Contacts of the helix formed by residues 164 - 179 (chain D) in PDB entry 2XXA
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 164 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136D THR* 4.1 0.2 - - - -
163D ALA* 1.4 70.8 - - - +
165D SER* 1.3 64.4 + - - +
166D ALA* 3.1 24.3 + - - +
167D SER* 3.9 19.6 + - - +
168D VAL* 3.1 25.7 + - - +
201D GLU* 4.5 4.8 - - - +
204D LYS* 2.8 32.8 + - - +
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Residues in contact with SER 165 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134D GLY* 2.7 34.7 + - - -
136D THR* 3.6 9.6 + - - -
163D ALA 3.5 3.8 + - - -
164D ASP* 1.3 70.9 + - - +
166D ALA* 1.4 60.0 + - - +
168D VAL* 3.1 6.5 + - - +
169D ILE* 3.0 41.4 + - - +
187D ASP 4.5 0.7 + - - -
188D THR* 4.8 2.1 - - - -
191D ARG* 4.9 2.1 + - - -
201D GLU* 3.7 20.7 + - - -
205D ILE* 4.1 10.2 - - - +
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Residues in contact with ALA 166 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164D ASP* 3.1 12.4 + - - +
165D SER* 1.4 76.6 - - - +
167D SER* 1.3 56.1 + - - +
169D ILE* 3.6 2.9 + - - +
170D PHE* 3.1 27.3 + - - +
201D GLU* 4.6 1.3 + - - +
204D LYS* 3.8 26.2 - - + +
205D ILE* 3.7 39.8 - - + +
208D VAL* 4.3 12.5 - - + +
209D MET* 5.8 0.7 - - - +
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Residues in contact with SER 167 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164D ASP* 3.6 26.4 + - - +
165D SER 3.3 0.4 - - - -
166D ALA* 1.3 73.3 - - - +
168D VAL* 1.3 63.5 + - - +
170D PHE* 3.7 12.0 - - - +
171D ASP* 3.3 29.9 + - - +
204D LYS* 4.5 5.5 + - - -
208D VAL* 5.1 6.0 - - - +
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Residues in contact with VAL 168 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132D ALA* 5.6 1.1 - - + -
133D ALA 3.4 28.9 - - - +
134D GLY* 5.0 1.3 - - - +
136D THR* 4.7 4.5 - - + -
157D ILE* 4.5 15.9 - - + +
158D ALA* 4.9 0.9 - - - -
159D GLN* 3.6 45.1 - - + +
163D ALA* 4.4 6.1 - - + -
164D ASP 3.1 20.6 + - - +
165D SER* 3.1 8.5 + - - +
167D SER* 1.3 75.6 - - - +
169D ILE* 1.4 61.5 + - + +
171D ASP* 3.1 9.4 + - - +
172D ALA* 3.0 24.9 + - - +
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Residues in contact with ILE 169 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102D LEU* 4.7 0.2 - - + -
132D ALA* 4.3 8.7 - - + -
134D GLY* 4.4 5.4 - - - -
165D SER* 3.0 37.4 + - - +
166D ALA 4.0 3.8 - - - +
168D VAL* 1.4 74.8 - - + +
170D PHE* 1.4 57.2 + - - +
172D ALA* 3.1 10.1 + - - +
173D ILE* 3.0 45.2 + - + +
184D LEU* 5.3 1.3 - - + -
186D ALA* 3.9 26.9 - - + -
187D ASP 3.7 20.2 - - - +
188D THR* 4.4 6.1 - - + -
205D ILE* 3.8 23.3 - - + -
209D MET* 4.4 15.9 - - + -
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Residues in contact with PHE 170 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166D ALA 3.1 18.8 + - - +
167D SER* 3.7 9.4 - - - +
169D ILE* 1.4 76.2 - - - +
171D ASP* 1.4 69.1 + - - +
173D ILE* 3.5 8.3 + - + -
174D GLN* 3.1 42.2 + - - +
208D VAL* 3.3 42.8 - - + +
209D MET* 5.3 2.7 - - - +
211D LYS* 4.1 15.0 - - + -
212D LEU* 3.6 37.2 - - + +
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Residues in contact with ASP 171 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157D ILE* 4.2 10.7 - - + +
159D GLN* 4.4 11.6 - - - +
167D SER* 3.3 15.3 + - - +
168D VAL* 3.1 10.9 + - - +
170D PHE* 1.4 89.5 - - - +
172D ALA* 1.3 57.0 + - - +
174D GLN* 3.7 16.9 + - - +
175D ALA* 3.2 25.8 + - - +
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Residues in contact with ALA 172 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130D MET* 3.7 1.0 - - - +
132D ALA* 3.7 28.0 - - + -
157D ILE* 3.9 26.0 - - + +
168D VAL* 3.0 12.0 + - + +
169D ILE 3.1 9.4 + - - +
171D ASP* 1.3 75.4 - - - +
173D ILE* 1.3 59.2 + - - +
175D ALA* 3.5 2.3 + - - +
176D ALA* 2.9 28.2 + - - +
184D LEU* 3.6 14.2 - - + +
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Residues in contact with ILE 173 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98D PRO* 5.0 4.9 - - + -
100D VAL* 4.5 11.7 - - + -
169D ILE* 3.0 27.8 + - + +
170D PHE* 3.8 8.5 - - - +
171D ASP 3.4 0.2 - - - -
172D ALA* 1.3 71.8 - - - +
174D GLN* 1.4 59.4 + - - +
175D ALA 3.1 1.6 - - - -
176D ALA* 3.1 7.5 + - - +
177D LYS* 2.9 44.7 + - + +
184D LEU* 3.7 18.2 - - + -
209D MET* 3.7 48.5 - - + +
212D LEU* 3.8 25.1 - - + -
213D ASP* 5.8 3.8 - - + -
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Residues in contact with GLN 174 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170D PHE* 3.1 29.7 + - - +
171D ASP* 3.8 23.0 - - - +
173D ILE* 1.4 74.5 - - - +
175D ALA* 1.4 58.2 + - - +
177D LYS* 4.1 4.7 - - - +
178D ALA* 3.4 23.4 + - - +
212D LEU* 3.8 21.0 - - + +
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Residues in contact with ALA 175 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130D MET* 3.8 6.5 - - + -
157D ILE* 3.8 27.8 - - + -
171D ASP 3.2 18.7 + - - +
172D ALA 3.6 6.1 - - - +
173D ILE 3.1 0.4 - - - -
174D GLN* 1.4 74.8 - - - +
176D ALA* 1.4 57.3 + - - +
177D LYS 3.2 0.4 - - - -
178D ALA* 3.5 2.8 + - - -
179D ARG* 2.9 45.5 + - - +
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Residues in contact with ALA 176 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98D PRO* 3.7 23.2 - - + +
130D MET* 3.8 4.2 - - - -
172D ALA 2.9 19.0 + - - +
173D ILE* 3.1 7.8 + - - +
175D ALA* 1.4 72.1 - - - +
177D LYS* 1.3 60.6 + - - +
180D ASN* 3.6 0.5 + - - -
181D ILE* 2.9 48.4 + - + +
184D LEU* 3.8 20.0 - - + -
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Residues in contact with LYS 177 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97D ALA 4.7 5.8 + - - +
98D PRO* 3.7 29.7 - - + +
173D ILE* 2.9 30.3 + - + +
174D GLN* 4.1 7.0 - - - +
176D ALA* 1.3 76.2 - - - +
178D ALA* 1.4 58.9 + - - +
180D ASN* 3.1 26.9 + - - +
212D LEU* 4.0 25.6 + - + -
213D ASP* 3.2 29.3 + - - -
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Residues in contact with ALA 178 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174D GLN 3.4 16.7 + - - +
175D ALA* 3.5 5.3 + - - +
177D LYS* 1.4 77.9 - - - +
179D ARG* 1.3 61.7 + - + +
180D ASN* 3.3 9.4 + - - -
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Residues in contact with ARG 179 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130D MET* 3.7 17.1 - - - +
155D PRO* 4.0 17.0 - - - +
157D ILE* 3.6 32.1 - - - +
175D ALA* 2.9 23.3 + - - +
178D ALA* 1.3 77.7 - - + +
180D ASN* 1.4 72.1 + - - +
181D ILE* 3.7 18.4 - - + +
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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