Contacts of the helix formed by residues 296 - 307 (chain H) in PDB entry 1I43
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 296 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268F ASP 5.3 1.0 + - - -
269F VAL* 4.1 15.4 - - - +
270F LEU 5.1 2.8 + - - +
296F ASN* 3.9 26.6 - - + +
298F ASN* 4.4 1.7 - - - +
299F ALA* 3.9 23.7 + - + +
302F LEU* 5.5 1.0 - - - +
83H ASN* 4.8 3.4 + - - -
294H ALA 4.1 2.4 + - - -
295H LEU* 1.3 76.4 - - - +
297H PRO* 1.3 74.2 - - - +
298H ASN* 3.2 37.1 + - - +
299H ALA* 2.9 22.4 + - + +
300H ALA* 3.0 10.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 297 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268F ASP 6.1 0.4 - - - +
81H VAL* 4.0 13.5 - - + +
82H VAL 3.2 13.7 - - - +
83H ASN* 4.3 8.5 - - - +
84H THR 5.3 2.2 - - - +
113H ASN* 3.1 27.6 - - + +
115H THR* 3.3 28.3 + - + -
116H THR* 4.5 2.0 - - - +
295H LEU 3.6 3.6 - - - +
296H ASN* 1.3 98.1 - - - +
298H ASN* 1.3 63.9 + - - +
300H ALA* 3.3 7.1 + - + +
301H TYR* 3.0 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 298 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298F ASN* 3.7 36.8 - - + +
302F LEU* 4.5 9.9 - - - +
298G ASN* 5.5 2.9 - - - +
81H VAL* 3.6 18.1 - - - +
83H ASN* 3.4 25.0 + - - +
296H ASN* 3.2 19.9 + - - +
297H PRO* 1.3 77.2 - - - +
299H ALA* 1.3 62.1 + - - +
301H TYR* 3.4 5.5 + - - +
302H LEU* 3.2 27.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 299 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296F ASN* 3.9 19.4 + - + +
269H VAL* 3.5 26.3 - - + +
270H LEU 4.7 0.9 - - - +
295H LEU* 4.0 16.4 - - + -
296H ASN* 2.9 15.8 + - + +
298H ASN* 1.3 77.0 - - - +
300H ALA* 1.3 65.8 + - - +
302H LEU* 3.1 17.5 + - - +
303H ILE* 3.1 18.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 300 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115H THR 3.8 13.2 - - - +
116H THR* 3.8 21.3 - - - +
119H LEU* 3.8 10.8 - - + +
295H LEU* 3.7 25.2 - - + +
296H ASN 3.0 7.4 + - - +
297H PRO 3.6 8.7 - - - +
299H ALA* 1.3 77.3 - - - +
301H TYR* 1.3 56.7 + - - +
303H ILE* 3.3 4.6 + - - +
304H ILE* 3.0 32.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 301 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266E HIS* 5.6 0.2 - - - +
268E ASP* 2.7 40.3 + - - +
302E LEU* 4.9 9.0 - - + -
83G ASN* 4.0 18.6 + - + -
78H THR* 4.1 14.1 - - - +
79H THR* 3.5 35.2 - - + -
81H VAL* 3.8 22.7 - - + -
115H THR* 4.5 6.0 + - - +
297H PRO 3.0 13.3 + - - +
298H ASN* 3.7 7.4 - - - +
299H ALA 3.2 0.2 - - - -
300H ALA* 1.3 72.2 - - - +
302H LEU* 1.3 71.5 + - + +
303H ILE 3.1 1.6 - - - -
304H ILE* 3.1 15.8 + - + +
305H ARG* 2.9 45.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 302 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301E TYR* 4.9 8.7 - - + -
302E LEU* 5.1 11.0 - - + -
305E ARG* 2.7 54.5 + - - +
83F ASN* 4.5 15.5 - - - +
296F ASN* 5.6 1.1 - - - +
298F ASN* 4.6 9.9 - - - +
268H ASP* 4.1 29.2 - - - +
269H VAL* 4.1 13.9 - - + -
298H ASN 3.2 15.8 + - - +
299H ALA* 3.1 10.7 + - - +
301H TYR* 1.3 88.6 - - + +
303H ILE* 1.3 57.1 + - - +
305H ARG* 4.5 1.6 - - - -
306H GLY* 3.0 8.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 303 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119H LEU* 3.4 34.5 - - + -
123H ILE* 5.4 1.6 - - + -
134H LEU* 4.7 0.4 - - + -
259H ALA* 3.9 15.5 - - + +
263H LEU* 4.3 9.4 - - + +
264H GLY* 4.5 9.6 - - - -
269H VAL* 4.1 18.8 - - + -
271H ALA* 3.3 34.1 - - + -
295H LEU* 4.8 1.8 - - + -
299H ALA 3.1 16.9 + - - +
300H ALA* 3.6 6.7 - - - +
301H TYR 3.1 0.4 - - - -
302H LEU* 1.3 75.8 - - - +
304H ILE* 1.3 59.4 + - - +
305H ARG 3.1 1.3 - - - -
306H GLY* 3.6 0.7 - - - +
307H MET* 2.8 42.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 304 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66H GLU* 3.9 27.4 - - - +
79H THR* 4.4 15.7 - - + +
115H THR 3.5 24.0 - - - +
118H VAL* 3.9 21.1 - - + -
119H LEU* 3.7 27.6 - - + +
122H LYS* 4.0 8.1 + - + +
300H ALA 3.0 20.3 + - - +
301H TYR* 3.1 17.9 + - + +
303H ILE* 1.3 77.7 - - - +
305H ARG* 1.3 62.6 - - - +
307H MET* 3.6 8.7 + - - +
308H LYS* 3.4 20.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 305 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264E GLY 4.0 5.7 + - - -
266E HIS* 3.6 45.8 + - + +
268E ASP* 2.7 43.1 + - - +
269E VAL* 4.4 4.0 - - - +
302E LEU* 2.8 47.4 + - - +
305E ARG* 3.9 23.5 - - - +
306E GLY* 3.4 19.0 - - - +
301H TYR* 2.9 34.4 + - + +
302H LEU* 3.8 6.1 - - - +
304H ILE* 1.3 77.3 - - - +
306H GLY* 1.3 64.8 + - - +
308H LYS* 3.0 26.4 + - + +
309H THR 4.3 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 306 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305E ARG* 3.5 7.8 - - - +
263H LEU 3.9 2.0 - - - -
264H GLY 3.6 17.9 - - - -
266H HIS* 4.0 8.3 - - - -
302H LEU 3.0 16.2 + - - -
303H ILE 3.1 3.8 + - - -
305H ARG* 1.3 77.2 - - - +
307H MET* 1.3 55.5 + - - +
308H LYS 3.5 0.7 + - - -
309H THR* 3.5 5.9 + - - -
313H ARG* 2.7 34.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 307 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61H ALA* 3.5 21.2 - - + +
119H LEU* 3.7 27.8 - - - -
122H LYS* 4.1 19.7 - - + -
123H ILE* 4.0 20.4 - - + -
126H LEU* 3.7 30.3 - - + -
263H LEU* 3.2 37.7 - - + +
303H ILE* 2.8 16.9 + - - +
304H ILE 3.9 6.1 - - - +
305H ARG 3.1 0.4 - - - -
306H GLY* 1.3 74.4 - - - +
308H LYS* 1.3 60.9 + - - +
309H THR 2.9 7.5 + - - -
310H LEU* 3.1 19.9 + - + +
313H ARG* 4.1 3.1 - - - +
----------------------------------------------------------
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