Contacts of the helix formed by residues 149 - 168 (chain B) in PDB entry 3IFS
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 149 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A HIS* 3.7 22.2 - - + +
82B ILE* 3.9 2.2 - - + -
144B SER* 3.8 2.1 + - - -
146B SER* 4.2 5.0 - - - -
147B GLY 3.9 1.4 - - - -
148B THR* 1.3 72.6 + - - +
150B THR* 1.3 68.4 + - - +
151B GLU* 3.6 16.6 - - - +
152B PRO* 3.4 15.9 - - + +
153B ALA* 3.1 23.7 + - - +
426B LYS* 5.3 11.7 + - - +
452B SO4 2.7 40.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 150 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A LEU* 4.9 14.5 - - + +
354A LEU* 5.7 3.4 - - + -
362A VAL* 4.3 23.6 - - + -
121B ILE* 5.2 1.6 - - + -
148B THR 3.3 5.7 + - - -
149B THR* 1.3 73.7 - - - +
151B GLU* 1.3 67.9 + - + +
153B ALA* 3.4 4.2 + - - +
154B LEU* 2.9 34.8 + - + +
429B MSE 3.6 30.2 - - + +
430B PHE* 3.6 15.8 - - - -
433B LEU* 5.2 6.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 151 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A SER* 2.7 26.0 + - - +
312A HIS* 3.0 30.0 + - - -
82B ILE* 3.5 7.0 - - + +
118B GLY* 3.3 14.8 - - - +
120B ASN 3.8 12.4 - - - +
121B ILE* 3.4 32.9 - - + +
126B MSE 5.2 1.2 - - - +
149B THR* 3.6 13.3 - - - +
150B THR* 1.3 79.7 + - - +
152B PRO* 1.3 69.1 - - + +
154B LEU* 3.8 5.1 - - - +
155B ALA* 3.1 24.8 + - - +
425B TYR* 4.5 5.4 + - - -
429B MSE 5.7 4.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 152 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B VAL* 3.5 15.8 - - + +
81B GLY* 4.1 18.8 - - - -
82B ILE* 3.9 13.7 - - + +
118B GLY* 3.3 13.2 - - - +
142B VAL* 4.9 4.4 - - + +
143B ILE 4.7 6.3 - - - +
144B SER* 5.1 5.4 - - - -
149B THR* 3.4 33.0 - - + +
151B GLU* 1.3 95.2 - - + +
153B ALA* 1.3 57.3 + - - +
156B PHE* 2.8 33.0 + - - +
452B SO4 4.5 4.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 153 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A ASP* 4.4 16.5 - - + +
351A LEU* 3.6 19.9 - - + +
147B GLY 5.7 2.2 - - - +
148B THR* 4.9 7.9 - - - +
149B THR 3.1 22.9 + - - +
150B THR* 3.8 4.3 - - - +
151B GLU 3.3 0.2 - - - -
152B PRO* 1.3 75.9 - - - +
154B LEU* 1.3 61.7 + - - +
156B PHE* 3.4 6.5 + - - +
157B ARG* 3.1 23.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 154 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A ILE* 3.8 43.5 - - + -
351A LEU* 3.6 16.1 - - + +
354A LEU* 6.1 1.8 - - + -
359A VAL* 4.2 14.4 - - + -
362A VAL* 4.5 12.1 - - + -
121B ILE* 4.1 24.9 - - + -
126B MSE 5.1 4.9 - - + -
150B THR* 2.9 22.2 + - + +
151B GLU* 3.8 5.4 - - - +
153B ALA* 1.3 74.1 - - - +
155B ALA* 1.3 64.6 + - - +
157B ARG* 3.4 5.5 + - - +
158B ILE* 3.2 37.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 155 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B VAL* 4.2 6.7 - - + -
117B VAL* 4.3 13.5 - - + -
118B GLY* 3.4 37.0 - - - +
126B MSE 4.4 14.6 - - + -
151B GLU 3.1 8.9 + - - +
152B PRO 4.0 2.2 - - - +
154B LEU* 1.3 77.9 - - - +
156B PHE* 1.3 57.4 + - - +
158B ILE* 3.3 5.2 + - - -
159B PHE* 2.9 36.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 156 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A ASP* 6.1 0.2 - - - -
80B VAL* 4.0 7.1 - - + +
140B ILE* 4.1 18.8 - - + -
142B VAL* 3.7 39.5 - - + -
152B PRO 2.8 20.4 + - - +
153B ALA* 3.8 6.5 - - - +
155B ALA* 1.3 74.5 - - - +
157B ARG* 1.3 58.6 + - - +
159B PHE* 5.1 0.4 - - - -
160B ARG* 2.8 72.1 + - + +
176B ILE* 4.0 17.7 - - + -
187B LEU* 4.2 12.6 - - + -
190B LEU* 3.8 26.0 - - + -
196B TYR* 3.8 20.0 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 157 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A ILE* 4.4 14.6 - - - +
342A GLU* 2.9 28.9 + - + +
343A SER* 3.7 0.6 - - - +
344A GLU* 3.3 42.6 - - + +
347A ASP* 3.2 18.2 + - - +
349A ASP* 2.4 46.4 + - - +
351A LEU* 3.6 21.9 + - - +
352A ASN* 2.9 24.4 + - - +
355A ALA* 5.6 0.2 - - - +
153B ALA 3.1 15.9 + - - +
154B LEU* 3.6 8.1 - - - +
155B ALA 3.4 0.2 - - - -
156B PHE* 1.3 78.7 - - - +
158B ILE* 1.3 63.4 + - + +
160B ARG* 3.9 9.1 + - - +
161B LYS* 3.3 21.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 158 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A LEU* 4.4 9.9 - - + -
340A THR 5.8 4.5 - - - +
341A ILE* 5.6 4.3 - - + -
359A VAL* 3.8 28.5 - - + -
126B MSE 4.0 16.4 - - - -
130B MSE 3.6 31.2 - - + -
154B LEU* 3.2 22.7 + - + +
155B ALA 3.7 6.5 - - - +
156B PHE 3.2 0.2 - - - -
157B ARG* 1.3 80.7 - - + +
159B PHE* 1.3 72.3 + - + +
161B LYS* 3.5 7.1 + - - +
162B LEU* 3.3 21.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 159 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B LEU* 3.6 30.1 - - + -
117B VAL* 3.8 29.6 - - + -
126B MSE 3.7 33.7 - - + -
129B LEU* 4.3 8.7 - - + -
130B MSE 3.9 19.5 - - + -
133B LEU* 3.7 26.0 - - + -
138B PHE* 4.7 2.5 - + + -
140B ILE* 3.7 11.4 - - + +
155B ALA 2.9 26.7 + - - +
156B PHE* 4.5 1.8 - - - +
158B ILE* 1.3 84.0 - - + +
160B ARG* 1.3 60.0 + - - +
161B LYS 3.2 0.2 - - - -
162B LEU* 3.3 11.6 + - + +
163B LEU* 2.9 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 160 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A GLU* 3.4 39.7 + - - +
349A ASP* 5.8 1.2 + - - -
140B ILE* 4.0 11.0 - - - +
156B PHE* 2.8 50.8 + - + +
157B ARG* 3.9 5.5 + - - +
159B PHE* 1.3 71.8 - - - +
161B LYS* 1.3 57.3 + - - +
163B LEU* 3.2 5.2 + - - +
164B GLU* 2.9 60.0 + - - +
169B LYS* 3.9 2.0 - - - +
176B ILE* 4.1 9.2 - - + -
190B LEU* 4.3 18.0 - - - +
194B GLU* 2.8 34.1 + - - +
196B TYR* 3.0 19.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 161 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A GLU* 4.8 22.0 - - + +
344A GLU* 5.2 8.1 - - - +
157B ARG 3.3 16.9 + - - +
158B ILE* 3.6 7.0 - - - +
160B ARG* 1.3 80.3 - - - +
162B LEU* 1.3 57.2 + - - +
164B GLU* 3.2 12.1 + - + +
165B GLU* 2.3 80.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 162 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B MSE 3.6 47.3 - - + -
133B LEU* 4.8 5.4 - - + -
138B PHE* 4.6 9.3 - - + -
158B ILE 3.3 10.4 + - - +
159B PHE* 3.3 27.9 + - + +
161B LYS* 1.3 79.5 - - - +
163B LEU* 1.3 61.7 + - - +
165B GLU* 3.3 21.4 + - - +
166B LYS* 3.1 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 163 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B PHE* 3.6 40.6 - - + +
140B ILE* 4.0 8.5 - - + -
159B PHE 2.9 13.6 + - - +
160B ARG 3.5 7.9 - - - +
162B LEU* 1.3 75.3 - - - +
164B GLU* 1.3 59.4 + - - +
166B LYS* 3.2 2.2 + - - -
167B TYR* 2.9 65.5 + - + +
172B ALA* 3.7 19.3 - - + +
175B ARG* 4.1 9.9 - - + +
176B ILE* 3.3 39.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 164 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B ARG* 2.9 49.9 + - + +
161B LYS* 3.6 11.7 - - + +
163B LEU* 1.3 76.8 - - - +
165B GLU* 1.3 58.9 + - - +
168B GLY* 2.8 33.8 + - - +
169B LYS* 3.0 44.8 + - + +
172B ALA* 4.0 21.1 - - + -
176B ILE* 5.6 1.0 - - + +
196B TYR* 4.4 2.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 165 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B LYS* 2.3 64.3 + - + +
162B LEU* 3.3 32.8 + - + +
164B GLU* 1.3 72.6 - - + +
166B LYS* 1.3 59.8 + - - +
168B GLY 4.7 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 166 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B LEU 5.5 0.4 - - - -
135B GLY* 5.3 5.8 - - - +
136B LYS 3.2 30.9 + - - +
137B ASP* 3.7 18.8 + - - -
138B PHE* 4.2 12.3 - - + -
162B LEU 3.1 12.6 + - - +
163B LEU* 3.6 7.2 - - - +
165B GLU* 1.3 79.8 - - - +
167B TYR* 1.3 87.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 167 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B ASP* 2.5 49.4 + - - +
138B PHE* 3.2 7.0 + + - -
163B LEU* 2.9 46.7 + - + +
166B LYS* 1.3 104.1 + - + +
168B GLY* 1.3 67.8 + - - +
171B GLU* 3.7 30.5 + - + +
172B ALA 3.9 4.3 - - - +
175B ARG* 3.5 30.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 168 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B GLU* 2.8 23.4 + - - -
165B GLU 4.7 0.6 + - - -
166B LYS 3.8 0.8 - - - -
167B TYR* 1.3 77.6 - - - +
169B LYS* 1.3 65.4 + - - -
170B GLU 3.6 1.3 - - - -
172B ALA* 3.1 20.1 + - - +
453B SO4 3.2 19.7 - - - -
----------------------------------------------------------
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