Contacts of the helix formed by residues 214 - 219 (chain B) in PDB entry 4B92
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 GLU 214 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B ILE* 4.0 14.4 - - + +
211B THR 5.3 0.2 + - - -
212B GLY* 3.3 21.9 + - - -
213B PRO* 1.3 79.3 - - - +
215B GLY* 1.3 58.9 + - - +
216B ILE 3.1 0.2 - - - -
217B GLU* 2.9 23.7 + - - +
218B ILE* 3.2 26.7 + - + +
283B TYR* 3.7 23.9 + - - +
284B TYR* 3.4 39.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 215 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B ALA* 5.3 0.2 - - - -
210B ILE* 3.9 13.5 - - - -
212B GLY 3.1 9.0 + - - -
214B GLU* 1.3 79.1 - - - +
216B ILE* 1.3 60.1 + - - +
218B ILE* 3.8 5.6 - - - -
219B SER* 2.8 33.8 + - - -
341B PHE* 3.4 27.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 216 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B PRO* 3.0 22.0 + - + +
215B GLY* 1.3 76.4 - - - +
217B GLU* 1.3 54.3 + - - +
219B SER* 3.9 1.1 - - - -
220B ARG* 2.7 49.4 - - - +
283B TYR* 3.9 35.0 - - + +
295B VAL* 4.0 18.4 - - + -
296B THR 3.8 17.3 - - - +
297B VAL* 3.9 11.0 - - + -
299B PRO* 3.4 5.9 - - + +
341B PHE* 3.5 22.2 - - + +
342B THR* 6.1 1.1 - - - -
346B HIS* 3.7 27.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 217 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B GLU* 2.9 9.9 + - - +
216B ILE* 1.3 78.7 - - + +
218B ILE* 1.3 65.8 + - + +
219B SER 3.2 1.8 - - - -
220B ARG 3.1 22.0 + - - +
221B PRO* 3.5 5.8 - - + +
280B GLY* 3.5 6.1 - - - -
283B TYR* 4.2 14.6 - - + -
284B TYR* 3.4 29.3 + - - +
299B PRO* 3.9 9.6 - - + -
300B LEU 2.6 28.9 - - - +
301B ARG* 3.3 7.2 - - - +
302B LEU* 2.9 34.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 218 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B ALA* 4.9 7.2 - - + -
210B ILE* 3.8 32.1 - - + -
214B GLU* 3.2 26.8 + - + +
215B GLY* 3.4 6.5 + - - +
217B GLU* 1.3 76.4 - - + +
219B SER* 1.3 60.1 + - - +
220B ARG 3.5 0.3 + - - -
221B PRO* 3.6 12.3 - - - +
284B TYR* 4.0 19.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 219 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B LEU 4.2 1.4 - - - +
198B VAL* 4.3 3.9 - - - +
201B GLY* 3.4 43.5 - - - -
202B ALA* 3.8 12.2 - - - +
205B ALA* 4.5 2.0 - - - +
215B GLY 2.8 23.5 + - - -
216B ILE 3.4 0.5 + - - -
218B ILE* 1.3 77.5 - - - +
220B ARG* 1.3 81.0 + - - +
221B PRO* 3.6 4.2 - - - +
224B LEU* 4.0 8.5 - - - +
341B PHE* 3.9 10.6 - - - -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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