Contacts of the helix formed by residues 161 - 180 (chain D) in PDB entry 1XDM
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 LEU 161 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168A ASN* 5.7 3.1 - - - +
218A ASP* 4.2 37.2 - - + +
219A HIS* 3.8 31.2 - - + +
159D SER* 2.6 14.4 + - - +
160D SER* 1.3 78.6 - - - +
162D ALA* 1.3 64.2 + - - +
163D ILE 3.3 1.1 - - - -
164D GLN* 3.5 27.4 - - + -
165D GLU* 3.0 33.2 + - + +
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Residues in contact with ALA 162 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158D PRO* 5.0 2.2 - - + -
159D SER* 2.7 32.4 + - - +
161D LEU* 1.3 79.1 - - - +
163D ILE* 1.3 66.4 + - + +
165D GLU* 3.9 2.1 - - - +
166D ASN* 2.9 26.8 + - - +
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Residues in contact with ILE 163 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158D PRO* 4.6 13.7 - - + -
159D SER 3.7 12.6 - - - +
160D SER* 5.1 3.1 - - - -
162D ALA* 1.3 78.3 - - + +
164D GLN* 1.3 67.4 + - - +
166D ASN* 3.6 8.1 + - - +
167D ALA* 2.9 24.2 + - + +
204D VAL* 5.9 0.9 - - + -
207D LYS* 3.1 42.6 - - + +
208D VAL* 4.0 32.1 - - + +
211D ALA* 3.4 31.6 - - + -
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Residues in contact with GLN 164 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A GLN* 4.2 20.4 + - - -
168A ASN* 5.4 3.3 - - - +
160D SER 3.5 21.1 + - - +
161D LEU* 3.5 28.1 + - + +
163D ILE* 1.3 82.4 - - - +
165D GLU* 1.3 69.6 + - + +
167D ALA* 3.1 11.5 + - - +
168D ASN* 2.6 46.9 + - - +
211D ALA* 6.0 0.9 - - - -
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Residues in contact with GLU 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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168A ASN* 3.2 19.7 + - - +
172A ARG* 2.7 36.1 + - - +
219A HIS* 3.0 30.7 + - + -
161D LEU* 3.0 36.6 + - + +
162D ALA* 3.9 2.2 - - - +
164D GLN* 1.3 80.3 - - - +
166D ASN* 1.3 65.9 + - - +
168D ASN* 3.0 15.9 + - - +
169D ALA* 2.9 19.7 + - - +
172D ARG* 4.4 1.9 + - - -
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Residues in contact with ASN 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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149D PRO* 3.0 37.5 - - + +
162D ALA 2.9 24.2 + - - +
163D ILE* 3.6 9.9 + - - +
165D GLU* 1.3 71.7 - - - +
167D ALA* 1.3 82.4 + - - +
169D ALA* 2.7 25.9 + - - +
170D LEU* 3.1 19.3 + - - +
188D PRO 3.9 9.0 + - - +
189D GLU* 4.6 3.5 - - - +
208D VAL* 4.7 11.1 - - - +
212D VAL* 4.5 6.9 - - - +
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Residues in contact with ALA 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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163D ILE* 2.9 13.3 + - + +
164D GLN* 3.2 11.0 - - - +
166D ASN* 1.3 87.0 - - - +
168D ASN* 1.3 61.4 + - - +
170D LEU* 2.9 10.4 + - - +
171D ALA* 2.8 27.5 + - - +
211D ALA* 3.4 28.0 - - + +
212D VAL* 4.1 9.7 - - + +
215D ALA* 3.7 10.9 - - + +
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Residues in contact with ASN 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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161A LEU* 5.9 1.7 - - - +
164A GLN* 5.5 0.2 + - - -
165A GLU* 4.5 10.7 + - - +
168A ASN* 5.1 3.2 - - - +
164D GLN* 2.6 50.0 + - - +
165D GLU* 3.0 16.2 + - - +
167D ALA* 1.3 74.9 - - - +
169D ALA* 1.3 57.4 + - - +
171D ALA* 3.6 7.7 - - - +
172D ARG* 2.8 50.3 + - - +
215D ALA* 3.8 13.7 - - - +
219D HIS* 4.3 12.3 + - - +
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Residues in contact with ALA 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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147D TRP* 5.0 12.3 - - + +
149D PRO* 4.8 13.7 - - + -
165D GLU 2.9 9.7 + - - +
166D ASN* 2.7 21.1 + - - +
168D ASN* 1.3 67.8 - - - +
170D LEU* 1.3 69.2 + - - +
172D ARG* 3.0 20.0 + - - +
173D TYR* 2.8 23.0 + - - +
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Residues in contact with LEU 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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147D TRP* 4.2 17.7 - - + +
149D PRO* 4.1 17.5 - - + -
166D ASN* 3.6 31.2 - - - +
167D ALA* 2.9 4.9 + - - +
169D ALA* 1.3 79.6 - - - +
171D ALA* 1.3 64.3 + - - +
172D ARG 2.8 0.5 + - - -
173D TYR* 2.8 12.8 + - + +
174D ALA* 2.8 24.0 + - - +
186D VAL* 4.2 13.7 - - + -
187D GLU 3.3 34.3 - - - +
188D PRO* 4.2 4.3 - - + -
212D VAL* 4.0 28.3 - - + -
216D LEU* 5.3 0.2 - - - -
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Residues in contact with ALA 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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167D ALA 2.8 18.8 + - - +
168D ASN 3.6 1.8 - - - +
170D LEU* 1.3 73.0 - - - +
172D ARG* 1.3 58.3 + - - +
174D ALA* 3.5 2.3 - - - +
175D SER* 3.3 19.4 + - - -
215D ALA* 3.7 23.1 - - + +
216D LEU* 3.7 20.4 - - + +
219D HIS* 3.1 34.2 - - + +
221D VAL* 3.6 8.0 - - - +
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Residues in contact with ARG 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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165A GLU* 3.3 24.5 + - - -
172A ARG* 3.5 32.6 - - - +
165D GLU 4.4 2.2 + - - -
168D ASN* 2.8 48.7 + - - +
169D ALA* 3.0 20.2 + - - +
170D LEU 2.8 3.8 + - - -
171D ALA* 1.3 69.2 - - - +
173D TYR* 1.3 65.6 + - - +
174D ALA 3.0 1.9 + - - -
175D SER* 3.4 7.4 + - - -
176D ILE* 3.2 28.8 + - + +
219D HIS* 3.5 22.4 - - + +
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Residues in contact with TYR 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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108D LEU* 4.4 7.9 - - + -
130D LEU* 4.1 20.1 - - + +
145D GLY 3.4 5.4 + - - -
147D TRP* 3.3 65.1 + + + -
169D ALA 2.8 10.9 + - - +
170D LEU* 2.8 30.2 + - + -
172D ARG* 1.3 73.4 - - - +
174D ALA* 1.3 69.2 + - + +
176D ILE* 3.3 14.9 - - - +
177D CYS* 3.2 37.5 + - - -
184D PRO* 4.3 6.5 - - + -
185D ILE 3.1 36.0 + - - -
186D VAL* 4.8 6.5 - - + -
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Residues in contact with ALA 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 LEU 2.8 15.6 + - - +
171D ALA 3.5 6.7 - - - +
173D TYR* 1.3 77.4 - - + +
175D SER* 1.3 57.3 + - - +
176D ILE 2.6 14.7 + - - -
177D CYS* 2.7 17.7 + - - +
178D GLN* 3.4 11.3 + - - +
184D PRO* 3.9 24.5 - - + -
186D VAL* 4.9 5.8 - - + -
216D LEU* 3.9 12.1 - - + -
221D VAL* 3.7 18.4 - - + -
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Residues in contact with SER 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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171D ALA 3.3 10.9 + - - -
172D ARG* 3.4 10.1 + - - -
174D ALA* 1.3 77.9 - - - +
176D ILE* 1.3 62.5 + - - +
178D GLN* 3.5 11.1 + - - +
179D GLN* 3.1 33.5 + - - +
219D HIS* 4.1 16.0 + - - -
220D HIS 5.7 0.2 - - - -
221D VAL* 3.8 15.1 - - - +
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Residues in contact with ILE 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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128D ASP* 5.8 7.0 - - - +
130D LEU* 4.4 16.6 - - + +
131D SER* 3.5 41.3 - - - +
134D CYS* 4.7 4.3 - - - -
172D ARG* 3.2 18.8 - - + +
173D TYR* 3.3 15.0 - - - +
174D ALA 2.6 4.6 + - - -
175D SER* 1.3 71.3 - - - +
177D CYS* 1.3 58.2 + - - +
179D GLN* 2.6 37.7 + - + +
180D ASN* 3.0 13.4 + - - +
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Residues in contact with CYS 177 (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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108D LEU* 4.4 14.6 - - - -
130D LEU* 5.4 0.7 - - - -
134D CYS* 4.4 10.8 - - - -
145D GLY* 5.2 2.2 - - - -
173D TYR* 3.2 44.6 - - - -
174D ALA 2.7 10.6 + - - +
176D ILE* 1.3 75.7 - - - +
178D GLN* 1.3 52.1 + - - +
180D ASN* 2.7 23.0 + - - +
182D LEU* 2.7 46.7 + - + +
184D PRO* 4.0 15.3 - - + -
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Residues in contact with GLN 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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7D LEU* 3.3 27.3 - - + +
11D GLN* 3.5 4.9 + - - +
15D LEU* 3.6 22.6 - - + +
174D ALA 3.4 6.2 + - - +
175D SER* 3.8 8.3 - - - +
176D ILE 3.2 0.8 - - - -
177D CYS* 1.3 75.5 - - - +
179D GLN* 1.3 60.7 + - - +
180D ASN 3.4 0.3 + - - -
181D GLY* 3.4 8.0 + - - -
182D LEU 3.5 6.7 - - - -
184D PRO* 3.8 19.8 - - + +
221D VAL* 3.5 13.8 - - - +
222D TYR* 2.8 46.9 + - - +
225D GLY 2.6 26.8 + - - -
226D THR* 3.0 10.5 + - - -
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Residues in contact with GLN 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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6D ALA* 4.5 9.2 - - - +
7D LEU* 4.3 22.9 + - + +
11D GLN* 3.7 21.4 + - - +
175D SER* 3.1 30.5 + - - +
176D ILE* 2.6 21.9 + - + +
178D GLN* 1.3 74.0 - - - +
180D ASN* 1.3 61.6 + - - +
181D GLY 3.4 0.8 + - - -
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Residues in contact with ASN 180 (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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131D SER* 2.9 27.9 + - - +
134D CYS* 3.4 18.1 - - + +
135D ALA* 3.2 39.0 - - - +
138D LYS* 3.3 23.0 - - - +
176D ILE* 3.0 20.6 + - - +
177D CYS 2.7 7.1 + - - +
179D GLN* 1.3 83.4 - - - +
181D GLY* 1.3 60.5 - - - +
182D LEU* 3.0 8.5 + - + +
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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