Contacts of the helix formed by residues 163 - 173 (chain B) in PDB entry 1DXO
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 ASP 163 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155B TYR 3.4 8.9 - - - +
156B SER* 3.9 5.0 + - - -
157B LEU* 3.7 23.7 + - + +
162B GLY* 1.3 71.4 - - - +
164B MET* 1.3 70.1 + - - +
165B ASN* 3.0 41.1 + - - +
166B VAL* 3.2 24.6 + - + +
167B ILE* 3.8 6.8 + - - +
255B VAL* 5.5 0.3 - - - +
263B ILE* 5.7 2.1 - - - +
266B ASP* 5.0 0.2 - - - +
169D TRP* 5.0 1.6 + - - -
256D GLY 3.1 13.9 + - - +
258D HIS* 3.1 31.5 + - + +
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Residues in contact with MET 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B LEU* 4.1 19.7 - - + -
146B ILE* 5.7 1.6 - - + -
148B THR* 4.4 4.0 - - + -
155B TYR* 3.1 27.3 + - + +
162B GLY 3.3 1.5 + - - -
163B ASP* 1.3 74.3 + - - +
165B ASN* 1.3 60.8 + - - +
166B VAL 3.1 0.9 - - - -
167B ILE* 3.0 25.5 + - - +
168B LEU* 2.9 58.1 + - + +
188B LEU* 4.3 10.5 - - + -
190B TYR* 3.3 46.2 - - + +
269B ILE* 3.9 12.1 - - + -
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Residues in contact with ASN 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B ASP* 3.0 32.3 + - - +
164B MET* 1.3 78.1 - - - +
166B VAL* 1.3 59.3 + - - +
168B LEU* 4.0 1.8 - - - -
169B TRP* 3.3 21.7 + - - +
255B VAL* 3.8 16.1 - - + +
263B ILE* 5.9 1.1 - - + -
264B PRO 5.7 0.2 - - - -
266B ASP* 3.2 34.3 + - - +
267B ASN 3.1 6.2 + - - -
268B GLN* 2.6 47.0 + - - +
269B ILE* 3.3 14.4 + - - +
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Residues in contact with VAL 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B ASP* 3.2 22.4 + - + +
164B MET 3.1 0.6 - - - -
165B ASN* 1.3 78.1 - - - +
167B ILE* 1.3 59.1 + - - +
169B TRP* 3.4 2.8 - - - +
170B PRO* 3.0 26.7 - - - +
255B VAL* 4.1 17.0 - - + -
263B ILE* 5.2 3.6 - - + -
166D VAL* 3.6 17.7 - - + +
169D TRP* 3.2 39.0 - - + +
170D PRO* 4.4 1.0 - - + +
255D VAL* 3.7 28.0 - - + +
256D GLY* 4.5 0.9 - - - -
258D HIS* 4.4 7.0 - - + +
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Residues in contact with ILE 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B LEU* 4.4 9.2 - - + -
106B PHE* 3.2 62.9 - - + +
107B GLY* 5.3 0.7 - - - -
155B TYR* 3.6 29.2 - - + -
161B HIS 5.0 2.2 - - - +
162B GLY 4.8 2.5 - - - +
163B ASP 4.1 7.2 - - - +
164B MET* 3.0 26.6 + - + +
166B VAL* 1.3 77.8 - - - +
168B LEU* 1.3 63.9 + - + +
170B PRO* 3.3 16.9 - - - +
171B ILE* 4.2 10.2 - - + +
169D TRP* 5.0 9.0 - - + +
170D PRO* 4.6 11.3 - - + +
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Residues in contact with LEU 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B LEU* 6.5 0.2 - - + -
144B LEU* 4.5 4.5 - - + -
146B ILE* 3.7 29.6 - - + -
164B MET* 2.9 37.3 + - + +
165B ASN 4.2 3.6 - - - +
167B ILE* 1.3 77.7 - - + +
169B TRP* 1.3 65.4 + - - +
171B ILE* 3.2 10.4 + - + +
172B GLN* 2.9 44.1 + - - +
186B PRO* 4.0 9.9 - - + -
188B LEU* 4.5 4.7 - - + -
268B GLN* 3.6 17.0 - - + +
269B ILE* 3.5 31.9 - - + -
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Residues in contact with TRP 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 ASN 3.3 11.7 + - - +
166B VAL 3.4 8.5 - - - +
168B LEU* 1.3 76.1 - - - +
170B PRO* 1.3 72.2 - - + +
173B SER* 2.9 62.6 + - - -
174B GLY 5.8 0.2 - - - +
222B PHE* 4.0 9.0 - + - -
223B ALA 6.1 0.2 - - - -
254B SER* 3.3 32.1 - - - -
255B VAL* 3.5 17.7 - - + -
256B GLY* 3.1 29.4 - - - -
257B HIS* 4.5 9.9 - + - -
268B GLN* 3.5 40.6 - - - +
106D PHE* 6.2 1.4 - + - -
161D HIS 4.1 19.7 + - - -
162D GLY* 5.3 0.2 - - - -
163D ASP 5.0 1.4 + - - -
166D VAL* 3.4 23.3 - - + +
167D ILE* 4.9 10.9 - - + +
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Residues in contact with PRO 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 VAL 3.0 19.3 - - - +
167B ILE 3.3 13.9 - - - +
169B TRP* 1.3 96.1 - - + +
171B ILE* 1.3 59.4 + - + +
174B GLY* 3.3 23.5 - - - +
175B ILE* 3.6 6.3 + - - +
105D TRP 4.3 1.3 - - - +
106D PHE* 3.7 35.1 - - + +
166D VAL* 4.8 3.4 - - + +
167D ILE* 4.7 10.3 - - + -
170D PRO* 3.9 21.8 - - + -
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Residues in contact with ILE 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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101B PHE* 5.2 2.7 - - + -
103B LEU* 6.0 1.6 - - + -
107B GLY* 4.4 17.5 - - - -
108B VAL* 3.7 32.1 - - + -
116B PHE* 5.1 4.9 - - + -
144B LEU* 4.2 29.4 - - + -
146B ILE* 6.1 1.3 - - + -
167B ILE* 4.2 16.4 - - + +
168B LEU* 3.2 9.8 + - + +
169B TRP 3.1 0.8 - - - -
170B PRO* 1.3 83.0 - - + +
172B GLN* 1.3 62.2 + - - +
173B SER 3.3 0.7 - - - -
175B ILE* 3.1 31.3 + - + +
176B LEU* 3.0 28.7 + - + +
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Residues in contact with GLN 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B LEU* 3.4 34.3 + - + +
168B LEU* 2.9 20.6 + - - +
171B ILE* 1.3 72.7 - - - +
173B SER* 1.3 57.6 + - - +
176B LEU* 3.4 9.7 - - + +
177B HIS* 2.9 27.2 + - - +
183B VAL* 3.6 21.3 - - + +
184B LEU 4.5 0.3 - - - +
186B PRO* 3.6 23.2 - - - +
220B LEU* 3.1 30.4 - - - +
222B PHE* 3.8 3.9 - - + -
268B GLN* 3.1 35.0 + - - +
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Residues in contact with SER 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B TYR* 3.4 20.2 + - - -
169B TRP* 2.9 49.4 + - - -
172B GLN* 1.3 77.5 - - - +
174B GLY* 1.3 60.4 + - - -
175B ILE 3.3 0.6 + - - -
177B HIS* 4.0 2.6 - - - -
178B PHE 2.9 28.8 + - - -
222B PHE* 3.7 23.5 - - - -
161D HIS 5.1 2.0 + - - -
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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