Contacts of the helix formed by residues 204 - 211 (chain A) in PDB entry 1EQB
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 VAL 204 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A PHE* 3.9 30.1 - - + -
183A TRP* 5.1 4.7 - - + -
201A MET* 3.0 24.4 + - + +
203A HIS* 1.3 79.6 - - - +
205A ALA* 1.3 59.3 + - - +
206A GLY 3.2 3.6 - - - -
207A LEU* 3.1 9.1 + - + -
208A VAL* 2.8 32.8 + - + +
213A TYR* 4.1 43.3 - - + -
230A THR* 3.7 1.3 - - - -
316A ASN* 4.4 4.0 - - + -
317A HIS* 4.2 12.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 205 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A PHE* 3.5 13.0 - - + -
201A MET* 2.8 19.9 + - - +
202A ALA 3.9 5.6 - - - +
203A HIS 3.5 0.6 - - - -
204A VAL* 1.3 76.4 - - - +
206A GLY* 1.3 59.0 + - - +
208A VAL 3.4 0.2 + - - -
209A ALA* 2.9 28.4 + - - +
225A THR* 3.0 31.6 - - - +
226A THR 4.4 1.3 - - - +
230A THR* 3.5 1.8 + - - -
231A LEU* 4.1 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 206 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A ALA* 1.3 74.7 - - - +
207A LEU* 1.3 61.0 + - - -
209A ALA* 3.1 12.8 + - - +
210A ALA 3.1 9.7 + - - -
230A THR* 2.8 41.2 + - - -
231A LEU* 3.8 12.7 - - - +
284A PHE* 3.9 1.3 - - - -
288A GLN* 3.5 16.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 207 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A VAL* 3.1 18.5 + - + +
206A GLY* 1.3 75.2 - - - +
208A VAL* 1.3 57.5 + - - +
210A ALA 3.2 1.6 + - - -
211A GLY 3.0 3.8 + - - -
212A VAL* 2.7 45.6 + - + +
213A TYR* 3.8 18.4 - - + -
230A THR* 3.9 9.4 + - + -
288A GLN* 3.0 45.1 - - + +
291A VAL* 4.6 11.7 - - + -
292A ALA* 5.1 2.7 - - + +
315A ASP 5.1 0.4 - - - +
316A ASN* 3.8 18.8 - - + -
317A HIS* 3.8 29.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 208 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A PHE* 4.2 12.8 - - + -
201A MET* 4.1 12.1 - - - -
204A VAL* 2.8 34.9 + - + +
205A ALA 3.7 5.2 - - - +
207A LEU* 1.3 76.1 - - - +
209A ALA* 1.3 58.9 + - - +
211A GLY* 2.8 21.0 + - - -
213A TYR* 3.7 13.6 - - + +
214A PRO 3.7 17.9 - - - +
215A ASN* 3.5 45.3 + - + +
216A PRO* 4.3 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 209 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A LEU* 4.1 43.3 - - + +
86A PHE* 4.1 10.7 - - + -
205A ALA 2.9 14.1 + - - +
206A GLY 3.1 10.5 + - - +
208A VAL* 1.3 77.1 - - - +
210A ALA* 1.3 59.3 + - - +
211A GLY 3.5 0.2 + - - -
231A LEU* 4.3 2.9 - - + -
279A ALA 5.1 1.3 - - - +
284A PHE* 3.9 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 210 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A GLY 3.1 5.3 + - - -
207A LEU 3.2 3.6 + - - +
208A VAL 3.2 0.2 - - - -
209A ALA* 1.3 76.1 - - - +
211A GLY* 1.3 60.7 + - - +
212A VAL* 3.3 5.8 - - + +
279A ALA 5.9 0.2 - - - -
284A PHE* 4.2 4.2 - - + +
285A LYS* 3.1 61.3 - - + +
288A GLN* 3.4 36.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 211 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A VAL 2.8 17.0 + - - -
209A ALA 3.2 0.8 + - - -
210A ALA* 1.3 80.1 - - - +
212A VAL* 1.3 61.3 + - - +
213A TYR 3.4 7.8 + - - -
285A LYS* 5.3 1.3 - - - -
----------------------------------------------------------
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