Contacts of the helix formed by residues 155 - 169 (chain D) in PDB entry 2JIF
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 THR 155 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153D HIS 5.5 0.9 - - - +
154D GLY* 1.3 78.6 - - - +
156D GLU* 1.3 64.4 + - - +
157D GLU* 3.5 8.8 + - - +
158D GLN* 3.0 38.8 + - - +
159D LYS* 3.0 20.4 + - - +
275D ILE 5.9 0.4 - - - +
277D GLY 6.2 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 156 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111D TYR* 4.1 13.9 + - - -
154D GLY 4.7 0.7 - - - +
155D THR* 1.3 74.2 - - - +
157D GLU* 1.3 62.2 + - + +
159D LYS* 2.8 35.1 + - - +
160D ALA* 3.1 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 157 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155D THR* 3.2 8.6 + - - +
156D GLU* 1.3 78.8 - - + +
158D GLN* 1.3 61.9 + - + +
160D ALA* 3.3 6.1 + - - +
161D THR* 2.8 33.7 + - - +
1435D EDO 5.7 4.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 158 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150D ILE* 4.5 4.9 - - + -
153D HIS 4.6 0.7 - - - +
154D GLY* 3.5 12.0 - - - -
155D THR* 3.0 45.9 + - - +
157D GLU* 1.3 75.9 - - + +
159D LYS* 1.3 58.3 + - - +
161D THR* 4.5 0.4 - - - -
162D TYR* 2.9 48.0 + - + +
236D LEU* 3.6 14.3 - - + +
273D ALA 3.0 26.9 + - - -
275D ILE 3.1 18.1 + - - +
276D LEU* 3.9 7.0 - - + +
277D GLY 4.7 0.5 + - - -
1435D EDO 3.2 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 159 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111D TYR* 3.7 28.2 - - + +
150D ILE* 3.7 18.4 - - + +
151D ARG* 3.3 26.3 + - - +
152D LYS 5.6 0.4 - - - -
154D GLY 3.6 16.9 + - - -
155D THR 3.0 16.7 + - - +
156D GLU* 2.8 30.0 + - - +
158D GLN* 1.3 76.0 - - - +
160D ALA* 1.3 58.7 + - - +
163D LEU* 3.0 53.1 + - + +
164D PRO* 3.4 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 160 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111D TYR* 3.8 16.8 - - + -
156D GLU 3.1 18.5 + - - +
157D GLU* 3.3 6.9 + - - +
159D LYS* 1.3 75.7 - - - +
161D THR* 1.3 59.0 + - - +
164D PRO* 3.2 22.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 161 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157D GLU* 2.8 24.2 + - - +
158D GLN* 3.9 2.2 - - - -
160D ALA* 1.3 81.0 - - - +
162D TYR* 1.3 74.0 + - + +
164D PRO* 4.1 2.6 - - - +
165D GLN* 3.3 34.7 + - - +
1435D EDO 4.2 18.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 162 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150D ILE* 4.1 21.8 - - + -
158D GLN* 2.9 36.6 + - + +
161D THR* 1.3 85.7 - - + +
163D LEU* 1.3 60.0 + - - +
165D GLN* 3.2 12.9 + - - +
166D LEU* 2.9 32.2 + - + +
170D LYS* 5.8 5.4 - - + -
216D LEU* 3.7 38.4 - - + -
236D LEU* 3.8 17.4 + - + +
238D ASP* 4.6 9.5 + - - -
274D ASN* 3.5 16.3 + - - -
1435D EDO 3.0 45.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 163 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107D VAL* 4.2 19.1 - - + -
111D TYR* 3.6 40.8 - - + -
147D ASN* 4.1 19.3 - - - +
150D ILE* 3.9 23.1 - - + -
151D ARG* 4.1 17.9 - - + -
159D LYS* 3.0 33.5 + - + +
162D TYR* 1.3 76.4 - - - +
164D PRO* 1.3 63.7 - - + +
166D LEU* 3.2 13.8 + - + -
167D THR* 3.0 28.2 + - - +
1439D CL 4.1 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 164 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110D GLU 5.2 1.3 - - - +
111D TYR* 3.2 34.1 - - + +
159D LYS 3.4 5.8 - - - +
160D ALA 3.2 28.3 - - - +
161D THR 4.1 2.9 - - - +
162D TYR 3.7 2.5 - - - -
163D LEU* 1.3 90.1 - - + +
165D GLN* 1.3 53.5 + - + +
167D THR* 3.2 2.9 + - - -
168D THR* 2.7 38.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 165 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161D THR* 3.3 30.1 + - - +
162D TYR* 3.2 13.3 + - - +
164D PRO* 1.3 78.1 - - + +
166D LEU* 1.3 59.3 + - - +
168D THR* 3.7 5.6 - - - -
169D GLU* 3.0 26.0 + - - +
170D LYS* 2.9 70.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 166 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98D PHE* 3.3 9.9 - - - -
103D MET 3.5 8.2 - - - +
142D GLN* 2.8 28.6 + - - +
146D ILE* 3.8 19.1 - - + -
147D ASN* 3.4 21.8 - - - +
150D ILE* 3.4 33.2 - - + -
162D TYR* 2.9 27.3 + - + +
163D LEU* 3.2 11.4 + - + +
165D GLN* 1.3 76.0 - - + +
167D THR* 1.3 57.7 + - - +
168D THR 3.4 0.2 - - - -
170D LYS* 3.4 27.1 - - + +
172D GLY 4.2 7.0 - - - +
216D LEU* 4.4 11.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 167 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98D PHE* 3.6 20.8 - - - +
101D GLY* 5.5 2.3 - - - -
103D MET* 4.2 9.5 + - - +
104D GLY* 3.8 22.1 + - - -
107D VAL* 3.7 32.3 - - + -
111D TYR 3.0 18.3 + - - +
112D GLY 3.6 17.1 + - - +
113D GLY* 4.2 2.5 - - - -
147D ASN* 4.9 0.7 - - - +
163D LEU* 3.0 13.7 + - - +
164D PRO 3.2 9.0 + - - -
166D LEU* 1.3 79.5 - - + +
168D THR* 1.3 64.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 168 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98D PHE* 3.3 22.8 - - - +
112D GLY* 5.3 6.7 - - - +
164D PRO* 2.7 25.4 + - + +
165D GLN 3.2 0.5 + - - -
166D LEU 3.4 0.2 - - - -
167D THR* 1.3 87.1 - - - +
169D GLU* 1.3 94.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 169 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98D PHE* 3.5 22.9 - - - -
165D GLN* 3.0 26.1 + - - +
168D THR* 1.3 106.8 + - - +
170D LYS* 1.3 67.7 + - + +
171D VAL* 3.8 4.2 + - - +
----------------------------------------------------------
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