Contacts of the helix formed by residues 180 - 193 (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 SER 180 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178D THR 3.5 2.2 + - - -
179D PHE* 1.3 77.2 - - - +
181D GLN* 1.3 62.9 - - - +
182D ALA* 3.9 7.3 + - - +
183D GLN* 3.0 48.2 + - - +
184D ARG* 3.3 12.7 + - - +
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Residues in contact with GLN 181 (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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172D GLN* 3.5 30.2 - - - +
180D SER* 1.3 70.2 - - - +
182D ALA* 1.3 68.5 + - - +
183D GLN 3.0 1.3 - - - -
184D ARG* 2.8 48.7 + - - +
185D ASP* 2.8 32.5 + - - +
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Residues in contact with ALA 182 (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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180D SER* 4.2 7.0 - - - +
181D GLN* 1.3 78.6 - - - +
183D GLN* 1.3 51.2 + - - +
185D ASP* 3.4 10.9 + - - +
186D LYS* 2.8 45.8 + - + +
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Residues in contact with GLN 183 (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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179D PHE* 3.0 53.1 - - + -
180D SER* 3.0 38.1 + - - +
181D GLN 3.0 0.8 - - - -
182D ALA* 1.3 74.1 - - - +
184D ARG* 1.3 60.3 + - - +
186D LYS* 3.7 4.6 - - - +
187D ARG* 2.8 32.4 + - - +
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Residues in contact with ARG 184 (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* 5.9 1.3 - - + +
171D ALA* 4.8 5.4 - - + -
172D GLN* 3.8 38.2 + - + +
175D LEU* 3.5 44.5 + - + +
176D PRO 3.5 17.6 + - - -
177D ARG* 3.8 14.6 + - - +
179D PHE* 3.2 25.5 + - + +
180D SER 3.5 8.3 + - - +
181D GLN* 2.8 43.3 + - - +
183D GLN* 1.3 72.6 - - - +
185D ASP* 1.3 59.6 - - - +
187D ARG* 3.0 2.3 + - - +
188D VAL* 2.8 40.0 + - + +
397D GLN* 5.5 6.2 - - - +
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Residues in contact with ASP 185 (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* 4.7 5.2 + - - +
168D ALA* 6.1 0.9 - - - +
181D GLN* 2.8 32.5 + - - +
182D ALA* 3.5 11.2 - - - +
184D ARG* 1.3 82.5 - - - +
186D LYS* 1.3 64.9 + - + +
188D VAL* 3.5 8.8 - - - +
189D GLU* 3.3 19.6 + - - +
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Residues in contact with LYS 186 (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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182D ALA* 2.8 27.7 + - + +
183D GLN* 4.0 4.3 - - - +
185D ASP* 1.3 75.1 - - + +
187D ARG* 1.3 59.5 + - - +
189D GLU* 3.6 7.8 + - + +
190D ASP* 2.8 42.8 + - - +
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Residues in contact with ARG 187 (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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29D SER* 6.1 1.1 - - - -
175D LEU* 3.6 19.7 - - + +
179D PHE* 4.2 22.7 - - + -
183D GLN 2.8 20.4 + - - +
184D ARG* 3.4 7.0 - - - +
186D LYS* 1.3 74.2 - - - +
188D VAL* 1.3 67.3 + - + +
190D ASP* 3.0 12.3 + - - +
191D VAL* 2.8 33.2 + - - +
227D LEU 4.9 1.3 - - - -
228D LEU* 2.9 48.1 + - + -
229D TRP* 3.9 1.8 - - - +
230D ASN* 3.9 35.9 + - - +
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Residues in contact with VAL 188 (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* 4.3 21.8 - - + +
167D LEU* 4.1 18.2 - - + +
168D ALA* 3.8 33.4 - - + +
171D ALA* 4.4 9.4 - - + -
184D ARG* 2.8 18.2 + - + +
185D ASP* 3.5 10.8 - - - +
187D ARG* 1.3 75.3 - - - +
189D GLU* 1.3 60.2 + - - +
191D VAL* 2.9 6.8 + - - +
192D ILE* 2.8 46.7 + - + +
228D LEU* 4.6 9.2 - - + -
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Residues in contact with GLU 189 (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* 3.6 28.4 + - - +
185D ASP 3.3 10.8 + - - +
186D LYS* 3.9 9.9 - - + +
187D ARG 3.3 0.2 - - - -
188D VAL* 1.3 79.8 - - - +
190D ASP* 1.3 58.3 + - - +
191D VAL 3.0 0.3 + - - -
192D ILE* 3.0 15.9 + - - +
193D ALA* 2.8 53.4 + - + +
198D ARG* 3.7 15.0 + - - -
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Residues in contact with ASP 190 (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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28D PHE* 3.5 38.3 - - - +
29D SER* 4.6 2.7 - - - -
186D LYS* 2.8 39.2 + - - +
187D ARG* 3.0 16.1 + - - +
189D GLU* 1.3 74.2 - - - +
191D VAL* 1.3 59.3 + - - +
193D ALA* 4.3 2.9 - - - -
194D GLU* 3.7 12.0 + - - +
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Residues in contact with VAL 191 (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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29D SER* 5.4 6.5 - - - +
167D LEU* 4.8 8.5 - - + -
187D ARG* 2.8 22.5 + - - +
188D VAL 3.3 6.7 - - - +
190D ASP* 1.3 76.0 - - - +
192D ILE* 1.3 71.1 + - - +
193D ALA 3.0 1.6 - - - -
194D GLU* 2.8 17.3 + - - +
195D LEU* 2.8 34.7 + - + +
197D LEU* 5.9 0.9 - - + -
224D GLY* 4.0 17.9 - - - +
227D LEU* 3.6 31.9 - - + +
228D LEU* 3.8 15.9 - - + -
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Residues in contact with ILE 192 (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* 4.7 2.7 - - + -
164D ARG* 4.5 24.2 - - + +
167D LEU* 3.9 19.3 - - + -
188D VAL* 2.8 38.6 + - + +
189D GLU* 3.6 24.2 - - - +
191D VAL* 1.3 74.6 - - - +
193D ALA* 1.3 58.9 + - - +
195D LEU* 3.4 1.4 + - - -
196D ARG 2.8 22.2 + - - -
197D LEU* 2.8 53.7 + - + +
198D ARG* 4.2 9.2 - - - +
201D ALA* 4.8 12.3 - - + -
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Residues in contact with ALA 193 (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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28D PHE* 2.7 41.7 - - + -
189D GLU* 2.8 26.8 + - + +
190D ASP* 5.1 1.8 - - - -
192D ILE* 1.3 75.1 - - - +
194D GLU* 1.3 58.3 + - - +
196D ARG* 3.7 14.4 - - - +
198D ARG* 3.3 26.2 + - - +
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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