Contacts of the helix formed by residues 207 - 221 (chain A) in PDB entry 5AVL
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 207 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A GLN 4.9 1.8 - - - -
206A LEU* 1.3 74.5 - - - +
208A PRO* 1.3 73.1 - - - +
209A GLU* 3.5 17.1 + - - +
210A GLN* 2.8 41.2 + - - +
211A LEU* 2.8 23.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 208 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A LEU 4.3 2.9 - - - +
207A SER* 1.3 85.0 - - - +
209A GLU* 1.3 75.1 + - - +
211A LEU* 3.4 10.8 + - + +
212A GLY* 3.1 21.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 209 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A SER* 3.5 19.7 - - - +
208A PRO* 1.3 87.7 - - - +
210A GLN* 1.3 62.1 + - + +
212A GLY* 3.8 0.5 + - - -
213A MET* 3.3 22.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 210 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A GLN 3.7 6.3 + - - -
206A LEU* 3.4 25.3 - - + +
207A SER* 2.8 46.0 + - - +
209A GLU* 1.3 77.5 - - + +
211A LEU* 1.3 58.8 + - - +
213A MET* 3.2 9.8 + - + +
214A ILE* 2.9 36.7 + - - +
384A THR 4.9 1.6 - - - +
387A GLU* 3.9 15.9 - - - +
388A ALA* 3.7 33.9 + - + -
391A ALA* 4.2 4.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 211 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A LEU* 3.9 26.7 - - + +
207A SER 2.8 12.2 + - - +
208A PRO* 3.4 14.8 - - + +
210A GLN* 1.3 76.2 - - - +
212A GLY* 1.3 57.0 + - - +
214A ILE* 3.3 5.6 + - + +
215A GLU* 3.0 59.8 + - + +
392A TYR* 6.6 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 212 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A PRO 3.1 11.4 + - - -
209A GLU* 4.3 0.9 - - - -
211A LEU* 1.3 77.6 - - - +
213A MET* 1.3 64.8 + - - +
215A GLU* 3.5 12.6 + - - +
216A LYS* 3.2 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 213 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A GLU 3.3 18.3 + - - +
210A GLN* 3.2 10.0 + - + +
212A GLY* 1.3 79.5 - - - +
214A ILE* 1.3 64.8 + - - +
216A LYS* 3.4 7.4 + - - +
217A LEU* 3.2 29.5 + - - +
276A PRO* 4.2 24.7 - - + -
358A LEU* 4.6 2.2 - - - -
384A THR* 4.4 11.0 - - - +
385A TYR* 3.5 34.8 - - + -
388A ALA* 3.7 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 214 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A LEU* 3.9 17.9 - - + -
210A GLN 2.9 21.4 + - - +
211A LEU* 3.7 5.8 - - + +
213A MET* 1.3 79.3 - - - +
215A GLU* 1.3 64.4 + - + +
217A LEU* 3.2 8.1 + - + +
218A VAL* 3.0 23.8 + - + +
354A ALA* 3.8 30.7 - - + +
357A ALA* 6.4 0.4 - - + -
358A LEU* 3.9 34.3 - - + -
388A ALA* 3.9 22.7 - - + +
392A TYR* 4.1 17.3 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
211A LEU* 3.0 49.0 + - + +
212A GLY* 3.9 11.4 - - - +
213A MET 3.3 0.2 - - - -
214A ILE* 1.3 78.8 - - + +
216A LYS* 1.3 56.4 + - - +
218A VAL* 3.4 7.8 + - - +
219A ALA* 3.0 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 216 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A GLY 3.2 18.2 + - - +
213A MET* 3.5 9.0 - - - +
215A GLU* 1.3 72.9 - - - +
217A LEU* 1.3 55.1 + - + +
219A ALA* 3.2 7.2 + - - +
220A ALA* 2.8 35.8 + - + +
274A GLN* 3.3 40.6 + - + +
276A PRO* 4.5 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 217 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A MET* 3.2 21.1 + - - +
214A ILE* 3.2 8.0 + - + +
216A LYS* 1.3 78.1 - - + +
218A VAL* 1.3 66.4 + - - +
220A ALA* 3.0 18.2 + - + +
221A GLN* 3.3 17.0 + - - +
271A PHE* 3.6 7.6 - - + -
274A GLN* 4.8 4.9 - - + +
275A LEU* 3.7 24.9 - - + -
276A PRO* 4.3 17.5 - - + -
357A ALA* 3.8 34.8 - - + +
358A LEU* 4.1 20.0 - - + -
361A ALA* 4.1 17.3 - - + -
385A TYR* 4.3 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 218 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A ILE* 3.0 16.5 + - + +
215A GLU* 3.8 8.5 - - - +
217A LEU* 1.3 75.2 - - - +
219A ALA* 1.3 59.5 + - - +
221A GLN* 3.4 14.5 + - - +
222A GLN* 3.3 32.8 - - - +
353A ASP* 3.9 21.1 - - + +
354A ALA* 3.7 36.3 - - + +
357A ALA* 4.5 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 219 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A GLU 3.0 17.6 + - - +
216A LYS* 3.6 7.4 - - - +
218A VAL* 1.3 73.7 - - - +
220A ALA* 1.3 58.9 + - - +
222A GLN* 2.9 37.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 220 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A LYS* 2.8 14.7 + - + +
217A LEU* 3.0 13.4 + - + +
219A ALA* 1.3 75.4 - - - +
221A GLN* 1.3 56.9 + - - +
222A GLN 3.3 4.4 + - - +
271A PHE* 4.0 23.5 - - + +
274A GLN* 4.1 38.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 221 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A LEU 3.3 15.0 + - - +
218A VAL* 3.7 8.8 - - - +
219A ALA 3.2 1.0 - - - -
220A ALA* 1.3 75.9 - - - +
222A GLN* 1.3 65.7 + - + +
271A PHE* 3.5 26.6 - - + -
301A GLU* 3.5 21.8 + - - -
304A ARG* 3.0 31.2 + - - +
353A ASP* 4.6 2.4 - - - +
357A ALA* 4.2 14.6 - - - +
360A ILE* 3.7 17.8 - - - +
----------------------------------------------------------
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