Contacts of the helix formed by residues 148 - 160 (chain B) in PDB entry 1F5Q
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 148 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68B ASN* 3.7 11.2 - - + +
71B PRO* 3.7 29.8 - - + +
72B LEU* 3.7 27.6 - - + +
75B ALA* 4.4 7.0 - - + -
106B ARG* 3.6 32.5 - - - +
146B ARG* 4.0 18.8 - - + -
147B CYS* 1.3 73.8 - - - +
149B SER* 1.3 61.6 + - - +
150B THR* 3.1 17.0 - - - +
151B ASP* 3.1 11.8 + - - +
152B LEU* 2.9 33.0 + - - +
192B PRO* 5.5 0.4 - - - -
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Residues in contact with SER 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B LEU* 1.3 71.8 - - - +
150B THR* 1.3 62.5 + - - +
152B LEU* 4.1 3.3 - - - +
153B ILE* 3.0 22.3 + - - +
178B ILE* 3.8 26.5 - - - -
182B LEU* 5.8 3.4 - - - +
192B PRO* 3.1 26.5 + - - +
195B ILE* 3.8 16.8 - - - +
196B THR* 2.9 27.4 + - - -
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Residues in contact with THR 150 (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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67B ASN 5.0 0.2 - - - +
68B ASN* 2.9 27.2 + - - +
71B PRO* 4.3 7.9 - - + -
148B LEU* 3.6 11.0 - - + +
149B SER* 1.3 79.0 - - - +
151B ASP* 1.3 74.8 + - - +
153B ILE* 3.3 26.5 + - - +
154B CYS* 4.2 1.7 + - - -
171B TYR* 3.7 26.2 - - + +
175B ARG* 4.7 6.3 - - + -
178B ILE* 4.0 18.6 - - + -
179B PHE* 4.0 25.8 - - + -
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Residues in contact with ASP 151 (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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122A ARG* 5.5 8.1 - - - +
152A PHE* 6.6 0.4 - - - -
9B PHE* 4.7 1.2 - - - -
68B ASN* 3.5 8.3 + - - -
106B ARG* 2.6 44.2 + - - -
146B ARG 3.7 2.3 - - - +
147B CYS* 4.0 9.3 - - - -
148B LEU* 3.1 23.2 + - - +
150B THR* 1.3 93.3 + - - +
152B LEU* 1.3 60.2 + - - +
154B CYS* 3.5 12.3 + - - +
155B TYR* 3.1 27.0 + - + -
171B TYR* 5.6 1.0 - - - -
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Residues in contact with LEU 152 (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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23B MET 4.8 0.2 - - - -
24B ILE* 4.0 29.6 - - + +
27B SER* 3.7 11.9 - - - +
147B CYS* 3.5 24.5 - - - -
148B LEU 2.9 17.1 + - - +
149B SER* 4.1 0.2 - - - -
150B THR 3.2 0.4 - - - -
151B ASP* 1.3 72.5 - - - +
153B ILE* 1.3 66.1 + - - +
154B CYS 3.0 2.7 - - - -
155B TYR* 2.9 21.8 + - + +
156B ILE* 3.1 18.5 + - + +
192B PRO* 3.5 21.8 - - + -
193B VAL* 3.5 32.1 - - + +
196B THR* 3.5 17.3 - - + +
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Residues in contact with ILE 153 (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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149B SER 3.0 14.8 + - - +
150B THR* 3.4 15.3 - - + +
151B ASP 3.3 0.4 - - - -
152B LEU* 1.3 75.8 - - - +
154B CYS* 1.3 62.7 + - - +
156B ILE 3.7 0.2 + - - -
157B LEU* 3.3 26.6 + - + +
170B ILE* 4.2 19.3 - - + -
171B TYR* 4.5 19.5 - - + -
174B CYS* 3.3 23.3 - - + -
175B ARG* 4.7 1.3 - - - +
178B ILE* 3.3 29.6 - - + -
196B THR* 3.4 17.7 - - + +
200B MET* 3.5 20.5 - - + +
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Residues in contact with CYS 154 (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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8B GLY 4.8 6.3 - - - -
9B PHE* 3.5 52.3 - - + -
150B THR 4.6 2.2 - - - -
151B ASP* 3.5 5.7 + - - +
152B LEU 3.0 1.2 - - - -
153B ILE* 1.3 81.2 - - - +
155B TYR* 1.3 61.2 + - - +
156B ILE 3.1 1.8 - - - -
157B LEU* 3.4 3.0 + - - +
158B HIS* 3.2 18.4 + - - +
167B TYR* 3.8 21.7 - - + -
171B TYR* 3.9 33.4 - - - -
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Residues in contact with TYR 155 (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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121A HIS 5.6 0.5 + - - -
122A ARG* 2.9 31.3 + - - +
152A PHE* 4.2 7.2 - + - -
9B PHE* 3.7 24.0 - + - -
15B LEU* 4.0 15.7 - - + -
19B ASP 4.9 1.1 - - - -
20B CYS* 3.5 41.8 - - + +
23B MET* 3.5 43.3 - - + +
24B ILE* 5.0 2.2 - - + -
147B CYS* 5.1 0.2 - - - -
151B ASP* 3.1 35.4 - - + -
152B LEU* 2.9 16.4 + - + +
154B CYS* 1.3 77.3 - - - +
156B ILE* 1.3 60.7 + - + +
158B HIS 3.9 0.4 - - - -
159B ILE* 3.2 32.6 + - - +
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Residues in contact with ILE 156 (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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24B ILE* 4.9 14.1 - - + -
152B LEU* 3.1 10.0 + - + +
153B ILE 3.9 0.2 - - - +
155B TYR* 1.3 78.1 - - + +
157B LEU* 1.3 64.4 + - - +
158B HIS 3.2 1.3 - - - -
159B ILE* 3.5 8.0 + - + +
160B MET* 3.0 43.5 + - + +
193B VAL* 4.5 12.3 - - + -
196B THR* 3.3 34.1 - - + -
197B LEU* 3.9 27.4 - - + -
200B MET* 3.5 25.1 - - + -
218B VAL* 4.9 8.7 - - + -
222B LEU* 5.8 1.6 - - + -
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Residues in contact with LEU 157 (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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153B ILE* 3.3 22.0 + - + +
154B CYS* 3.4 2.2 + - - +
156B ILE* 1.3 77.4 - - - +
158B HIS* 1.3 63.9 + - - +
160B MET* 3.3 4.3 + - - -
161B HIS 3.3 2.9 + - - -
162B ALA* 3.0 37.6 + - + +
167B TYR* 3.7 58.1 - - + +
170B ILE* 3.9 26.2 - - + -
200B MET* 3.4 18.8 - - + -
204B MET* 3.5 23.3 - - + -
210B TYR* 4.2 0.7 - - + -
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Residues in contact with HIS 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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9B PHE* 4.8 7.4 - + + -
12B SER 4.1 15.4 + - - -
13B SER* 4.5 7.4 - - - -
15B LEU* 2.5 38.2 + - + -
16B ASN* 3.9 7.4 + - - -
17B GLU 4.6 2.2 + - - -
20B CYS* 3.3 26.7 - - - -
154B CYS 3.2 16.8 + - - +
155B TYR* 3.8 5.2 - - - +
157B LEU* 1.3 75.5 - - - +
159B ILE* 1.3 58.4 + - - +
161B HIS* 2.7 40.6 + + - +
167B TYR* 3.3 15.2 + - - +
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Residues in contact with ILE 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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17B GLU* 3.9 40.3 - - + +
20B CYS* 3.5 25.8 - - + -
21B ARG* 4.4 16.4 - - + +
24B ILE* 3.9 22.9 - - + -
155B TYR 3.2 18.7 + - - +
156B ILE* 3.7 8.7 - - + +
158B HIS* 1.3 81.4 - - - +
160B MET* 1.3 57.5 + - - +
161B HIS* 3.1 16.6 + - - -
214B ARG* 3.9 8.6 + - - -
218B VAL* 4.3 27.1 - - + -
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Residues in contact with MET 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 ILE* 3.0 34.5 + - + +
157B LEU* 3.8 5.4 - - - +
158B HIS 3.0 1.2 - - - -
159B ILE* 1.3 76.4 - - - +
161B HIS* 1.3 69.9 + - - +
162B ALA 3.0 3.0 + - - -
197B LEU* 4.9 0.4 - - + -
200B MET* 5.1 0.4 - - - -
204B MET* 4.5 10.3 - - - -
210B TYR* 3.8 19.5 - - + +
211B TYR* 4.0 34.3 - - + +
214B ARG* 3.5 30.4 + - + +
215B ILE* 4.0 33.2 - - + +
218B VAL* 3.9 30.1 - - + -
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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
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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