Contacts of the helix formed by residues 201 - 215 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199B GLY 3.5 4.4 + - - -
200B LEU* 1.3 83.2 - - - +
202B GLY* 1.3 65.3 + - - -
203B VAL 3.5 1.8 - - - -
204B GLY 4.0 2.0 - - - +
205B LEU* 3.1 18.4 + - - +
228B LYS* 4.3 5.8 - - - -
268B VAL 5.5 0.2 + - - -
368B ILE* 3.9 10.3 - - - -
2377B NAD 3.4 32.6 + - - -
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Residues in contact with GLY 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175B GLY 4.7 2.0 - - - -
201B GLY* 1.3 73.7 - - - +
203B VAL* 1.3 61.2 + - - +
205B LEU 3.6 0.2 + - - -
206B SER* 2.8 24.4 + - - -
345B LEU* 3.8 8.2 - - - +
368B ILE* 3.5 23.3 - - - +
369B ARG* 4.0 21.3 - - - +
2377B NAD 3.2 14.0 + - - -
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Residues in contact with VAL 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B GLY* 3.7 22.9 - - - +
178B THR* 3.8 2.9 - - + -
179B GLY* 3.6 25.8 - - - +
202B GLY* 1.3 69.8 - - - -
204B GLY* 1.3 64.3 + - - +
206B SER* 2.9 6.2 + - - -
207B VAL* 2.9 20.3 + - - +
268B VAL* 3.3 22.0 - - + -
292B VAL* 3.8 13.9 - - + -
369B ARG* 4.3 1.1 - - - +
2377B NAD 2.8 57.8 + - + +
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Residues in contact with GLY 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B VAL* 3.6 5.7 - - - +
199B GLY 3.0 28.0 + - - -
200B LEU* 4.6 1.8 - - - -
201B GLY 3.5 4.3 + - - +
202B GLY 3.4 0.6 - - - -
203B VAL* 1.3 79.1 - - - +
205B LEU* 1.3 59.8 + - - +
207B VAL* 3.3 5.1 + - - +
208B ILE* 3.2 26.2 + - - +
268B VAL* 3.6 16.3 + - - +
2377B NAD 4.0 2.2 + - - -
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Residues in contact with LEU 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200B LEU* 3.6 14.1 - - + +
201B GLY 3.1 22.3 + - - +
204B GLY* 1.3 75.9 - - - +
206B SER* 1.3 62.1 + - - +
208B ILE* 3.2 7.2 + - + +
209B MET* 3.1 17.8 + - - +
228B LYS 4.9 0.7 - - - +
231B LYS* 3.8 26.9 - - + +
232B ALA* 3.4 41.5 - - + +
235B VAL* 3.4 20.8 - - + +
345B LEU* 3.7 17.0 - - + -
368B ILE* 3.8 31.2 - - + -
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Residues in contact with SER 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B GLY 3.5 19.3 + - - -
176B PHE* 3.6 26.8 - - - -
179B GLY 3.6 2.0 - - - -
180B TYR* 3.5 11.9 - - - +
202B GLY 2.8 14.9 + - - -
203B VAL 2.9 8.5 + - - -
205B LEU* 1.3 76.1 - - - +
207B VAL* 1.3 64.1 - - - +
209B MET* 3.2 14.7 + - - +
210B GLY 3.0 16.3 + - - -
345B LEU* 3.7 13.0 - - - +
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Residues in contact with VAL 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B GLY* 2.8 30.9 + - - +
182B ALA* 4.3 9.4 - - + -
183B ALA* 3.7 2.2 - - + +
197B VAL* 3.6 24.5 - - + -
203B VAL 2.9 13.7 + - - +
204B GLY 3.3 8.5 - - - +
205B LEU 3.2 0.4 - - - -
206B SER* 1.3 73.8 - - - +
208B ILE* 1.3 54.5 - - - +
210B GLY* 2.7 23.2 + - - -
211B CYS* 2.8 18.1 + - - -
266B PHE* 3.8 28.9 - - + -
268B VAL* 4.0 21.1 - - + -
292B VAL* 4.7 1.6 - - + -
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Residues in contact with ILE 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197B VAL* 3.5 19.7 - - + -
200B LEU* 3.6 30.5 - - + -
204B GLY 3.3 11.7 - - - +
205B LEU* 3.2 12.1 + - + +
207B VAL* 1.3 76.3 - - - +
209B MET* 1.3 56.9 + - - +
211B CYS* 3.2 7.4 + - - +
212B LYS* 2.8 28.4 + - - +
219B ILE* 3.6 15.5 - - + -
221B GLY* 4.9 2.5 - - - -
232B ALA* 4.2 16.8 - - + -
235B VAL* 4.2 3.6 - - + -
236B GLY* 3.7 13.0 - - - +
237B ALA* 3.5 32.3 - - + +
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Residues in contact with MET 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B PHE* 3.2 33.7 - - + -
180B TYR* 4.1 6.6 - - + -
205B LEU 3.1 10.9 + - - +
206B SER* 3.5 12.8 - - - +
207B VAL 3.2 0.4 - - - -
208B ILE* 1.3 75.8 - - - +
210B GLY* 1.3 57.6 + - - +
212B LYS* 3.5 8.6 + - - +
213B SER* 2.8 31.2 + - - -
235B VAL* 3.2 32.3 - - + +
340B PHE* 4.2 15.3 - - + -
341B ASP 4.1 22.0 - - - +
344B GLN* 5.9 1.3 - - - -
345B LEU* 4.5 15.7 - - + -
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Residues in contact with GLY 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B TYR* 3.5 27.3 - - - -
183B ALA* 3.6 15.9 - - - -
184B VAL* 3.8 4.1 - - - +
206B SER 3.0 6.2 + - - -
207B VAL 2.7 15.4 + - - -
209B MET* 1.3 68.3 - - - +
211B CYS* 1.3 57.4 + - - -
213B SER* 3.1 3.5 + - - -
214B ALA* 2.8 29.8 + - - +
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Residues in contact with CYS 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B ALA* 3.5 9.2 - - - +
189B VAL* 4.3 2.9 - - - -
195B CYS* 3.5 37.0 - - - -
197B VAL* 4.8 1.1 - - - -
207B VAL* 2.8 25.7 + - - -
208B ILE* 3.2 6.5 + - - +
210B GLY* 1.3 72.9 - - - +
212B LYS* 1.3 61.3 + - - +
214B ALA* 3.1 6.8 + - - +
215B GLY 3.0 19.1 + - - -
216B ALA* 3.2 9.5 + - - -
219B ILE* 3.6 21.8 - - + -
266B PHE* 3.9 19.5 - - - -
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Residues in contact with LYS 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208B ILE 2.8 20.3 + - - +
209B MET* 3.6 7.9 - - - +
211B CYS* 1.3 72.4 - - - +
213B SER* 1.3 64.9 + - - +
215B GLY* 3.3 12.8 + - - -
216B ALA 5.0 3.5 - - - +
219B ILE* 3.4 13.5 - - + +
235B VAL 4.5 9.6 - - - +
236B GLY* 4.3 21.9 + - - +
78D GLU* 4.6 15.1 + - - -
79D GLY* 5.7 4.2 - - - -
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Residues in contact with SER 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B TYR* 3.2 27.8 + - - -
184B VAL* 4.6 4.0 - - - +
209B MET 2.8 19.1 + - - -
210B GLY 3.1 5.4 + - - -
212B LYS* 1.3 81.4 - - - +
214B ALA* 1.3 60.8 + - - +
215B GLY* 4.6 0.3 - - - -
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Residues in contact with ALA 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183B ALA 5.1 1.1 - - - +
184B VAL* 4.8 10.1 - - + +
189B VAL* 3.2 42.1 - - + +
191B PRO* 3.4 25.3 - - - +
210B GLY 2.8 12.7 + - - +
211B CYS 3.1 8.9 + - - +
213B SER* 1.3 79.0 - - - +
215B GLY* 1.3 57.2 + - - +
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Residues in contact with GLY 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B PRO* 3.6 8.3 - - - +
192B GLY* 2.9 22.2 + - - -
211B CYS 3.0 3.2 + - - -
212B LYS 3.3 10.1 + - - -
213B SER 4.6 0.7 - - - -
214B ALA* 1.3 80.0 - - - +
216B ALA* 1.3 71.0 + - - +
217B SER* 3.4 2.1 + - - -
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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
------------------------------------------------------------
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