Contacts of the helix formed by residues 141 - 153 (chain D) in PDB entry 2IBS
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 141 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108D TYR* 3.6 1.4 - - - +
109D GLY* 2.7 45.0 + - - +
110D ILE* 3.9 5.0 - - - +
111D VAL* 5.6 1.1 - - - +
136D TRP* 4.6 5.0 - - - -
140D TYR* 1.3 87.9 + - - +
142D LEU* 1.3 74.3 + - - +
143D TYR* 3.2 33.2 + - + -
144D GLY 3.4 2.1 + - - -
145D ALA* 3.3 17.3 + - - +
165D PRO* 6.0 0.2 - - - +
174D PHE* 3.7 21.3 - - + -
5E G 4.1 22.8 + - - -
6E 2PR 4.4 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 142 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91D LEU* 4.3 17.0 - - + -
107D PRO* 3.4 38.4 - - + +
109D GLY 3.0 9.5 + - - +
111D VAL* 3.7 28.3 - - + -
119D ILE* 3.8 38.1 - - + -
129D TYR* 4.4 10.1 - - + +
136D TRP* 5.1 2.5 - - + -
141D ASN* 1.3 79.3 + - - +
143D TYR* 1.3 55.6 + - - +
145D ALA* 3.2 5.0 + - + +
146D PHE* 2.8 41.0 + - + -
1002D NEA 5.1 7.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 143 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106D PRO* 4.3 3.5 - - + +
107D PRO 3.4 4.2 + - - +
108D TYR* 3.7 24.0 - + + -
141D ASN* 3.2 37.3 + - + -
142D LEU* 1.3 78.9 - - - +
144D GLY* 1.3 56.8 + - - +
146D PHE* 3.8 7.8 - - - +
147D LEU* 3.0 39.1 + - + +
164D VAL* 3.7 25.1 - - + +
165D PRO* 3.7 30.4 + - + -
167D THR* 2.6 26.3 + - - -
168D TRP* 3.2 39.9 + + + +
174D PHE* 3.3 21.6 - + - -
5E G 4.9 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 144 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140D TYR* 3.4 27.5 + - - -
141D ASN* 3.4 7.9 + - - +
142D LEU 3.2 0.6 - - - -
143D TYR* 1.3 83.2 - - - +
145D ALA* 1.3 58.5 + - - +
147D LEU* 3.4 3.6 + - - +
148D GLU* 3.2 24.4 + - - +
174D PHE* 4.2 4.5 - - - -
177D LEU* 3.8 18.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 145 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91D LEU* 3.5 12.5 - - + +
133D PHE* 3.5 38.3 - - + -
136D TRP* 3.9 16.2 - - + -
140D TYR* 3.6 5.2 - - - -
141D ASN 3.3 11.6 + - - +
142D LEU* 3.2 9.3 + - - +
144D GLY* 1.3 75.1 - - - +
146D PHE* 1.3 59.7 + - - +
148D GLU* 3.6 1.0 + - - +
149D LYS* 3.1 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 146 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46D PRO* 3.8 18.8 - - + -
47D ALA* 4.1 7.2 - - + -
90D PHE* 3.5 32.5 - + + -
91D LEU* 3.5 28.5 - - + -
106D PRO* 3.8 27.1 - - + -
107D PRO* 3.6 34.3 - - + -
142D LEU* 2.8 30.0 + - + +
143D TYR 3.8 3.1 - - - +
145D ALA* 1.3 76.5 - - - +
147D LEU* 1.3 57.1 + - - +
149D LYS* 3.6 2.3 + - - +
150D ALA* 3.1 30.3 + - - +
162D PHE* 3.7 7.6 - + + -
1002D NEA 3.7 31.0 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 147 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143D TYR* 3.0 38.0 + - + +
144D GLY 3.5 6.3 - - - +
145D ALA 3.3 0.4 - - - -
146D PHE* 1.3 76.8 - - - +
148D GLU* 1.3 61.4 + - - +
150D ALA* 3.3 3.9 + - - +
151D VAL* 3.1 28.3 + - - +
160D LEU* 4.0 15.2 - - + +
162D PHE* 3.8 24.0 - - + -
164D VAL* 4.6 10.3 - - + -
168D TRP* 5.1 4.9 - - + -
177D LEU* 3.8 30.3 - - + -
181D LEU* 5.2 6.1 - - + -
206D ILE* 3.9 35.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 148 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132D ALA 3.9 0.5 - - - +
133D PHE* 3.2 24.4 - - + +
134D SER 3.0 14.7 + - - -
135D THR* 2.5 48.8 + - + +
144D GLY 3.2 8.6 + - - +
145D ALA 4.2 2.9 - - - +
146D PHE 3.5 0.2 - - - -
147D LEU* 1.3 76.2 - - - +
149D LYS* 1.3 64.8 + - - +
151D VAL* 3.4 2.6 + - - +
152D ARG* 2.8 59.9 + - - +
177D LEU* 4.4 2.8 - - + +
180D PHE* 3.7 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 149 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90D PHE* 3.4 43.7 - - + +
91D LEU* 3.8 19.3 + - + +
92D LEU* 4.6 1.0 - - - +
93D TRP 2.8 30.3 + - - +
94D GLU* 3.7 21.8 + - - -
133D PHE* 3.6 16.5 - - + -
145D ALA 3.1 19.7 + - - +
146D PHE 3.9 0.4 - - - +
148D GLU* 1.3 77.2 - - - +
150D ALA* 1.3 55.8 + - - +
152D ARG* 3.2 11.0 + - + +
153D LEU* 3.0 52.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 150 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90D PHE* 4.2 7.2 - - + -
102D ILE* 3.3 36.3 - - + +
146D PHE 3.1 18.2 + - - +
147D LEU 3.7 0.4 - - - +
148D GLU 3.3 0.2 - - - -
149D LYS* 1.3 75.1 - - - +
151D VAL* 1.3 63.7 + - - +
153D LEU* 3.5 0.6 + - - -
154D LEU* 3.4 13.3 + - - +
160D LEU* 3.6 22.4 - - + -
162D PHE* 3.9 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 151 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147D LEU 3.1 15.1 + - - +
148D GLU 3.7 7.4 - - - +
149D LYS 3.3 0.2 - - - -
150D ALA* 1.3 75.8 - - - +
152D ARG* 1.3 54.0 + - - +
154D LEU* 3.2 17.0 - - - +
160D LEU* 3.9 15.0 - - + -
180D PHE* 3.7 25.8 - - + -
181D LEU* 3.9 25.1 - - + -
184D GLU* 4.1 9.9 - - + +
208D PHE* 3.7 28.5 - - + -
210D LYS* 2.7 34.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 152 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98D ALA* 5.3 1.7 - - - +
132D ALA 4.6 8.7 + - - -
133D PHE* 5.6 2.0 - - - -
134D SER* 3.0 21.4 + - - +
148D GLU* 2.8 46.7 + - - +
149D LYS* 3.7 12.1 - - + +
151D VAL* 1.3 76.6 - - + +
153D LEU* 1.3 61.7 + - + +
154D LEU 3.2 4.6 + - - +
180D PHE* 3.5 25.7 - - + -
210D LYS* 3.9 11.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 153 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44D LEU* 4.5 2.0 - - + -
90D PHE* 3.7 34.3 - - + -
93D TRP* 3.7 19.5 - - + -
94D GLU* 4.6 4.9 - - - +
95D PRO* 3.6 27.1 - - + -
98D ALA* 3.3 10.4 - - - +
99D PHE* 2.8 32.9 + - + +
102D ILE* 4.1 8.1 - - + -
149D LYS* 3.0 43.2 + - + +
150D ALA 3.8 5.6 - - - +
151D VAL 3.3 0.4 - - - -
152D ARG* 1.3 79.1 - - + +
154D LEU* 1.3 57.6 + - - +
----------------------------------------------------------
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