALA 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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165B GLY 3.2 7.6 + - - +
166B GLY 3.2 9.1 + - - +
168B MET* 1.3 79.7 - - - +
170B GLY* 1.3 63.9 + - - +
172B TYR* 3.0 14.8 + - - +
173B LEU* 3.1 17.8 + - - +
200B PHE* 4.9 0.2 - - - -
244B PHE* 3.9 34.3 - - + -
272B ILE* 4.1 22.0 - - + +
290B ILE* 4.2 9.8 - - + +
325B LEU* 6.0 0.2 - - - -
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Residues in contact with GLY 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 GLY 3.0 8.0 + - - -
167B TYR 3.7 2.7 - - - -
169B ALA* 1.3 78.7 - - - +
171B ARG* 1.3 60.0 - - - +
173B LEU* 3.6 5.4 + - - +
174B ILE* 3.3 31.6 + - - +
200B PHE* 3.4 32.6 - - - -
203B ALA* 4.3 7.0 - - - -
204B MET* 4.6 2.7 - - - +
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Residues in contact with ARG 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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167B TYR* 2.9 46.0 + - + +
168B MET* 3.7 6.7 - - - +
169B ALA 3.0 0.2 - - - -
170B GLY* 1.3 75.6 - - - +
172B TYR* 1.3 65.6 + - - +
173B LEU 3.1 1.6 - - - -
174B ILE* 3.8 27.2 - - + +
175B GLU* 2.9 68.2 + - - +
203B ALA* 3.6 22.2 + - + -
206B GLU* 4.5 15.3 + - - +
207B ALA* 5.1 4.6 - - - +
340B ARG* 6.0 2.2 - - - +
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Residues in contact with TYR 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 MET 2.9 13.6 + - - +
169B ALA* 3.5 10.1 - - - +
171B ARG* 1.3 76.7 - - - +
173B LEU* 1.3 61.8 + - + +
175B GLU* 3.4 9.1 + - + +
176B ARG* 3.0 64.7 + - + +
272B ILE* 4.4 17.0 - - + -
288B THR* 4.0 12.3 + - + +
325B LEU* 4.5 15.3 - - + -
327B GLU* 2.5 51.3 + - + +
328B ARG 5.7 1.0 + - - -
331B VAL* 3.7 32.9 + - + +
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Residues in contact with LEU 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 ALA 3.1 11.2 + - - +
170B GLY* 3.8 5.8 - - - +
171B ARG 3.1 0.6 - - - -
172B TYR* 1.3 82.9 - - + +
174B ILE* 1.3 63.6 + - - +
176B ARG* 3.3 9.0 + - - +
178B HIS* 3.0 28.9 + - + +
181B ILE* 3.6 40.6 - - + -
200B PHE* 4.2 13.7 - - + -
242B ALA* 3.9 22.0 - - + -
243B VAL 5.4 0.7 - - - +
244B PHE* 4.7 5.2 - - + +
270B SER* 5.1 0.9 - - - +
272B ILE* 4.2 26.5 - - + +
331B VAL* 4.4 24.5 - - + -
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Residues in contact with ILE 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 GLY 3.3 20.1 + - - +
171B ARG* 3.3 28.8 + - - +
173B LEU* 1.3 78.0 - - - +
175B GLU* 1.3 66.9 + - - +
177B GLY* 3.0 15.2 + - - -
178B HIS 3.8 7.8 + - - +
181B ILE* 4.8 2.0 - - + -
203B ALA* 3.4 35.4 - - + +
204B MET* 4.3 5.6 - - - -
207B ALA* 3.8 13.7 - - + -
209B ILE* 3.4 27.1 - - + -
339B TYR* 4.3 26.3 + - + +
340B ARG* 6.2 0.2 - - - -
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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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3B MG 4.3 8.5 - - - -
171B ARG* 2.9 57.3 + - - +
172B TYR* 3.9 8.1 - - + +
174B ILE* 1.3 79.9 - - + +
176B ARG* 1.3 59.4 + - + +
177B GLY* 3.0 4.4 + - - -
337B ARG* 3.6 19.1 + - - +
340B ARG* 5.3 10.9 - - - +
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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
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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