Contacts of the helix formed by residues 158 - 179 (chain A) in PDB entry 4B6L
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 LEU 158 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A ARG* 4.3 4.7 - - - +
156A THR* 6.1 1.1 - - - +
157A LEU* 1.3 74.8 - - - +
159A GLU* 1.3 68.0 + - - +
160A PRO* 3.3 12.8 - - + -
161A GLU* 2.8 27.4 + - + +
162A VAL* 3.1 11.7 + - - +
331A VAL* 4.6 16.2 - - + -
332A PRO* 3.7 34.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 159 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A LEU 3.9 1.0 + - - -
158A LEU* 1.3 70.1 - - - +
160A PRO* 1.4 64.2 - - + +
162A VAL* 3.3 1.7 + - - +
163A ARG* 2.9 42.2 + - - +
254A LEU* 3.9 20.2 - - + +
283A LEU* 4.6 1.9 - - - -
284A SER* 2.6 47.6 + - - -
286A PRO* 5.3 1.4 - - - +
287A ALA* 3.5 6.6 - - - +
313A PHE* 3.5 31.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 160 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A LEU* 3.5 14.1 - - + -
159A GLU* 1.4 91.9 - - + +
161A GLU* 1.3 51.6 + - + +
163A ARG* 3.6 8.2 + - + +
164A TYR* 2.8 33.4 + - - +
318A TYR* 3.4 46.9 - - + +
320A PRO* 3.4 15.1 - - + +
323A LEU* 6.2 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 161 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A ARG* 2.7 44.8 + - - -
157A LEU* 3.5 16.0 - - + +
158A LEU* 2.8 28.7 + - + +
160A PRO* 1.3 73.0 - - + +
162A VAL* 1.3 60.4 + - - +
164A TYR* 3.2 7.0 + - - +
165A TYR* 2.9 38.8 + - - -
323A LEU* 3.7 28.0 - - + +
327A SER* 3.6 15.1 + - - +
332A PRO* 3.6 17.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 162 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A LEU* 3.6 21.5 - - + +
158A LEU 3.1 12.9 + - - +
159A GLU 3.6 6.7 - - - +
161A GLU* 1.3 72.8 - - - +
163A ARG* 1.4 53.6 + - - +
165A TYR* 3.2 2.0 + - - +
166A LEU* 2.8 61.4 + - + +
250A MET* 4.2 10.3 - - + +
253A LEU* 3.7 25.9 - - + +
254A LEU* 3.6 35.4 - - + -
313A PHE* 4.2 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 163 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A GLU* 2.9 24.8 + - - +
160A PRO* 3.7 23.5 - - - +
162A VAL* 1.4 76.3 - - - +
164A TYR* 1.3 54.8 + - - +
167A ARG* 3.1 36.1 + - - +
313A PHE* 2.7 67.5 + - + +
314A PHE* 3.5 27.3 - - + +
317A GLY* 3.5 16.6 - - - -
318A TYR* 2.8 35.1 + - - +
319A THR* 3.2 20.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 164 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A PRO 2.8 21.8 + - - +
161A GLU* 3.2 8.0 + - - +
163A ARG* 1.3 73.7 - - - +
165A TYR* 1.3 72.9 + + - +
167A ARG* 4.0 3.5 - - - +
168A GLN* 3.2 47.0 + - - +
196A ASN 4.0 0.7 + - - -
197A MET* 2.6 28.9 + - + +
198A GLU* 4.9 0.3 - - - -
319A THR* 3.9 12.2 - - + +
320A PRO* 3.2 31.2 - - + -
321A ASP 3.7 5.9 + - - -
322A ARG* 3.6 27.2 - - - +
323A LEU* 3.4 42.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 165 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A LEU* 3.9 28.5 - - + -
150A ILE* 4.1 9.9 - - + +
157A LEU* 3.6 29.8 - - + -
161A GLU* 2.9 28.7 + - + +
162A VAL 3.9 2.5 - - - +
164A TYR* 1.3 90.0 - + - +
166A LEU* 1.4 60.2 - - - +
168A GLN* 3.1 12.2 + - - +
169A ILE* 2.9 34.4 + - + +
193A ILE* 3.8 19.7 - - + -
197A MET* 3.2 34.1 - - - +
199A LEU* 3.9 17.2 - - + +
253A LEU* 4.8 3.8 - - + -
323A LEU* 3.6 22.7 - - + +
327A SER* 4.3 2.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 166 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A VAL* 2.8 32.2 + - + +
165A TYR* 1.4 71.5 - - - +
167A ARG* 1.4 51.5 + - - +
169A ILE* 3.3 18.4 + - + +
170A LEU* 2.8 46.1 + - + +
246A LEU* 4.4 11.9 - - + +
249A VAL* 4.3 12.8 - - + -
250A MET* 3.7 47.8 - - + +
253A LEU* 5.1 2.0 - - + -
290A LEU* 5.0 0.2 - - + -
313A PHE* 3.7 20.6 - - + -
314A PHE* 3.5 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 167 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A ARG 3.1 17.4 + - - +
164A TYR 4.0 6.1 - - - +
166A LEU* 1.4 73.7 - - - +
168A GLN* 1.3 54.5 + - + +
170A LEU* 3.4 2.6 + - - +
171A SER* 2.8 34.5 + - - -
309A LEU* 4.2 24.6 + - + +
314A PHE* 2.8 58.3 + - + +
315A THR* 5.1 0.4 - - - +
317A GLY 5.0 0.6 + - - -
319A THR* 3.0 40.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 168 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A HIS* 3.1 49.8 - - + +
164A TYR* 3.2 55.8 + - - +
165A TYR* 3.1 12.2 + - - +
167A ARG* 1.3 74.4 - - + +
169A ILE* 1.4 59.3 + - - +
171A SER 3.3 0.5 + - - -
172A GLY* 2.9 23.9 + - - -
197A MET 3.8 3.2 + - - -
198A GLU* 3.4 6.0 - - - +
199A LEU* 2.6 39.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 169 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A LEU* 4.5 2.2 - - + -
165A TYR* 2.9 32.2 + - + +
166A LEU* 3.6 13.7 - - + +
168A GLN* 1.4 73.6 - - - +
170A LEU* 1.4 53.5 + - - +
172A GLY* 3.2 2.3 + - - -
173A LEU* 2.8 33.2 + - + +
186A LEU* 4.9 2.5 - - + -
191A PHE* 3.8 35.0 - - + -
199A LEU* 3.5 30.5 - - + -
201A VAL* 4.1 5.7 - - + +
246A LEU* 3.2 37.9 - - + -
249A VAL* 4.0 14.4 - - + -
253A LEU* 5.2 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 170 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A LEU* 2.8 29.7 + - + +
167A ARG 3.7 3.6 - - - +
169A ILE* 1.4 67.6 - - - +
171A SER* 1.3 60.3 + - - +
173A LEU* 4.0 3.5 - - - -
174A LYS* 2.9 31.7 + - - +
246A LEU* 3.7 24.5 - - + -
305A ILE* 3.6 38.1 - - + +
308A ILE* 3.7 39.5 - - + -
309A LEU* 3.7 18.8 - - + -
314A PHE* 3.7 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 171 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A HIS* 3.0 29.6 + - - -
120A ARG* 3.5 13.2 + - - -
121A HIS* 3.3 20.1 - - - -
167A ARG 2.8 17.9 + - - -
168A GLN* 3.6 0.4 - - - -
170A LEU* 1.3 76.6 - - - +
172A GLY* 1.3 61.8 + - - +
174A LYS* 3.6 8.6 - - - +
175A TYR* 3.2 17.7 + - - +
309A LEU* 5.4 2.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 172 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A HIS* 4.1 4.5 - - - -
121A HIS* 3.7 25.2 - - - +
122A ILE* 3.5 14.2 - - - +
168A GLN 2.9 13.5 + - - -
169A ILE 3.5 3.4 - - - -
171A SER* 1.3 75.1 + - - +
173A LEU* 1.3 61.2 + - - +
175A TYR* 3.2 7.3 + - - +
176A LEU* 3.1 23.1 + - - +
201A VAL* 4.4 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 173 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A ILE* 2.8 21.6 + - + +
170A LEU* 4.0 2.9 - - - +
172A GLY* 1.3 70.5 - - - +
174A LYS* 1.4 54.3 + - - +
176A LEU* 3.1 21.9 + - + +
177A HIS* 2.8 48.1 + - + +
183A HIS* 4.2 1.1 - - + -
186A LEU* 3.5 27.8 - - + -
201A VAL* 4.7 2.4 - - + +
242A ASP* 3.6 36.8 - - + +
243A VAL* 4.5 2.5 - - + +
246A LEU* 3.7 26.9 - - + -
305A ILE* 3.8 19.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 174 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A LEU 2.9 22.0 + - - +
171A SER* 3.6 9.0 - - - +
173A LEU* 1.4 69.7 - - - +
175A TYR* 1.3 52.8 + - - +
177A HIS* 3.2 4.0 + - - +
178A GLN* 2.8 65.9 + - + +
305A ILE* 3.6 24.9 - - + +
306A ASP* 3.4 28.1 + - - +
309A LEU* 5.5 6.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 175 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A ASP 3.8 4.2 + - - -
117A LEU* 3.5 33.1 - - + +
118A GLN* 2.8 43.1 + - - +
119A HIS* 3.5 42.0 - + + +
122A ILE* 3.9 10.1 - - + -
171A SER 3.2 7.5 + - - +
172A GLY 3.2 7.6 + - - +
174A LYS* 1.3 76.4 - - - +
176A LEU* 1.4 66.9 + - + +
178A GLN* 3.4 15.8 + - - +
179A ARG* 3.1 53.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 176 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A LEU* 3.7 19.1 - - + -
122A ILE* 3.7 21.3 - - + -
172A GLY 3.1 14.5 + - - +
173A LEU* 3.1 18.5 + - + +
175A TYR* 1.4 82.5 - - + +
177A HIS* 1.3 59.0 + - - +
179A ARG* 3.0 20.7 + - - +
181A ILE* 3.0 35.8 + - + +
183A HIS* 3.9 28.7 - - + +
201A VAL* 4.6 2.7 - - + -
204A PHE* 3.6 35.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 177 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A LEU* 2.8 32.9 + - + +
174A LYS* 3.7 5.2 - - - +
176A LEU* 1.3 74.2 - - - +
178A GLN* 1.3 57.1 + - + +
180A GLY* 3.0 19.6 + - - -
181A ILE 3.3 13.1 + - - +
182A LEU* 3.7 15.3 - - + +
210A LEU* 4.6 9.1 - - + +
239A PRO* 3.5 26.1 + - + +
242A ASP* 2.8 35.7 + - - +
305A ILE* 3.7 11.2 - - + -
1334A SO4 2.9 39.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 178 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A LYS* 2.8 54.6 + - + +
175A TYR* 3.6 19.8 - - + +
176A LEU 3.3 0.2 - - - -
177A HIS* 1.3 70.6 - - + +
179A ARG* 1.3 62.1 + - + +
180A GLY 3.3 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 179 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A ASP* 2.8 40.0 + - - -
117A LEU* 4.8 3.2 - - + +
175A TYR* 3.1 47.2 + - + +
176A LEU* 3.0 11.7 + - - +
178A GLN* 1.3 78.7 - - + +
180A GLY* 1.3 60.7 + - - +
181A ILE* 3.3 23.5 + - + +
----------------------------------------------------------
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