Contacts of the helix formed by residues 163 - 173 (chain B) in PDB entry 3OX3
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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169A TRP* 5.1 0.2 + - - -
155B TYR 3.5 13.9 - - - +
156B THR* 3.4 12.6 + - - +
157B LYS* 3.7 12.4 + - + +
161B ASN 4.6 1.4 - - - +
162B GLY* 1.3 74.3 - - - +
164B SER* 1.3 67.7 + - - +
165B ARG* 3.2 37.0 + - - +
166B TYR* 3.1 47.2 + - + +
167B PHE* 4.3 2.9 + - - -
227B HIS 4.8 1.4 - - - +
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Residues in contact with SER 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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155B TYR* 3.2 25.7 + - - -
162B GLY 3.5 0.2 + - - -
163B ASP* 1.3 76.9 + - - +
165B ARG* 1.3 69.7 + - - +
166B TYR 3.1 0.9 + - - -
167B PHE* 3.3 39.3 + - - -
168B LEU* 3.6 8.3 - - - +
188B ILE* 3.8 28.1 - - - +
190B PHE* 4.3 8.7 - - - -
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Residues in contact with ARG 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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163B ASP* 3.2 17.8 + - - +
164B SER* 1.3 81.5 + - - +
166B TYR* 1.3 63.9 + - - +
168B LEU* 3.1 20.0 + - + -
226B TRP* 2.9 82.9 + - + +
227B HIS* 3.4 36.9 - - - +
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Residues in contact with TYR 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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166A TYR 4.9 2.9 - - - +
169A TRP* 3.4 27.7 - + + +
170A PRO* 5.1 0.7 - - - +
224A ALA* 4.4 13.0 - - + +
228A PHE* 3.4 33.4 - + + +
157B LYS* 3.7 27.7 - - - +
162B GLY* 3.9 11.7 - - - -
163B ASP* 3.1 42.8 + - + +
165B ARG* 1.3 77.7 - - - +
167B PHE* 1.3 62.4 + - - +
168B LEU 3.4 0.3 + - - -
169B TRP* 3.5 16.5 + - - +
170B PRO* 4.3 2.1 - - - +
227B HIS 3.6 12.6 - - - -
228B PHE* 3.5 44.0 + + + -
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Residues in contact with PHE 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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169A TRP* 4.4 4.0 - - - -
170A PRO* 4.4 5.6 - - + -
103B LEU* 3.7 37.2 - - + -
106B PHE* 3.5 45.3 - + + +
146B VAL* 4.8 7.2 - - + -
148B THR* 4.8 8.5 - - + -
155B TYR* 3.5 39.5 - + - -
163B ASP 4.6 1.6 - - - -
164B SER* 3.3 29.1 + - - -
166B TYR* 1.3 76.2 - - - +
168B LEU* 1.3 86.5 + - + +
169B TRP 3.2 1.3 - - - -
170B PRO* 3.4 10.9 - - - +
171B LEU* 4.4 11.2 - - + +
188B ILE* 4.5 9.4 - - + -
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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
----------------------------------------------------------
144B LEU* 4.0 20.9 - - + -
146B VAL* 4.8 8.7 - - + -
164B SER 3.6 9.9 - - - +
165B ARG* 3.1 26.5 + - + +
167B PHE* 1.3 99.3 - - + +
169B TRP* 1.3 54.8 + - - +
170B PRO* 3.5 0.4 - - - -
171B LEU* 3.1 8.1 + - + -
172B GLN* 2.7 55.6 + - - +
186B PRO* 3.6 34.3 - - + -
188B ILE* 4.5 9.2 - - + -
226B TRP* 4.2 6.1 - - + -
227B HIS* 4.1 2.9 - - + -
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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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106A PHE* 3.4 21.3 - + - -
160A VAL 5.5 0.2 - - - -
161A ASN 3.4 17.1 + - - -
162A GLY* 4.2 2.9 - - - -
163A ASP 5.0 0.4 + - - -
166A TYR* 3.4 46.5 - + + +
167A PHE 4.1 1.3 - - - +
165B ARG 3.7 2.4 + - - -
166B TYR 3.5 7.0 + - - +
167B PHE 3.2 0.2 - - - -
168B LEU* 1.3 77.3 - - - +
170B PRO* 1.3 70.7 - - + +
173B HIS* 2.9 69.5 + + + +
174B GLY 3.1 5.5 + - - -
223B THR 3.7 2.2 - - - -
224B ALA* 3.6 37.2 - - + -
227B HIS* 3.4 35.7 - + + -
228B PHE* 3.5 23.6 - + + -
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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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105A TRP 4.1 6.6 - - - +
106A PHE* 3.6 39.3 - - + +
107A SER* 5.2 4.0 - - - -
166A TYR 5.2 0.4 - - - +
167A PHE* 4.4 14.4 - - - -
170A PRO* 4.1 21.3 - - + -
107B SER* 6.2 0.2 - - - +
166B TYR 4.3 2.2 - - - +
167B PHE 3.4 17.3 - - - +
169B TRP* 1.3 94.7 - - + +
171B LEU* 1.3 61.7 + - + +
174B GLY* 3.2 3.8 - - - -
175B THR* 3.0 30.2 + - - -
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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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105A TRP 6.0 1.1 - - - +
101B PHE* 4.2 10.1 - - + -
103B LEU* 5.7 0.7 - - + -
107B SER* 4.5 20.6 - - - +
108B VAL* 3.8 36.1 - - + -
113B LYS* 6.0 2.9 - - + -
116B MET* 4.1 21.9 - - + +
144B LEU* 3.8 26.0 - - + -
167B PHE* 4.4 17.7 - - + +
168B LEU* 3.1 9.7 + - + +
170B PRO* 1.3 82.4 - - + +
172B GLN* 1.3 61.4 + - - +
175B THR* 3.4 7.8 - - - +
176B LEU* 3.0 34.6 + - - +
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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
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144B LEU* 3.6 23.7 - - + +
168B LEU* 2.7 27.9 + - + +
171B LEU* 1.3 72.8 - - - +
173B HIS* 1.3 56.8 + - - +
176B LEU* 3.6 8.2 - - + +
177B HIS* 2.8 28.9 + - - +
183B VAL* 3.8 27.6 - - + +
184B LEU 4.2 0.8 + - - -
186B PRO* 3.5 39.0 - - - +
220B ILE* 3.6 4.5 - - - +
222B CYS* 3.5 10.1 - - - -
226B TRP* 3.3 15.8 - - - -
227B HIS* 3.1 24.4 + - - +
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Residues in contact with HIS 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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106A PHE* 4.3 4.5 - + - -
160A VAL 3.0 25.9 + - - -
161A ASN 4.4 0.2 - - - -
132B TYR* 3.2 40.7 - + - -
169B TRP* 2.9 60.6 + + + +
172B GLN* 1.3 76.1 - - - +
174B GLY* 1.3 67.4 + - - +
175B THR 3.2 1.6 - - - -
177B HIS* 3.3 7.1 + + - +
178B PHE 3.2 22.2 + - - -
222B CYS* 3.3 6.8 + - - -
223B THR* 5.3 2.0 - - - -
227B HIS* 4.5 0.2 - - + -
231B ZN 2.1 37.8 - - - -
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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