Contacts of the helix formed by residues 163 - 173 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155A TYR 3.5 9.1 - - - +
156A SER* 3.9 4.4 + - - -
157A LEU* 3.6 21.5 + - + +
162A GLY* 1.3 70.8 - - - +
164A MET* 1.3 72.2 + - - +
165A ASN* 2.9 42.3 + - - +
166A VAL* 3.2 21.9 + - + +
167A ILE* 3.7 7.8 + - - +
263A ILE* 5.9 1.4 - - - +
269A ILE* 5.4 0.5 - - - +
169C TRP* 5.1 1.7 + - - -
256C GLY 3.1 12.3 + - - +
258C HIS* 3.1 35.3 + - + +
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Residues in contact with MET 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A LEU* 4.1 19.1 - - + -
146A ILE* 5.5 2.0 - - + -
148A THR* 4.4 5.2 - - + -
155A TYR* 3.2 27.4 + - + +
162A GLY 3.3 0.8 + - - -
163A ASP* 1.3 74.0 + - - +
165A ASN* 1.3 58.1 + - - +
166A VAL 3.1 0.2 - - - -
167A ILE* 3.2 31.0 + - - +
168A LEU* 2.9 54.3 + - + +
188A LEU* 4.2 12.8 - - + -
190A TYR* 3.5 44.9 - - + +
269A ILE* 4.0 10.5 - - + -
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Residues in contact with ASN 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157A LEU* 5.9 0.4 - - - +
163A ASP* 2.9 33.0 + - - +
164A MET* 1.3 80.3 - - - +
166A VAL* 1.3 59.6 + - + +
168A LEU* 4.4 1.3 - - - -
169A TRP* 3.3 17.8 + - - +
255A VAL* 3.7 15.1 - - + +
263A ILE* 6.1 0.9 - - + -
264A PRO 5.7 0.4 - - - -
266A ASP* 3.2 35.2 + - - +
267A ASN 3.4 2.4 + - - -
268A GLN* 2.6 53.1 + - - +
269A ILE* 3.0 17.4 + - - +
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Residues in contact with VAL 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A ASP* 3.2 15.4 + - + +
164A MET 3.1 0.6 - - - -
165A ASN* 1.3 76.3 - - - +
167A ILE* 1.3 58.8 + - - +
169A TRP* 3.2 3.3 + - - +
170A PRO* 2.9 27.4 - - - +
255A VAL* 4.1 17.3 - - + -
263A ILE* 5.3 3.8 - - + -
166C VAL* 3.6 24.9 - - + +
169C TRP* 3.5 33.2 - - + +
170C PRO* 4.3 0.4 - - + +
255C VAL* 3.6 28.7 - - + +
256C GLY* 4.6 0.7 - - - -
258C HIS* 4.4 12.8 - - + +
263C ILE* 6.0 0.2 - - + -
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Residues in contact with ILE 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A LEU* 4.5 9.0 - - + -
106A PHE* 3.3 61.3 - - + +
107A GLY* 5.3 0.7 - - - -
155A TYR* 3.5 30.7 - - + -
161A HIS 4.9 2.0 - - - +
162A GLY 4.8 2.5 - - - +
163A ASP 4.0 8.3 - - - +
164A MET* 3.2 24.6 + - - +
166A VAL* 1.3 78.2 - - - +
168A LEU* 1.3 58.5 + - + +
170A PRO* 3.2 16.3 - - - +
171A ILE* 4.2 12.7 - - + +
169C TRP* 4.9 9.2 - - + +
170C PRO* 4.1 14.4 - - + +
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Residues in contact with LEU 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A LEU* 6.5 0.2 - - + -
144A LEU* 4.5 3.8 - - + -
146A ILE* 3.9 28.0 - - + -
164A MET* 2.9 36.5 + - + +
165A ASN 4.0 3.8 - - - +
167A ILE* 1.3 77.4 - - + +
169A TRP* 1.3 59.9 + - - +
171A ILE* 3.3 9.7 + - + +
172A GLN* 2.8 47.9 + - - +
186A PRO* 3.9 9.4 - - + -
188A LEU* 4.5 5.4 - - + -
268A GLN* 3.4 32.1 - - + +
269A ILE* 3.5 23.8 - - + -
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Residues in contact with TRP 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A ASN 3.3 12.2 + - - +
166A VAL 3.2 8.4 + - - +
168A LEU* 1.3 76.7 - - - +
170A PRO* 1.4 69.6 - - + +
171A ILE 2.9 0.3 + - - -
173A SER* 2.8 60.2 + - - -
174A GLY 3.4 3.4 + - - +
222A PHE* 3.9 15.5 - + + -
223A ALA 6.1 0.4 - - - -
254A SER* 3.8 20.6 - - - -
255A VAL* 3.8 13.9 - - + -
256A GLY* 3.4 35.0 - - - -
257A HIS* 4.5 9.9 - + - -
268A GLN* 3.0 41.7 - - - +
161C HIS 4.1 20.2 + - - -
162C GLY* 4.9 2.1 - - - -
163C ASP 5.1 0.8 + - - -
166C VAL* 3.2 25.4 - - + +
167C ILE* 4.8 9.2 - - + +
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Residues in contact with PRO 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A VAL 2.9 20.4 - - - +
167A ILE 3.2 14.1 - - - +
168A LEU 3.5 0.4 - - - -
169A TRP* 1.4 95.5 - - + +
171A ILE* 1.3 59.9 + - + +
174A GLY* 3.1 23.8 - - - +
175A ILE* 3.5 8.9 + - - +
105C TRP 4.6 1.0 - - - +
106C PHE* 3.8 30.2 - - + +
166C VAL 4.2 9.4 - - - +
167C ILE* 4.3 12.8 - - + +
170C PRO* 4.0 17.3 - - + -
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Residues in contact with ILE 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A PHE* 5.1 3.4 - - + -
103A LEU* 5.8 2.5 - - + -
107A GLY* 4.4 10.3 - - - -
108A VAL* 3.8 39.3 - - + +
116A PHE* 5.2 4.7 - - + -
144A LEU* 3.9 30.3 - - + -
146A ILE* 5.9 1.3 - - + -
167A ILE* 4.2 20.0 - - + +
168A LEU* 3.6 9.0 - - + +
169A TRP 3.0 0.4 - - - -
170A PRO* 1.3 81.8 - - + +
172A GLN* 1.3 61.4 + - - +
173A SER 3.4 0.2 - - - -
175A ILE* 3.1 26.1 + - + +
176A LEU* 3.1 29.9 + - + +
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Residues in contact with GLN 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A LEU* 3.4 32.8 + - + +
168A LEU* 2.8 28.5 + - - +
171A ILE* 1.3 73.7 - - - +
173A SER* 1.3 56.7 + - - +
176A LEU* 3.3 10.3 - - + +
177A HIS* 3.0 25.8 + - - +
183A VAL* 3.5 20.8 - - + +
184A LEU 4.7 0.3 - - - +
186A PRO* 3.7 23.2 - - - +
220A LEU* 2.9 32.8 - - - +
222A PHE* 4.0 3.5 - - + -
268A GLN* 3.2 27.6 + - - +
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Residues in contact with SER 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A TYR* 3.4 21.2 + - - -
169A TRP* 2.8 63.7 + - - -
172A GLN* 1.3 75.0 - - - +
174A GLY* 1.3 64.6 + - - +
175A ILE 3.4 0.7 - - - -
177A HIS* 4.0 2.7 - - - -
178A PHE 3.1 22.9 + - - -
222A PHE* 3.7 12.2 - - - -
161C HIS 5.1 1.2 + - - -
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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