Contacts of the helix formed by residues 178 - 189 (chain D) in PDB entry 1DGB
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 178 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5B ARG* 5.0 0.9 + - - -
8B ALA 5.3 0.7 - - - +
9B SER* 4.4 16.6 - - - +
11B GLN* 5.0 3.3 - - - +
12B MET* 3.8 8.8 + - - +
167D SER 5.5 0.2 + - - -
169D LYS 4.2 5.7 + - - -
171D ASN* 3.3 24.9 + - + +
176D LEU 3.5 5.5 + - - +
177D LYS* 1.3 74.4 - - - +
179D PRO* 1.3 57.3 - - - +
180D ASP* 3.0 25.0 + - - +
181D MET* 2.8 53.0 + - - +
182D VAL* 3.0 17.2 + - - +
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Residues in contact with PRO 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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5B ARG* 5.2 2.0 - - - +
9B SER* 6.3 3.1 - - - -
177D LYS* 3.5 12.3 - - + +
178D ASP* 1.3 82.9 - - - +
180D ASP* 1.3 57.8 + - - +
182D VAL* 3.8 3.6 - - + -
183D TRP* 2.9 35.5 + - + +
466D HIS* 3.9 35.2 - - + +
469D ASP* 3.9 40.2 - - + +
470D ALA* 4.0 2.9 - - - +
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Residues in contact with ASP 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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5B ARG* 2.9 32.0 + - - -
9B SER 4.4 3.2 - - - +
12B MET* 3.7 14.5 - - + +
13B GLN 5.8 0.2 + - - -
409C PHE* 4.2 3.6 - - + -
178D ASP* 2.9 12.6 + - - +
179D PRO* 1.3 78.4 - - - +
181D MET* 1.3 56.4 + - - +
184D ASP* 2.7 40.0 + - - +
470D ALA* 3.0 6.0 - - - +
471D GLN* 2.9 46.1 + - - -
474D ILE* 3.7 17.1 - - + +
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Residues in contact with MET 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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12B MET* 3.4 20.4 - - + +
402C PRO* 6.5 0.2 - - - -
403C ASN* 3.4 28.3 - - - +
404C TYR* 3.5 22.3 - - + -
166D HIS 3.5 21.8 - - - +
167D SER* 3.5 14.9 - - - +
169D LYS 4.5 1.3 - - - +
170D ARG 3.9 15.5 - - - +
171D ASN* 3.8 26.2 - - - -
172D PRO* 4.3 2.2 - - - -
178D ASP* 2.8 28.7 + - + +
180D ASP* 1.3 78.0 - - - +
182D VAL* 1.3 66.1 + - - +
185D PHE* 3.2 24.6 + - - +
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Residues in contact with VAL 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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167D SER* 3.2 26.9 + - - +
168D GLN* 3.6 22.9 - - - +
169D LYS 5.6 0.2 - - - +
177D LYS* 6.4 0.4 - - + -
178D ASP 3.0 16.0 + - - +
179D PRO* 3.8 11.0 - - + +
181D MET* 1.3 79.5 - - - +
183D TRP* 1.3 59.3 + - + +
185D PHE* 3.6 2.9 - - - +
186D TRP* 3.1 58.6 + - + -
466D HIS* 4.0 19.5 - - + +
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Residues in contact with TRP 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 PRO* 2.9 30.3 + - + +
182D VAL* 1.3 71.4 - - + +
184D ASP* 1.3 54.5 + - - +
185D PHE 3.1 1.6 - - - -
186D TRP* 3.6 42.6 - + + +
187D SER* 2.6 44.4 + - - -
196D VAL* 4.2 15.0 - - + -
200D PHE* 3.9 16.2 - + - -
463D ILE* 4.0 26.5 - - + -
466D HIS* 2.6 34.7 + + - -
467D LEU* 3.5 36.6 - - + +
470D ALA* 4.4 2.5 - - + -
474D ILE* 3.6 15.9 - - + -
478D ALA* 4.3 9.6 - - + -
482D PHE* 4.2 21.8 - + - -
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Residues in contact with ASP 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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404C TYR* 2.7 24.6 + - - +
407C ASN* 3.3 3.8 - - - -
408C SER* 2.7 47.9 + - - -
409C PHE* 3.6 7.4 - - + -
180D ASP 2.7 24.7 + - - +
183D TRP* 1.3 71.2 - - - +
185D PHE* 1.3 62.5 + - - +
187D SER* 2.8 19.3 + - - -
188D LEU* 3.0 26.1 + - - +
473D PHE* 4.9 0.3 - - - -
474D ILE* 3.6 18.8 - - + +
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Residues in contact with PHE 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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404C TYR* 4.1 21.5 - + + -
405C TYR 3.9 20.6 - - - -
406C PRO* 4.3 8.7 - - + -
155D ILE* 4.2 18.6 - - + -
160D LEU* 4.4 6.7 - - + -
163D SER* 4.3 2.2 - - - -
164D PHE* 3.3 57.7 - + + -
167D SER* 3.8 14.4 - - - +
181D MET 3.2 16.1 + - - +
182D VAL 3.6 2.5 - - - +
183D TRP 3.1 0.2 - - - -
184D ASP* 1.3 77.2 - - - +
186D TRP* 1.3 79.6 + + - +
188D LEU* 3.0 4.2 + - - -
189D ARG* 2.9 44.4 + - + +
192D SER* 5.6 1.3 - - - -
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Residues in contact with TRP 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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154D PHE* 3.8 27.2 - + - -
164D PHE* 3.1 17.9 - + - -
168D GLN* 2.9 30.7 - - - -
182D VAL* 3.1 32.8 + - + +
183D TRP* 3.3 48.7 + + + +
185D PHE* 1.3 91.9 - + - +
187D SER* 1.3 64.2 + - - +
189D ARG 3.0 24.2 + - - +
190D PRO* 3.6 3.1 - - - +
192D SER* 3.5 25.0 + - - +
196D VAL* 3.8 12.8 - - + -
199D LEU* 4.0 21.1 - - + -
200D PHE* 3.8 14.1 - + - -
466D HIS* 5.4 0.2 - + - -
481D ASN* 4.3 0.9 + - - -
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Residues in contact with SER 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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183D TRP* 2.6 29.0 + - - -
184D ASP* 2.8 20.6 + - - -
186D TRP* 1.3 72.0 - - - +
188D LEU* 1.3 59.1 + - - +
190D PRO* 4.2 2.1 - - - +
474D ILE* 3.7 8.6 - - - +
477D LYS* 3.7 36.4 - - - +
478D ALA* 3.8 18.6 - - - +
481D ASN* 2.8 27.2 + - - +
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Residues in contact with LEU 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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406C PRO* 4.0 17.4 - - + +
407C ASN* 3.8 29.6 - - - +
408C SER* 3.6 14.6 - - - +
184D ASP* 3.0 37.5 + - - +
185D PHE* 3.6 4.0 - - - +
187D SER* 1.3 79.7 - - - +
189D ARG* 1.3 68.7 + - + +
190D PRO* 3.2 10.1 - - - +
477D LYS* 4.4 21.8 - - + +
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Residues in contact with ARG 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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39B LEU* 3.8 36.8 + - - +
40B ASN* 5.7 0.4 - - - +
406C PRO* 3.8 28.0 - - + +
155D ILE* 5.4 0.9 - - + -
156D ARG* 6.1 1.8 - - - +
160D LEU* 3.8 21.5 - - + +
185D PHE* 2.9 38.1 + - + +
186D TRP 3.0 3.8 - - - +
188D LEU* 1.3 87.9 - - - +
190D PRO* 1.3 52.7 - - - +
191D GLU* 3.0 39.8 + - - +
192D SER* 2.6 30.2 + - - -
433D ASN* 5.2 0.8 + - - -
434D THR* 5.2 2.0 + - - -
435D ALA* 3.4 37.2 - - - +
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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