Contacts of the helix formed by residues 236 - 252 (chain D) in PDB entry 1G3I
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 ASN 236 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237D PRO* 1.3 75.2 - - - +
238D GLU* 3.8 14.3 + - - +
239D GLU* 3.6 37.7 + - - +
240D LEU* 3.8 15.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 237 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112D ARG* 5.8 3.8 - - - +
236D ASN* 1.3 86.5 - - - +
238D GLU* 1.3 67.7 + - + +
239D GLU 3.3 2.2 - - - -
240D LEU* 2.8 33.5 + - + +
241D LYS* 3.0 16.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 238 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236D ASN* 3.7 11.2 + - - +
237D PRO* 1.3 78.3 - - + +
239D GLU* 1.3 63.1 + - - +
241D LYS* 3.7 16.0 + - - +
242D GLN* 3.2 20.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 239 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115D GLU* 6.1 0.9 - - - +
236D ASN* 3.6 26.5 + - - +
237D PRO 3.3 0.4 - - - -
238D GLU* 1.3 75.6 - - - +
240D LEU* 1.3 73.1 + - - +
242D GLN* 3.0 13.0 + - + +
243D LYS* 2.8 45.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 240 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108D MET* 3.4 27.3 - - + +
111D VAL* 3.4 26.4 - - + +
112D ARG* 4.0 43.3 - - - +
115D GLU* 4.3 15.9 - - + -
236D ASN 3.8 8.2 + - - +
237D PRO* 2.8 26.7 + - + +
239D GLU* 1.3 74.8 - - - +
241D LYS* 1.3 56.9 + - + +
243D LYS* 2.5 33.9 + - + +
244D ALA 3.1 8.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 241 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108D MET* 3.2 14.9 - - + +
237D PRO* 3.0 16.0 + - + +
238D GLU* 3.9 17.1 + - - +
240D LEU* 1.3 78.4 - - + +
242D GLN* 1.3 66.2 + - - +
243D LYS 2.7 1.7 + - - -
244D ALA* 2.9 2.1 + - - +
245D ILE* 2.9 27.6 + - + +
294D LYS 4.0 12.5 + - - -
295D HIS* 3.7 51.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 242 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238D GLU 3.2 12.0 + - - +
239D GLU* 3.0 19.2 + - + +
240D LEU 2.9 0.2 + - - -
241D LYS* 1.3 77.1 - - - +
243D LYS* 1.3 56.1 + - + +
245D ILE* 3.2 22.6 - - - +
246D ASP* 3.1 37.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 243 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111D VAL* 3.8 20.2 - - + -
114D GLN* 6.4 0.2 - - - +
115D GLU* 2.9 37.4 + - + +
239D GLU* 2.8 38.5 + - + +
240D LEU* 2.5 23.4 + - - +
242D GLN* 1.3 69.4 - - + +
244D ALA* 1.3 53.1 + - - +
245D ILE 2.9 1.8 - - - -
246D ASP* 2.6 17.1 + - + +
247D ALA* 2.4 36.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 244 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104D THR* 4.4 7.9 - - + +
107D ALA* 3.6 1.6 - - + +
108D MET* 3.4 56.1 - - + +
111D VAL* 3.3 15.5 - - + +
240D LEU 3.1 1.8 + - - -
241D LYS* 2.9 6.0 + - - +
243D LYS* 1.3 74.8 - - - +
245D ILE* 1.3 53.6 + - + +
247D ALA* 3.2 3.0 - - - +
248D VAL* 2.8 39.1 + - - +
295D HIS* 5.6 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 245 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104D THR* 5.0 0.9 - - - -
241D LYS* 2.9 24.0 + - + +
242D GLN* 3.2 32.1 - - - +
243D LYS 2.9 0.2 - - - -
244D ALA* 1.3 76.8 - - - +
246D ASP* 1.3 65.9 + - - +
248D VAL* 3.0 4.3 + - - +
249D GLU* 2.8 34.3 + - - +
295D HIS* 3.6 32.3 - - + +
296D GLY* 4.7 5.2 - - - -
297D MET 3.5 24.9 - - - +
298D VAL* 3.9 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 246 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242D GLN* 3.4 26.7 - - - +
243D LYS* 2.6 20.8 + - + +
245D ILE* 1.3 75.9 - - - +
247D ALA* 1.3 57.0 + - - +
248D VAL 3.0 0.3 + - - -
249D GLU* 3.1 11.4 + - - +
250D GLN* 2.6 49.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 247 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77D PRO* 3.5 23.0 - - + +
107D ALA* 3.9 9.4 - - + -
110D LEU* 6.0 1.3 - - + -
111D VAL* 3.8 14.4 - - + -
243D LYS 2.4 16.2 + - - +
244D ALA* 3.2 16.6 - - - +
246D ASP* 1.3 72.7 - - - +
248D VAL* 1.3 60.9 + - - +
250D GLN* 5.0 0.4 - - - -
251D ASN* 3.2 25.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 248 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77D PRO* 4.4 4.7 - - + -
100D ILE* 4.8 2.2 - - + -
103D LEU* 3.5 29.8 - - + -
104D THR* 3.2 45.5 - - + +
107D ALA* 3.5 11.4 - - + -
244D ALA 2.8 18.7 + - - +
245D ILE 3.6 5.2 - - - +
247D ALA* 1.3 70.4 - - - +
249D GLU* 1.3 68.6 + - - +
250D GLN 3.0 2.1 + - - -
252D GLY* 3.0 23.4 + - - +
298D VAL* 4.6 15.0 - - + -
299D LYS 5.7 0.4 - - - +
303D ILE* 3.2 15.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 249 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245D ILE* 2.8 29.3 + - - +
246D ASP* 3.7 11.7 - - - +
248D VAL* 1.3 74.6 - - - +
250D GLN* 1.3 64.3 + - + +
297D MET 3.5 6.2 - - - +
298D VAL* 3.4 14.1 - - + -
299D LYS* 3.0 65.9 + - - +
302D HIS* 3.3 33.3 + - - +
303D ILE* 4.4 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 250 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34D ARG* 3.3 26.4 + - - +
37D ARG* 3.2 33.1 + - - +
38D MET* 3.5 27.7 - - + +
45D ARG* 4.3 15.1 + - - -
46D HIS* 5.4 4.3 - - - -
246D ASP* 2.6 33.4 + - + +
247D ALA* 5.0 0.2 - - - -
248D VAL 3.0 0.8 + - - -
249D GLU* 1.3 79.8 + - + +
251D ASN* 1.3 72.2 + - - +
252D GLY 3.9 0.7 - - - -
302D HIS* 4.2 3.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 251 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31D LEU* 6.0 3.1 - - + -
34D ARG* 2.9 25.5 + - + +
38D MET* 4.6 10.0 - - - +
74D ALA* 5.3 3.7 + - + +
75D ASN 4.7 8.9 + - - -
76D ALA* 3.1 29.4 - - + +
77D PRO* 3.3 9.8 - - - +
247D ALA* 3.2 23.7 + - - +
250D GLN* 1.3 94.1 - - - +
252D GLY* 1.3 56.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 252 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34D ARG* 3.2 5.8 + - - +
77D PRO* 3.4 13.2 - - - -
103D LEU* 4.3 7.9 - - - -
248D VAL 3.0 15.6 + - - -
250D GLN 3.9 0.6 - - - -
251D ASN* 1.3 77.2 - - - +
253D ILE* 1.3 63.0 + - - -
303D ILE* 3.4 13.7 - - - +
304D LEU 2.8 27.5 + - - -
----------------------------------------------------------
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