Contacts of the helix formed by residues 151 - 171 (chain B) in PDB entry 5I3R
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 151 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145B LYS* 6.0 1.1 - - - -
149B GLY 5.3 1.8 - - - +
150B PHE* 1.3 77.1 - - - +
152B GLU* 1.3 65.4 + - - +
153B PRO* 3.1 19.7 - - - +
154B GLU* 3.0 32.6 + - - +
155B VAL* 3.0 20.1 + - - +
285B ARG* 4.1 24.2 - - - +
286B TYR* 4.1 0.7 - - - -
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Residues in contact with GLU 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B THR* 1.3 71.2 - - - +
153B PRO* 1.4 72.8 - - + +
155B VAL* 3.2 4.3 + - + +
156B LEU* 2.9 33.3 + - + +
285B ARG* 5.0 5.7 - - + +
286B TYR* 3.6 29.6 - - + -
287B SER* 2.8 46.7 + - - -
290B ILE* 3.6 17.5 - - + +
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Residues in contact with PRO 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B THR* 3.1 16.4 - - - +
152B GLU* 1.4 90.2 - - + +
154B GLU* 1.3 61.0 + - + +
156B LEU* 3.4 8.1 + - + +
157B GLN* 3.0 31.2 + - + +
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Residues in contact with GLU 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B LYS* 3.4 25.2 + - - -
150B PHE* 3.3 29.2 - - + -
151B THR* 3.0 42.7 + - - +
153B PRO* 1.3 79.1 - - - +
155B VAL* 1.3 62.6 + - - +
157B GLN* 3.2 13.9 + - - +
158B ILE* 3.0 33.2 + - + +
194B TYR* 5.0 6.9 - - - +
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Residues in contact with VAL 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B PHE* 3.6 18.8 - - + -
151B THR 3.0 18.5 + - - +
152B GLU* 3.6 8.7 - - + +
154B GLU* 1.3 75.5 - - - +
156B LEU* 1.4 56.2 + - - +
158B ILE* 3.4 8.2 + - - +
159B PHE* 2.9 28.2 + - - +
256B LEU* 3.5 28.7 - - + -
259B LEU* 4.1 20.4 - - + +
260B CYS* 3.9 12.8 - - - -
286B TYR* 3.7 21.1 - - + +
290B ILE* 5.3 7.6 - - + -
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Residues in contact with LEU 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B GLU* 2.9 31.0 + - - +
153B PRO* 3.8 7.0 - - + +
155B VAL* 1.4 73.2 - - + +
157B GLN* 1.3 60.9 + - + +
159B PHE* 4.5 6.7 - - + -
160B CYS* 2.9 38.2 + - - +
256B LEU* 6.0 0.9 - - + -
290B ILE* 3.7 28.7 - - + -
293B LEU* 5.3 3.1 - - + -
315B ALA* 3.9 24.7 - - + +
318B PHE* 3.6 37.0 - - + +
319B ALA* 4.0 12.8 - - + +
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Residues in contact with GLN 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B PRO* 3.0 20.0 + - + +
154B GLU* 3.2 16.4 + - - +
156B LEU* 1.3 75.4 - - + +
158B ILE* 1.4 61.1 + - - +
160B CYS* 4.2 1.6 - - - +
161B ASP* 3.2 33.1 + - - +
192B GLY 6.0 1.8 - - - -
194B TYR* 4.1 22.0 + - + -
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Residues in contact with ILE 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138B VAL* 4.1 18.6 - - + -
150B PHE* 3.7 37.7 - - + -
154B GLU* 3.0 18.7 + - + +
155B VAL* 3.8 4.9 - - - +
157B GLN* 1.4 75.4 - - - +
159B PHE* 1.3 61.7 + - - +
161B ASP* 3.5 2.8 + - - +
162B THR* 2.8 34.5 + - - +
186B ILE* 4.6 15.3 - - + -
194B TYR* 3.5 38.0 - - + +
259B LEU* 3.7 25.8 - - + -
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Residues in contact with PHE 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155B VAL 2.9 18.4 + - - +
156B LEU* 4.1 7.0 - - + +
158B ILE* 1.3 76.4 - - - +
160B CYS* 1.3 65.2 + - - +
162B THR* 3.1 5.4 + - - -
163B CYS* 2.9 45.4 + - - -
252B LEU* 3.6 38.6 - - + -
255B LEU* 5.1 3.4 - - + -
256B LEU* 3.7 31.4 - - + -
259B LEU* 4.7 5.6 - - + -
293B LEU* 4.0 19.5 - - + -
297B MET* 3.3 28.9 - - + -
311B VAL* 3.9 10.1 - - + -
315B ALA* 3.8 14.6 - - + -
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Residues in contact with CYS 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156B LEU* 2.9 30.5 + - - +
157B GLN* 4.3 3.1 - - - +
159B PHE* 1.3 72.8 - - - +
161B ASP* 1.4 64.6 + - - +
163B CYS* 3.3 7.5 + - - +
164B GLU* 3.1 27.2 + - - +
315B ALA* 3.5 38.8 - - - -
316B PHE* 3.6 33.3 - - + -
319B ALA* 4.2 12.1 - - - -
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Residues in contact with ASP 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B LYS* 4.4 8.3 + - - -
107B ASN* 3.4 38.7 + - - +
157B GLN* 3.2 17.4 + - - +
158B ILE 3.6 4.3 - - - +
159B PHE 3.2 0.4 - - - -
160B CYS* 1.4 77.1 - - - +
162B THR* 1.4 63.1 + - - +
164B GLU* 3.4 3.8 + - - +
165B ALA* 3.2 17.2 + - - +
192B GLY 4.6 0.9 - - - +
193B ASN* 3.7 8.8 - - - +
194B TYR* 2.8 46.8 + - + +
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Residues in contact with THR 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B ILE* 2.8 20.5 + - - +
159B PHE* 3.1 5.8 + - - -
161B ASP* 1.4 71.1 - - - +
163B CYS* 1.4 54.3 + - - +
165B ALA* 3.2 7.4 + - - +
166B VAL* 2.9 38.3 + - + +
181B LEU* 4.2 17.3 - - + -
186B ILE* 3.8 20.3 - - + +
194B TYR* 5.4 0.7 - - - +
196B LEU* 4.3 12.9 - - + +
252B LEU* 3.8 15.7 - - + -
255B LEU* 3.7 25.1 - - + +
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Residues in contact with CYS 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159B PHE* 2.9 50.0 + - - -
160B CYS* 3.3 10.7 + - - +
162B THR* 1.4 74.8 - - - +
164B GLU* 1.3 52.3 + - - +
166B VAL* 3.3 2.2 + - - +
167B ALA* 2.8 35.8 + - - +
252B LEU* 4.6 3.8 - - - -
308B ILE* 3.6 16.6 - - + +
311B VAL* 3.9 16.2 - - - -
312B SER* 3.6 20.6 - - - +
315B ALA* 4.5 6.3 - - - -
316B PHE* 4.7 3.4 - - + -
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Residues in contact with GLU 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B HIS* 3.7 19.7 + - + +
106B LYS* 2.7 39.7 + - - -
107B ASN* 3.4 13.6 - - - +
160B CYS 3.1 13.9 + - - +
161B ASP* 3.6 6.7 - - - +
162B THR 3.4 0.2 - - - -
163B CYS* 1.3 74.7 - - - +
165B ALA* 1.4 56.7 + - - +
167B ALA* 3.4 8.0 + - - +
168B ARG 3.1 22.5 + - - -
316B PHE* 3.7 23.6 - - + -
324B PRO* 3.4 28.2 - - + +
325B VAL* 4.5 6.5 - - + +
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Residues in contact with ALA 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B HIS* 4.1 9.6 - - - -
107B ASN* 3.4 25.4 - - + +
108B ILE* 4.1 6.5 - - + -
161B ASP 3.2 8.7 + - - +
162B THR* 3.2 11.6 + - - +
164B GLU* 1.4 77.2 - - - +
166B VAL* 1.3 61.7 + - - +
168B ARG* 3.2 18.8 + - - +
169B LEU* 3.3 15.6 + - - +
196B LEU* 3.8 23.1 - - + +
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Residues in contact with VAL 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162B THR* 2.9 25.2 + - + +
163B CYS 3.7 3.4 - - - +
165B ALA* 1.3 73.9 - - - +
167B ALA* 1.4 60.3 + - - +
169B LEU* 2.9 13.5 + - + +
170B HIS* 2.9 59.7 + - + +
178B HIS* 5.9 0.4 - - + -
181B LEU* 3.8 35.9 - - + -
196B LEU* 4.7 2.9 - - + -
248B ASP* 4.9 3.4 - - + +
252B LEU* 4.2 11.7 - - + -
308B ILE* 3.9 16.4 - - + -
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Residues in contact with ALA 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163B CYS 2.8 20.5 + - - +
164B GLU 3.7 5.2 - - - +
166B VAL* 1.4 71.8 - - - +
168B ARG* 1.3 63.5 + - - +
170B HIS 4.5 0.2 - - - +
171B GLN* 3.0 37.5 + - - +
308B ILE* 3.8 19.9 - - + +
325B VAL* 3.7 34.1 - - + -
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Residues in contact with ARG 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B GLU* 3.0 30.9 + - - +
102B LEU* 3.6 27.8 + - + +
105B HIS* 3.8 35.0 - - + +
108B ILE* 5.0 1.8 - - + -
164B GLU 3.1 13.5 + - - +
165B ALA* 3.2 13.9 + - - +
167B ALA* 1.3 77.4 - - - +
169B LEU* 1.3 57.5 + - + +
171B GLN* 4.7 1.0 - - - -
172B CYS* 3.1 32.3 + - - -
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Residues in contact with LEU 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B LEU* 3.7 34.3 - - + -
108B ILE* 4.1 11.0 - - + -
165B ALA 3.3 15.3 - - - +
166B VAL* 2.9 12.0 + - + +
168B ARG* 1.3 77.9 - - - +
170B HIS* 1.3 63.3 + - + +
172B CYS* 3.6 14.1 - - - +
176B ILE* 2.9 53.9 + - + +
178B HIS* 3.7 43.7 - - + +
196B LEU* 4.6 4.7 - - + -
199B PHE* 4.3 7.4 - - + -
248B ASP* 5.5 0.2 - - - +
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Residues in contact with HIS 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166B VAL* 2.9 42.5 + - + +
169B LEU* 1.3 74.6 - - + +
171B GLN* 1.3 57.9 + - + +
172B CYS 3.3 2.3 + - - -
175B PRO* 3.4 23.0 - - - +
176B ILE 3.2 21.8 - - - +
245B THR* 3.1 46.4 + - + +
248B ASP* 2.8 29.2 + - + +
249B ILE* 3.9 12.0 - - + +
308B ILE* 4.1 24.4 + - + +
328B ILE* 4.9 3.5 - - - +
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Residues in contact with GLN 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167B ALA* 3.0 31.4 + - - +
168B ARG 4.7 1.3 - - - -
170B HIS* 1.3 75.7 - - + +
172B CYS* 1.4 64.3 + - - +
173B LYS 3.9 0.2 + - - -
308B ILE* 4.0 15.7 - - + +
309B PHE* 4.6 4.0 - - - +
325B VAL* 3.8 11.8 - - - +
326B SER* 2.8 43.3 + - - -
328B ILE* 3.6 42.2 - - + +
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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
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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) + - + + + + + -
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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