Contacts of the helix formed by residues 201 - 214 (chain D) in PDB entry 1D1T
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 GLY 201 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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199D GLY 3.5 4.0 + - - -
200D LEU* 1.3 79.3 - - - +
202D GLY* 1.3 60.3 + - - -
203D VAL 3.4 2.7 - - - -
204D GLY 4.3 2.2 - - - +
205D LEU* 2.9 27.5 + - - +
228D LYS* 4.3 5.2 - - - -
268D VAL 5.5 0.6 + - - -
368D ILE* 4.1 9.4 - - - -
4377D NAD 3.2 35.2 + - - -
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Residues in contact with GLY 202 (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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175D GLY 4.8 2.7 - - - -
201D GLY* 1.3 72.0 - - - +
203D VAL* 1.3 60.4 + - - +
206D SER* 2.8 26.6 + - - -
345D LEU* 4.0 7.9 - - - +
368D ILE* 3.4 25.4 - - - +
369D ARG* 4.2 21.4 - - - +
4377D NAD 3.2 11.4 + - - -
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Residues in contact with VAL 203 (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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175D GLY* 3.9 20.2 - - - +
178D THR* 4.1 3.8 - - + -
179D GLY* 3.7 24.2 - - - +
202D GLY* 1.3 70.5 - - - -
204D GLY* 1.3 67.9 + - - +
206D SER* 2.8 15.2 + - - -
207D VAL* 2.9 11.4 + - - +
268D VAL* 3.4 21.8 - - + -
292D VAL* 3.8 16.4 - - + -
369D ARG* 4.2 1.8 - - - +
4377D NAD 2.9 56.2 + - + +
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Residues in contact with GLY 204 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197D VAL* 3.7 5.8 - - - +
199D GLY 3.0 28.0 - - - -
200D LEU* 4.6 1.1 - - - -
201D GLY 3.5 6.0 + - - +
202D GLY 3.4 0.4 - - - -
203D VAL* 1.3 77.8 - - - +
205D LEU* 1.3 62.3 + - - +
207D VAL* 3.1 13.7 + - - +
208D ILE* 3.2 16.0 + - - +
268D VAL* 3.3 17.2 + - - +
4377D NAD 4.2 0.8 + - - -
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Residues in contact with LEU 205 (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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200D LEU* 3.8 12.7 - - + +
201D GLY 2.9 17.4 + - - +
204D GLY* 1.3 74.6 - - - +
206D SER* 1.3 61.9 + - - +
208D ILE* 3.2 20.2 + - + +
209D MET* 3.2 17.5 + - - +
231D LYS* 4.0 18.4 - - + -
232D ALA* 3.4 41.3 - - + +
235D VAL* 3.7 13.9 - - + +
344D GLN 5.0 0.2 - - - +
345D LEU* 3.7 19.3 - - + -
368D ILE* 3.6 40.4 - - + -
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Residues in contact with SER 206 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175D GLY 3.5 2.6 + - - -
176D PHE* 3.3 41.9 + - - -
179D GLY* 3.6 8.1 - - - -
180D TYR* 3.6 6.9 + - - +
202D GLY 2.8 17.3 + - - -
203D VAL 2.8 12.1 + - - -
205D LEU* 1.3 76.7 - - - +
207D VAL* 1.3 57.1 + - - -
209D MET* 3.1 15.9 + - - +
210D GLY 2.9 22.5 + - - -
345D LEU* 3.9 12.0 - - - +
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Residues in contact with VAL 207 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179D GLY* 3.2 33.7 - - - +
182D ALA* 4.4 7.6 - - + -
183D ALA* 3.8 3.1 - - + +
197D VAL* 3.9 11.9 - - + -
203D VAL* 2.9 14.9 + - + +
204D GLY 3.1 8.0 + - - +
206D SER* 1.3 72.1 - - - +
208D ILE* 1.3 60.3 + - - +
210D GLY* 3.1 1.4 + - - -
211D CYS* 2.8 33.0 + - - -
266D PHE* 3.6 38.6 - - + -
268D VAL* 4.0 20.6 - - + -
292D VAL* 4.9 1.3 - - + -
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Residues in contact with ILE 208 (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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197D VAL* 4.0 16.2 - - + -
200D LEU* 3.8 28.3 - - + -
204D GLY 3.7 9.0 - - - +
205D LEU* 3.2 17.0 + - + +
206D SER 3.2 0.4 - - - -
207D VAL* 1.3 76.2 - - - +
209D MET* 1.3 52.3 + - - +
211D CYS* 3.3 2.3 + - - +
212D LYS* 2.8 35.7 + - - +
219D ILE* 3.8 15.9 - - + +
221D GLY* 5.0 1.6 - - - -
232D ALA* 4.0 21.3 - - + +
235D VAL* 3.4 24.7 - - + +
236D GLY 3.8 3.1 - - - -
237D ALA* 3.5 28.3 - - + +
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Residues in contact with MET 209 (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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176D PHE* 4.0 20.0 - - + -
180D TYR* 3.9 12.8 - - + -
205D LEU 3.5 13.2 - - - +
206D SER* 3.1 9.1 + - - +
208D ILE* 1.3 72.9 - - - +
210D GLY* 1.3 54.6 + - - +
212D LYS* 3.5 10.0 - - + +
213D SER* 2.7 36.0 + - - -
235D VAL* 4.1 26.5 - - + +
340D PHE* 4.0 14.6 - - + -
341D ASP* 3.1 40.6 - - + +
344D GLN* 6.0 1.3 - - + -
345D LEU* 4.4 17.3 - - - -
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Residues in contact with GLY 210 (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 TYR* 3.5 25.3 - - - -
183D ALA* 3.8 14.8 - - - -
184D VAL* 3.7 3.0 - - - +
206D SER 2.9 11.2 + - - -
207D VAL 3.1 4.2 + - - -
209D MET* 1.3 76.0 - - - +
211D CYS* 1.3 49.8 + - - +
213D SER* 2.8 11.3 + - - -
214D ALA* 2.8 32.7 + - - +
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Residues in contact with CYS 211 (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 ALA* 3.6 9.5 - - - +
189D VAL* 4.2 3.4 - - - -
195D CYS* 3.6 34.5 - - - -
197D VAL* 4.8 0.9 - - - -
207D VAL* 2.8 26.9 + - - +
208D ILE* 3.7 4.0 - - - +
210D GLY* 1.3 71.2 - - - -
212D LYS* 1.3 61.8 + - - +
214D ALA* 3.2 13.0 + - - +
215D GLY 3.3 0.2 + - - -
216D ALA* 3.1 23.9 + - - +
219D ILE* 3.8 21.1 - - + -
266D PHE* 3.7 23.3 - - - -
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Residues in contact with LYS 212 (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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208D ILE 2.8 21.8 + - - +
209D MET* 3.5 7.4 - - + +
211D CYS* 1.3 70.8 - - - +
213D SER* 1.3 65.8 + - - +
215D GLY* 3.2 12.0 + - - +
216D ALA 4.9 2.7 - - - +
219D ILE* 3.6 15.0 - - + +
234D ALA 5.0 4.6 + - - -
235D VAL* 3.7 27.6 + - - +
236D GLY* 4.0 10.7 - - - +
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Residues in contact with SER 213 (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 TYR* 3.6 24.6 + - - -
184D VAL* 3.2 19.4 - - - +
209D MET 2.7 18.5 + - - -
210D GLY 2.8 13.9 + - - -
212D LYS* 1.3 74.4 - - - +
214D ALA* 1.3 60.4 + - - +
215D GLY 3.3 1.0 + - - -
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Residues in contact with ALA 214 (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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184D VAL* 4.7 13.2 - - + -
189D VAL* 3.2 37.7 - - + +
191D PRO* 3.3 27.0 - - - +
210D GLY 2.8 11.1 + - - +
211D CYS 3.6 8.3 - - - +
212D LYS 3.1 0.8 - - - -
213D SER* 1.3 78.8 + - - +
215D GLY* 1.3 57.0 + - - +
216D ALA 3.5 1.1 + - - -
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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