Contacts of the helix formed by residues 162 - 175 (chain D) in PDB entry 5DO7
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 THR 162 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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161D LEU* 1.3 75.1 - - - +
163D VAL* 1.3 67.2 + - - +
164D ARG* 4.1 3.1 + - - +
165D GLU* 2.7 47.4 + - - +
166D THR* 2.8 22.0 + - - -
201D ALA 4.1 1.1 - - - -
202D ASP* 3.6 39.2 + - + +
203D THR 3.3 13.7 - - - -
204D ARG* 4.2 10.8 - - + +
412D ARG* 4.5 7.4 - - - +
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Residues in contact with VAL 163 (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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162D THR* 1.3 70.5 - - - +
164D ARG* 1.3 55.3 + - - +
166D THR* 2.9 5.4 + - - -
167D LEU* 2.8 52.2 + - + +
192D ILE* 4.7 7.0 - - + -
197D LEU* 4.1 13.5 - - + -
200D CYS* 3.6 33.2 - - + +
201D ALA 3.8 7.5 + - - +
203D THR 3.4 6.3 + - - +
205D VAL* 3.7 21.0 - - + +
213D LEU* 4.1 5.2 - - + -
221D VAL* 4.1 30.1 - - + -
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Residues in contact with ARG 164 (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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162D THR* 4.3 4.3 - - - +
163D VAL* 1.3 77.2 - - - +
165D GLU* 1.3 59.4 + - + +
167D LEU* 3.8 2.0 - - - +
168D ALA* 2.8 33.7 + - + +
185D ASP* 4.7 4.6 + - - +
188D VAL* 4.3 19.1 - - + +
189D GLU* 3.6 34.1 + - - +
192D ILE* 4.5 15.3 - - + +
201D ALA* 3.1 29.0 + - - +
202D ASP* 3.2 29.3 + - - +
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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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161D LEU* 3.0 31.4 - - + +
162D THR* 2.7 39.8 + - - +
164D ARG* 1.3 75.7 - - + +
166D THR* 1.3 57.1 + - - +
168D ALA* 2.9 6.4 + - - +
169D PHE* 2.8 48.1 + - + +
412D ARG* 3.1 27.6 + - - -
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Residues in contact with THR 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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157D LEU* 4.7 17.3 - - + -
158D LEU* 4.6 20.2 - - + +
161D LEU* 3.7 24.0 - - + +
162D THR 2.8 19.1 + - - -
163D VAL* 2.9 6.0 + - - -
165D GLU* 1.3 71.3 - - - +
167D LEU* 1.3 62.6 + - - +
169D PHE* 4.3 4.8 - - - +
170D ILE* 3.5 31.9 + - + +
205D VAL* 3.9 13.1 - - - +
221D VAL* 5.3 7.0 - - + -
225D VAL* 4.9 3.5 - - + +
405D ARG* 5.6 5.2 - - - +
480D TYR* 6.1 1.1 - - - +
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Residues in contact with LEU 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 VAL* 2.8 29.3 + - + +
164D ARG 3.8 3.4 - - - +
166D THR* 1.3 75.5 - - - +
168D ALA* 1.3 67.9 + - - +
169D PHE 3.1 1.3 - - - -
170D ILE* 2.8 5.7 + - - +
171D ALA* 2.8 21.6 + - - +
188D VAL* 4.1 20.9 - - + +
191D VAL* 4.8 9.4 - - + -
192D ILE* 3.9 30.5 - - + -
197D LEU* 5.2 4.0 - - + -
221D VAL* 4.3 7.9 - - + +
224D GLY* 3.7 9.9 - - - +
225D VAL* 3.6 40.4 - - + +
228D LEU* 3.7 11.9 - - + +
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Residues in contact with ALA 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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164D ARG* 2.8 25.3 + - + +
165D GLU* 2.9 6.2 + - - +
167D LEU* 1.3 70.8 - - - +
169D PHE* 1.3 55.9 + - + +
171D ALA* 3.2 3.6 + - - +
172D GLN* 2.8 43.5 + - + +
184D ARG* 5.9 2.2 - - + +
185D ASP* 6.1 0.9 - - - +
188D VAL* 3.8 18.2 - - + +
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Residues in contact with PHE 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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161D LEU* 4.4 17.9 - - + -
165D GLU* 2.8 41.0 + - + +
166D THR* 4.6 3.4 - - - +
168D ALA* 1.3 74.9 - - + +
170D ILE* 1.3 60.2 + - - +
172D GLN* 4.0 13.1 + - - -
173D MET* 3.6 7.9 + - - +
401D THR* 3.4 35.9 - - + +
404D ARG* 3.9 39.3 - - + -
405D ARG* 3.7 52.5 - - + -
408D SER* 4.4 6.7 - - - -
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Residues in contact with ILE 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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157D LEU* 6.1 1.1 - - + -
166D THR* 3.5 23.1 - - + +
167D LEU* 2.8 11.0 + - - +
169D PHE* 1.3 72.0 - - + +
171D ALA* 1.3 68.7 + - - +
172D GLN 3.2 1.6 - - - -
173D MET* 2.8 14.3 + - + +
174D ARG* 2.8 34.7 + - + +
225D VAL* 3.3 43.3 - - + +
228D LEU* 3.8 16.2 - - + -
405D ARG* 4.3 15.5 - - - +
480D TYR* 4.6 20.0 - - + +
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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 LEU 2.8 12.0 + - - +
168D ALA* 3.3 15.0 - - - +
170D ILE* 1.3 77.0 - - - +
172D GLN* 1.3 58.7 + - - +
173D MET 3.0 0.2 + - - -
174D ARG* 4.5 1.1 - - - +
175D LEU* 2.8 60.1 + - + +
184D ARG* 4.7 6.5 - - + -
188D VAL* 4.4 10.5 - - + -
228D LEU* 3.6 18.1 - - + +
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Residues in contact with GLN 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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168D ALA* 2.8 26.8 + - + +
169D PHE* 4.1 14.8 - - + +
170D ILE 3.2 0.4 - - - -
171D ALA* 1.3 71.1 - - - +
173D MET* 1.3 61.5 + - - +
175D LEU 4.0 7.7 - - - +
181D GLN* 3.5 26.3 + - - +
184D ARG* 3.8 28.5 + - + +
393D PRO* 4.5 5.7 - - - +
397D GLN* 4.0 34.7 + - - +
401D THR* 4.1 16.1 + - + +
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Residues in contact with MET 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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169D PHE 3.6 16.4 - - - +
170D ILE* 2.8 15.2 + - + +
172D GLN* 1.3 81.1 - - - +
174D ARG* 1.3 59.8 + - + +
175D LEU 3.6 1.6 - - - -
393D PRO* 3.4 28.4 - - - +
398D GLN* 4.3 16.6 - - + +
401D THR* 3.8 25.6 - - + +
402D LEU* 3.9 13.0 - - + -
405D ARG* 4.1 19.7 - - - +
480D TYR* 5.5 2.9 - - + -
484D ASP 5.6 0.5 - - - +
485D GLY* 3.8 25.5 - - - +
486D LEU* 3.4 33.9 - - + -
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Residues in contact with ARG 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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145D ARG* 4.6 10.7 + - - +
146D LYS* 6.2 0.2 - - - +
148D VAL 5.7 0.4 + - - -
170D ILE* 2.8 29.1 + - + +
171D ALA* 5.0 2.0 - - - -
173D MET* 1.3 72.4 - - + +
175D LEU* 1.3 65.4 + - - +
176D PRO* 3.7 3.5 - - - +
225D VAL 4.9 4.7 + - - -
226D GLN* 5.1 2.4 - - - +
228D LEU* 5.1 8.7 - - + +
229D TRP* 2.8 71.7 - - + +
392D MET* 5.6 5.2 - - - +
393D PRO* 5.6 2.5 - - - +
483D GLU* 2.9 40.4 + - - +
484D ASP* 3.2 30.2 + - - +
485D GLY* 5.1 9.1 - - - +
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Residues in contact with LEU 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* 2.8 44.0 + - + +
172D GLN 4.0 7.8 - - - +
174D ARG* 1.3 72.6 - - - +
176D PRO* 1.3 73.0 - - + +
177D ARG 3.8 0.5 + - - -
179D PHE* 3.8 25.4 - - + -
184D ARG* 3.5 44.5 + - + +
187D ARG* 3.6 25.4 - - + +
228D LEU* 3.1 26.9 - - + +
229D TRP* 5.2 1.3 - - + -
393D PRO* 4.1 7.4 - - - +
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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