Contacts of the helix formed by residues 203 - 214 (chain B) in PDB entry 5DTI
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 203 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120B GLY* 4.6 3.8 - - - -
121B GLY 4.8 3.9 + - - -
122B GLY* 5.3 2.8 + - - -
202B GLU* 1.3 81.0 - - - +
204B ALA* 1.3 61.1 + - - +
206B ALA* 2.7 24.1 + - - +
207B ALA* 2.8 11.8 + - - +
228B GLN 2.8 13.9 + - - -
229B SER 3.3 14.7 + - - -
230B GLY* 3.8 3.3 - - - -
236B TRP* 3.9 12.5 - - - -
295B PHE* 4.5 6.2 - - - -
297B PHE* 6.1 0.3 - - - -
338B PHE* 5.4 0.5 - - - -
447B HIS* 2.6 35.2 + - - -
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Residues in contact with ALA 204 (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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119B TYR 4.3 0.9 - - - -
120B GLY* 3.9 1.8 - - - -
121B GLY 3.8 5.8 - - - +
122B GLY* 3.5 29.6 - - - +
123B PHE* 3.5 33.3 - - + +
151B TYR* 4.6 3.1 - - - +
202B GLU 3.2 0.4 + - - -
203B SER* 1.3 80.2 + - - +
205B GLY* 1.3 58.4 + - - +
207B ALA 3.4 0.5 + - - -
208B SER* 2.9 32.0 + - - -
236B TRP* 3.9 14.0 - - + -
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Residues in contact with GLY 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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118B ILE* 3.3 30.5 - - - +
119B TYR 3.3 9.4 - - - -
120B GLY* 3.4 4.4 - - - -
201B GLY* 3.9 7.4 - - - -
202B GLU 2.9 7.8 + - - -
204B ALA* 1.3 75.6 - - - +
206B ALA* 1.3 58.9 + - - +
208B SER* 3.2 3.7 + - - -
209B VAL* 2.9 31.5 + - - +
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Residues in contact with ALA 206 (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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201B GLY 3.5 16.7 - - - +
203B SER 2.7 16.2 + - - +
205B GLY* 1.3 69.8 - - - +
207B ALA* 1.3 65.0 + - - +
209B VAL* 3.2 7.8 + - - +
210B GLY 2.9 18.5 + - - -
227B LEU* 3.4 14.8 - - - +
228B GLN 3.4 30.5 - - - +
230B GLY* 3.4 20.0 - - - +
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Residues in contact with ALA 207 (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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123B PHE* 4.0 8.1 - - + -
203B SER 2.8 10.7 + - - +
204B ALA 3.5 8.1 - - - +
206B ALA* 1.3 76.0 - - - +
208B SER* 1.3 57.3 + - - +
210B GLY* 3.2 2.8 + - - -
211B MET* 2.9 35.1 + - + +
231B THR 3.3 32.1 - - - +
232B PRO* 3.9 1.2 - - - +
236B TRP* 3.9 15.5 - - + -
237B ALA* 3.9 11.9 - - + -
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Residues in contact with SER 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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118B ILE* 3.9 5.8 - - - -
123B PHE* 3.3 15.9 - - - -
151B TYR* 4.5 1.0 + - - -
173B LEU* 3.9 10.7 - - - +
176B GLN* 3.2 37.5 + - - -
204B ALA 2.9 21.5 + - - -
205B GLY* 3.3 10.3 - - - -
207B ALA* 1.3 73.4 - - - +
209B VAL* 1.3 65.6 - - - +
211B MET* 3.0 5.4 + - - +
212B HIS* 2.9 28.4 + - - -
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Residues in contact with VAL 209 (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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118B ILE* 4.0 16.6 - - + -
199B LEU* 4.0 17.6 - - + +
200B PHE 4.1 4.9 - - - -
201B GLY 4.0 21.8 - - - +
205B GLY 2.9 20.4 + - - +
206B ALA* 3.4 7.6 - - - +
208B SER* 1.3 74.5 - - - +
210B GLY* 1.3 63.9 + - - +
212B HIS* 3.1 12.5 + - - +
213B ILE* 3.0 21.3 + - - +
225B ALA* 3.5 31.4 - - + -
226B VAL 4.1 6.3 - - - +
227B LEU* 4.0 11.0 - - + -
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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
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206B ALA 2.9 10.9 + - - -
207B ALA 3.5 4.5 - - - -
208B SER 3.2 0.4 - - - -
209B VAL* 1.3 76.8 - - - +
211B MET* 1.3 57.0 + - - +
213B ILE* 3.1 14.6 + - - +
214B LEU* 3.0 29.1 + - - +
227B LEU* 3.9 8.5 - - - +
232B PRO* 3.7 26.7 - - - -
414B LEU* 5.9 0.2 - - - -
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Residues in contact with MET 211 (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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123B PHE* 4.5 0.7 - - + -
173B LEU* 3.9 11.7 - - + -
207B ALA* 2.9 24.6 + - + +
208B SER* 3.0 7.3 + - - +
210B GLY* 1.3 74.6 - - - +
212B HIS* 1.3 60.7 + - - +
214B LEU* 3.2 7.2 + - + +
215B SER* 2.9 31.2 + - - -
232B PRO* 3.8 14.1 - - + -
237B ALA* 3.5 39.3 - - + +
238B THR* 3.6 14.8 - - + -
301B PRO* 3.5 29.8 - - + -
307B PHE* 3.7 17.5 - - + -
308B LEU* 4.1 18.8 - - + +
312B PRO* 5.4 0.7 - - + -
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Residues in contact with HIS 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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118B ILE* 4.1 11.6 - - + +
173B LEU* 3.6 24.0 - - + +
176B GLN* 2.7 30.2 + - + +
177B ARG* 3.9 15.3 - - - -
180B LEU* 4.2 6.9 - - + +
199B LEU* 4.0 10.5 - - + -
208B SER 2.9 30.1 + - - -
209B VAL* 3.1 7.2 + - - +
211B MET* 1.3 73.4 - - - +
213B ILE* 1.3 66.9 + - - +
215B SER* 3.2 18.8 - - - +
218B SER* 2.8 37.9 + - - -
219B ARG* 3.7 5.9 - - - -
222B PHE* 3.8 13.4 - - + -
307B PHE* 4.1 10.1 - + - -
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Residues in contact with ILE 213 (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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209B VAL 3.0 17.6 + - - +
210B GLY* 3.2 14.4 - - - +
212B HIS* 1.3 76.5 - - - +
214B LEU* 1.3 62.8 + - + +
215B SER 3.6 0.2 + - - -
219B ARG* 3.2 27.0 + - - +
222B PHE* 3.8 24.2 - - + -
225B ALA* 3.8 21.8 - - + -
227B LEU* 4.1 16.8 - - + -
321B PHE* 3.8 20.7 - - + -
324B LEU* 3.7 31.4 - - + -
326B VAL* 4.4 5.6 - - + -
414B LEU* 6.2 1.1 - - + -
418B LEU* 5.0 8.3 - - + -
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Residues in contact with LEU 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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210B GLY 3.0 14.3 + - - +
211B MET* 3.2 7.4 + - - +
212B HIS 3.1 0.4 - - - -
213B ILE* 1.3 80.5 - - + +
215B SER* 1.3 59.2 + - - +
216B LEU 4.0 1.7 + - - -
232B PRO* 3.9 27.1 - - + -
307B PHE 4.5 3.7 - - - +
308B LEU* 4.8 5.6 - - + -
309B SER* 5.3 1.7 + - - -
312B PRO* 3.9 29.2 - - + +
315B LEU* 3.7 37.3 - - + +
316B ILE* 3.9 16.4 - - + -
321B PHE* 3.8 33.7 - - + -
414B LEU* 6.2 0.4 - - + -
418B LEU* 6.0 0.4 - - + -
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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