Contacts of the helix formed by residues 209 - 221 (chain A) in PDB entry 2QVH
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 GLY 209 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A ALA* 3.5 8.8 - - - +
56A GLU* 3.4 12.6 - - - -
204A VAL* 2.9 27.4 + - - +
207A LEU 4.6 0.3 - - - +
208A GLY* 1.3 79.1 - - - +
210A VAL* 1.3 60.9 + - - -
211A ARG 3.5 2.0 - - - -
212A ALA* 3.5 1.7 + - - +
213A ALA* 2.9 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 210 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A GLU* 2.7 13.9 + - - +
62A TRP* 3.5 29.8 - - + +
63A PRO* 3.7 19.5 - - + -
204A VAL* 4.2 7.2 - - + -
209A GLY* 1.3 67.9 - - - -
211A ARG* 1.3 61.1 + - - +
213A ALA* 3.2 3.3 + - - +
214A LEU* 2.8 40.1 + - + +
238A ALA 3.6 24.0 - - - +
241A ALA 4.5 4.9 - - - +
242A LEU* 3.8 31.2 - - + +
245A ALA* 4.7 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 211 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A GLU* 3.1 19.6 + - - +
60A LEU* 4.7 13.8 + - - +
61A GLY 3.0 29.3 + - - -
62A TRP 3.9 3.4 + - - -
63A PRO* 3.5 37.7 - - + +
210A VAL* 1.3 78.4 - - - +
212A ALA* 1.3 62.5 + - - +
214A LEU* 3.3 9.4 + - + +
215A ARG* 3.0 46.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 212 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A GLU* 4.8 0.2 + - - -
207A LEU* 3.3 24.7 - - - +
208A GLY* 3.8 13.7 + - - +
209A GLY 3.5 6.1 + - - +
210A VAL 3.2 0.4 - - - -
211A ARG* 1.3 79.8 - - - +
213A ALA* 1.3 61.8 + - - +
215A ARG* 3.2 25.1 + - - +
216A LEU* 3.0 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 213 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A LEU* 3.9 7.4 - - + +
204A VAL* 5.1 2.0 - - - -
207A LEU* 4.1 29.1 + - + -
209A GLY 2.9 19.0 + - - +
210A VAL 3.6 2.0 - - - +
212A ALA* 1.3 77.3 - - - +
214A LEU* 1.3 59.2 + - - +
216A LEU* 3.3 3.9 + - - +
217A ALA* 3.0 29.1 + - - +
242A LEU* 3.5 32.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 214 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A PRO* 3.9 21.1 - - + -
210A VAL* 2.8 34.0 + - + +
211A ARG* 3.7 6.3 - - - +
213A ALA* 1.3 76.5 - - - +
215A ARG* 1.3 58.4 + - + +
217A ALA* 3.3 5.9 + - - +
218A GLU* 3.0 27.9 + - - +
242A LEU* 3.7 13.5 - - + -
245A ALA* 4.0 27.8 - - + +
246A LEU* 3.7 28.0 - - + -
247A PRO* 5.3 2.2 - - + -
20B THR* 4.8 2.6 + - - -
21B VAL* 6.3 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 215 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A ARG* 3.0 36.6 + - - +
212A ALA* 3.2 31.1 + - - +
214A LEU* 1.3 78.6 - - + +
216A LEU* 1.3 56.8 + - - +
218A GLU* 3.2 15.0 + - - +
219A GLU* 2.9 45.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 216 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A ARG* 6.0 0.4 - - - +
182A ILE* 3.9 27.8 - - + -
188A PRO* 3.9 29.4 - - + -
189A LEU* 4.2 11.7 - - + -
200A VAL* 5.8 0.2 - - + -
202A LEU* 4.8 4.3 - - + -
207A LEU* 3.9 23.6 - - + -
212A ALA 3.0 15.9 + - - +
213A ALA* 3.7 6.3 - - - +
214A LEU 3.3 0.2 - - - -
215A ARG* 1.3 74.2 - - - +
217A ALA* 1.3 66.3 + - - +
219A GLU* 3.2 11.2 + - + +
220A CYS* 3.0 39.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 217 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A VAL* 5.8 0.9 - - - -
202A LEU* 3.8 22.6 - - + +
213A ALA 3.0 17.4 + - - +
214A LEU 3.5 6.1 - - - +
215A ARG 3.3 0.2 - - - -
216A LEU* 1.3 76.4 - - - +
218A GLU* 1.3 62.7 + - - +
220A CYS* 3.5 4.6 + - - +
221A GLY* 3.4 18.5 + - - -
222A LEU 4.5 5.7 + - - +
224A VAL* 4.0 17.4 - - + +
246A LEU* 4.2 14.8 - - + -
15B ARG* 5.0 1.2 + - - -
20B THR* 5.6 1.2 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
214A LEU 3.0 12.7 + - - +
215A ARG* 3.4 17.6 - - - +
217A ALA* 1.3 78.9 - - - +
219A GLU* 1.3 65.9 + - + +
220A CYS 3.3 0.5 + - - -
221A GLY 3.4 1.6 + - - -
15B ARG* 3.3 24.1 + - - +
18B GLY 4.0 10.8 - - - +
19B ILE* 3.3 15.7 - - - +
20B THR* 2.8 54.4 + - + +
21B VAL* 3.5 15.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 219 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A LEU* 3.8 26.7 - - + +
192A ARG* 2.7 32.9 + - - +
215A ARG* 2.9 39.6 + - - +
216A LEU* 3.2 11.9 + - - +
218A GLU* 1.3 81.7 - - + +
220A CYS* 1.3 57.0 + - - +
221A GLY 3.4 0.4 + - - -
15B ARG* 4.6 4.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 220 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A ILE* 4.6 5.4 - - - -
188A PRO 4.5 11.2 - - - -
189A LEU* 4.0 19.7 - - - -
191A VAL* 5.7 0.2 - - - -
192A ARG* 3.4 32.5 - - + +
200A VAL* 4.4 26.5 - - + -
216A LEU* 3.0 32.7 + - - +
217A ALA* 4.1 5.6 - - - +
218A GLU 3.3 0.4 - - - -
219A GLU* 1.3 78.1 - - - +
221A GLY* 1.3 63.9 + - - +
222A LEU* 3.2 13.5 + - + +
224A VAL* 6.1 0.2 - - + -
15B ARG* 4.8 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 221 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A ALA 3.4 8.5 + - - -
218A GLU 3.4 4.0 + - - -
219A GLU 3.4 0.4 - - - -
220A CYS* 1.3 78.0 - - - +
222A LEU* 1.3 63.2 + - - +
223A PRO* 4.7 0.5 - - - +
15B ARG* 3.3 44.3 + - - -
----------------------------------------------------------
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