Contacts of the helix formed by residues 212 - 221 (chain A) in PDB entry 6XAV
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 ARG 212 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A GLU* 1.3 81.8 + - - +
213A PRO* 1.3 71.2 - - + +
214A GLU* 3.4 24.7 - - - +
215A GLU* 2.5 54.3 + - + +
216A VAL* 3.1 24.1 + - - +
232A PHE* 3.9 7.0 - - + -
133G HIS* 4.3 15.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 213 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A GLU 4.0 3.6 - - - +
212A ARG* 1.3 86.1 - - + +
214A GLU* 1.3 72.9 + - - +
216A VAL* 3.1 13.8 + - + +
217A THR* 3.1 20.1 + - + +
231A THR* 3.8 24.7 - - + -
232A PHE* 4.1 14.8 - - + -
233A ASP* 4.2 18.2 - - - +
133G HIS* 5.0 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 214 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A ARG* 3.4 21.2 - - + +
213A PRO* 1.3 84.5 - - - +
215A GLU* 1.3 67.1 + - + +
217A THR* 2.8 22.0 + - - -
218A GLU* 3.1 14.5 + - - +
133G HIS* 3.2 34.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 215 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A THR* 5.4 8.3 + - + -
208A LEU* 5.3 4.3 - - + -
211A GLU* 3.6 20.2 - - + +
212A ARG* 2.5 59.7 + - + +
213A PRO 3.2 0.6 - - - -
214A GLU* 1.3 79.6 - - + +
216A VAL* 1.3 65.0 + - + +
218A GLU* 3.7 12.9 - - - +
219A MET* 3.0 32.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 216 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A LEU* 4.8 9.9 - - + -
211A GLU* 4.7 12.6 - - + -
212A ARG 3.1 15.4 + - - +
213A PRO* 3.1 9.7 + - + +
215A GLU* 1.3 77.4 - - - +
217A THR* 1.3 60.9 + - + +
219A MET* 3.3 4.8 + - - +
220A GLN* 2.9 37.0 + - - +
227A VAL* 4.5 8.5 - - + +
229A ALA* 3.7 34.5 - - + -
231A THR* 4.2 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 217 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A PRO* 3.1 12.8 + - + +
214A GLU* 2.8 25.5 + - - -
216A VAL* 1.3 79.1 - - + +
218A GLU* 1.3 61.1 + - - +
220A GLN* 4.0 9.1 - - - +
221A ARG* 3.1 42.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 218 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A THR* 5.8 3.0 - - - +
189A GLN* 4.0 21.8 + - - +
214A GLU 3.1 13.5 + - - +
215A GLU* 3.7 14.6 - - - +
217A THR* 1.3 83.3 + - - +
219A MET* 1.3 62.3 + - + +
221A ARG* 3.5 5.1 + - - +
222A LEU* 3.2 31.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 219 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A THR* 5.0 7.6 - - - +
188A LEU* 4.1 24.7 - - + -
189A GLN* 3.5 44.2 - - + -
206A VAL* 5.0 10.1 - - + -
208A LEU* 4.1 22.2 - - + -
215A GLU* 3.0 23.0 + - + +
216A VAL 3.9 3.1 - - - +
218A GLU* 1.3 75.4 - - + +
220A GLN* 1.3 64.1 + - - +
222A LEU* 4.5 3.1 - - - -
223A VAL* 3.1 52.7 + - + +
227A VAL* 4.5 6.7 - - + -
265A ASP* 5.9 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 220 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A VAL* 2.9 25.7 + - - +
217A THR* 4.0 9.5 - - - +
218A GLU 3.3 0.2 - - - -
219A MET* 1.3 77.4 - - - +
221A ARG* 1.3 62.7 + - + +
222A LEU 3.3 1.3 + - - -
223A VAL 3.9 10.9 - - - +
225A GLY 5.4 1.6 - - - +
227A VAL* 3.7 41.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 221 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A THR* 3.1 30.4 + - - +
218A GLU* 3.8 5.2 - - - +
219A MET 3.2 0.4 - - - -
220A GLN* 1.3 80.8 - - + +
222A LEU* 1.3 56.8 + - - +
223A VAL 4.9 0.4 - - - -
----------------------------------------------------------
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