Contacts of the helix formed by residues 203 - 217 (chain B) in PDB entry 3N4E
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
---------------------------
Residue Dist Surf HB Arom Phob DC
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170B CYS* 3.3 14.2 - - - -
171B ASP* 2.7 31.0 + - - -
202B TYR* 1.3 74.6 - - - +
204B VAL* 1.3 57.3 + - - +
205B GLY* 3.8 3.3 + - - -
206B GLY 3.0 11.4 + - - -
207B ALA* 2.7 34.5 + - - +
226B VAL* 4.1 2.2 - - - -
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Residues in contact with VAL 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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203B SER* 1.3 72.7 - - - +
205B GLY* 1.3 58.6 + - - +
207B ALA* 3.3 1.6 + - - +
208B ILE* 3.0 45.6 + - + +
226B VAL* 4.2 9.7 - - + +
233B ALA* 3.6 33.0 - - + -
236B GLU* 3.8 23.6 - - + +
237B VAL* 4.1 13.2 - - + +
240B ARG* 4.1 3.4 - - - +
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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
----------------------------------------------------------
203B SER* 3.2 4.3 + - - -
204B VAL* 1.3 80.1 - - - +
206B GLY* 1.3 56.6 + - - +
208B ILE* 3.6 8.5 + - - +
209B ARG* 3.1 26.7 + - - +
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Residues in contact with GLY 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B ASP* 4.0 5.8 - - - -
174B ILE* 3.9 22.3 - - - +
202B TYR* 3.9 6.3 - - - -
203B SER* 3.0 19.0 + - - -
205B GLY* 1.3 75.4 - - - +
207B ALA* 1.3 59.0 + - - +
209B ARG* 3.2 4.3 + - - +
210B VAL* 2.9 34.5 + - - +
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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
----------------------------------------------------------
202B TYR* 3.5 17.0 - - + +
203B SER 2.7 19.7 + - - +
204B VAL 3.7 3.8 - - - +
206B GLY* 1.3 72.8 - - - +
208B ILE* 1.3 52.0 + - - +
210B VAL 3.4 0.2 + - - -
211B GLY* 2.8 30.0 + - - -
222B PHE* 3.2 10.8 - - - -
225B PRO* 3.6 29.6 - - + -
226B VAL* 4.1 9.4 - - + -
237B VAL* 4.1 10.8 - - + -
241B LEU* 4.2 1.9 - - - +
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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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204B VAL* 3.0 30.6 + - + +
205B GLY* 3.9 7.2 - - - +
207B ALA* 1.3 72.9 - - - +
209B ARG* 1.3 66.9 + - - +
211B GLY* 3.4 0.7 + - - -
212B ARG* 3.1 41.1 + - + +
237B VAL* 4.8 12.6 - - + -
240B ARG* 3.2 56.1 - - + +
241B LEU* 4.0 16.5 - - + +
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Residues in contact with ARG 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B ILE* 4.1 30.2 - - + +
178B ILE* 4.6 7.3 - - + +
205B GLY 3.1 18.5 + - - +
206B GLY* 3.2 6.9 + - - +
208B ILE* 1.3 79.9 - - - +
210B VAL* 1.3 62.7 + - - +
212B ARG* 3.6 6.1 + - - +
213B ALA* 3.4 16.8 + - - +
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Residues in contact with VAL 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B ILE* 3.9 24.9 - - + +
177B ASP* 5.4 0.4 - - + -
178B ILE* 4.5 14.4 - - + -
196B PHE* 4.4 7.9 - - + -
202B TYR* 3.7 31.9 - - + +
206B GLY 2.9 18.8 + - - +
207B ALA 3.9 3.1 - - - +
209B ARG* 1.3 72.8 - - - +
211B GLY* 1.3 61.7 + - - +
213B ALA* 2.9 9.3 + - - +
214B LEU* 2.8 49.8 + - + +
222B PHE* 3.8 13.9 - - + -
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Residues in contact with GLY 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B ALA 2.8 23.1 + - - -
208B ILE 3.9 1.3 - - - -
210B VAL* 1.3 72.9 - - - +
212B ARG* 1.3 49.9 + - - +
214B LEU* 3.2 6.5 + - - +
215B GLU* 2.7 38.0 + - - +
222B PHE* 3.8 19.5 - - - -
241B LEU* 4.1 14.8 - - - -
243B ILE* 4.0 4.3 - - - +
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Residues in contact with ARG 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B ILE* 3.1 30.0 + - + +
209B ARG* 3.9 5.8 - - - +
211B GLY* 1.3 74.6 - - - +
213B ALA* 1.3 57.3 + - - +
215B GLU* 2.8 43.7 + - - +
216B ASP* 2.9 33.8 + - - +
240B ARG* 3.2 22.2 + - - +
241B LEU* 3.9 9.0 - - + +
242B ASP* 3.7 22.4 + - - +
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Residues in contact with ALA 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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178B ILE* 3.8 42.2 - - + -
209B ARG 3.4 6.4 + - - +
210B VAL 2.9 9.0 + - - +
212B ARG* 1.3 75.1 - - - +
214B LEU* 1.3 65.9 + - + +
216B ASP* 3.3 13.3 + - - +
217B LEU* 3.1 29.0 + - + +
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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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178B ILE* 6.1 2.0 - - + -
181B ALA* 3.8 18.6 - - + -
196B PHE* 3.5 40.8 - - + -
210B VAL* 2.8 24.6 + - + +
211B GLY 3.5 6.3 - - - +
213B ALA* 1.3 76.7 - - + +
215B GLU* 1.3 62.0 + - - +
217B LEU* 3.1 6.5 + - + +
218B GLY 3.1 4.7 + - - -
219B TYR* 3.1 36.6 + - + +
222B PHE* 3.4 48.2 - - + -
243B ILE* 3.9 14.4 - - + -
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Residues in contact with GLU 215 (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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211B GLY 2.7 17.8 + - - +
212B ARG* 2.8 43.7 + - - +
214B LEU* 1.3 73.8 - - - +
216B ASP* 1.3 62.2 + - - +
218B GLY* 3.2 13.3 + - - +
219B TYR 5.0 2.9 - - - +
241B LEU* 3.6 5.2 - - - +
242B ASP* 2.8 23.4 + - + +
243B ILE* 2.8 48.2 + - + +
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Residues in contact with ASP 216 (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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212B ARG* 2.9 18.2 + - - +
213B ALA* 3.3 15.0 + - - +
215B GLU* 1.3 77.1 - - - +
217B LEU* 1.3 62.3 + - + +
218B GLY 3.3 0.8 + - - -
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Residues in contact with LEU 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B ILE* 4.3 10.8 - - + +
181B ALA* 3.9 14.6 - - + -
182B ARG* 3.7 58.6 - - + +
185B ARG* 2.7 49.6 + - + -
186B GLU* 6.1 0.4 - - - +
213B ALA* 3.1 23.7 + - + +
214B LEU* 3.1 5.5 + - + +
216B ASP* 1.3 78.4 - - + +
218B GLY* 1.3 55.0 + - - +
219B TYR* 3.3 13.9 + - + -
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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