Contacts of the helix formed by residues 148 - 160 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34D ARG* 6.0 0.9 - - - +
68D ASN* 3.8 13.0 - - - +
71D PRO* 3.5 29.8 - - + +
72D LEU* 3.7 29.6 - - + +
75D ALA* 4.5 8.1 - - + -
106D ARG* 3.7 26.5 - - - +
146D ARG* 4.1 19.1 - - + +
147D CYS* 1.3 78.8 - - - +
149D SER* 1.3 60.7 + - - +
150D THR* 3.0 13.2 - - - +
151D ASP* 2.9 28.2 + - - +
152D LEU* 3.0 17.9 + - - +
192D PRO* 5.1 0.2 - - - -
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Residues in contact with SER 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147D CYS 4.2 0.2 + - - -
148D LEU* 1.3 74.2 - - - +
150D THR* 1.3 57.3 + - - +
152D LEU* 3.9 4.4 - - - +
153D ILE* 3.1 22.7 + - - +
178D ILE* 3.7 29.5 - - - +
182D LEU* 5.8 2.8 - - - +
192D PRO* 2.7 31.1 + - - +
195D ILE* 3.8 10.4 - - - +
196D THR* 2.9 29.9 + - - +
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Residues in contact with THR 150 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68D ASN* 2.9 27.1 + - - +
71D PRO* 4.6 3.7 - - + +
148D LEU* 3.5 13.5 - - - +
149D SER* 1.3 77.2 - - - +
151D ASP* 1.3 64.8 + - - +
153D ILE* 3.4 22.6 - - + +
154D CYS* 4.1 2.6 + - - -
171D TYR* 3.7 31.5 - - + +
175D ARG* 4.6 7.2 - - + -
178D ILE* 3.8 26.7 - - + -
179D PHE* 4.3 19.5 - - + -
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Residues in contact with ASP 151 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122C ARG* 5.3 9.2 + - - +
68D ASN* 3.9 11.6 + - - -
106D ARG* 3.2 35.2 + - - -
146D ARG 3.9 1.6 - - - +
147D CYS* 4.0 6.4 - - - -
148D LEU* 2.9 30.1 + - - +
150D THR* 1.3 77.7 + - - +
152D LEU* 1.3 65.8 + - - +
154D CYS* 3.1 18.1 + - - +
155D TYR* 3.1 30.0 - - + -
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Residues in contact with LEU 152 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D ILE* 3.7 28.5 - - + +
27D SER* 3.9 7.2 - - - +
147D CYS* 3.7 20.2 - - - -
148D LEU 3.0 18.9 + - - +
149D SER* 4.1 0.2 - - - -
150D THR 3.3 0.4 - - - -
151D ASP* 1.3 74.9 - - - +
153D ILE* 1.3 64.7 + - - +
155D TYR* 2.9 10.4 + - + +
156D ILE* 2.9 30.6 + - + +
192D PRO* 3.8 13.9 - - + -
193D VAL* 3.1 48.2 - - + +
196D THR* 3.6 21.5 - - + +
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Residues in contact with ILE 153 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149D SER 3.1 13.7 - - - +
150D THR* 3.4 15.5 - - + +
152D LEU* 1.3 76.8 - - - +
154D CYS* 1.3 62.8 + - - +
157D LEU* 3.2 30.0 + - + +
167D TYR 5.7 0.2 - - - +
170D ILE* 4.3 26.9 - - + +
171D TYR* 4.5 21.8 - - + +
174D CYS* 3.4 30.7 - - + -
175D ARG 4.8 0.2 - - - +
178D ILE* 3.5 17.0 - - + -
196D THR* 3.6 16.6 - - + +
200D MET* 4.0 13.4 - - + +
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Residues in contact with CYS 154 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122C ARG* 6.2 2.9 - - - +
5D GLU 4.9 5.6 - - - -
9D PHE* 4.0 27.4 - - + -
150D THR 4.6 6.7 - - - -
151D ASP* 3.1 12.8 + - - +
152D LEU 3.1 0.4 - - - -
153D ILE* 1.3 82.2 - - - +
155D TYR* 1.3 63.3 + - + +
158D HIS* 3.2 24.9 + - - +
167D TYR* 3.6 27.4 - - + -
171D TYR* 4.7 17.3 - - - -
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Residues in contact with TYR 155 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122C ARG* 3.0 33.9 + - - +
152C PHE* 4.1 3.6 - - - -
12D SER* 5.2 0.4 - - - -
15D LEU* 3.6 23.6 - - + -
20D CYS* 3.8 34.4 - - + +
23D MET* 3.7 45.9 - - + +
24D ILE* 4.8 8.7 - - + -
147D CYS* 4.7 1.1 - - - -
151D ASP* 3.1 40.8 - - + -
152D LEU* 2.9 15.4 + - + +
154D CYS* 1.3 80.2 - - + +
156D ILE* 1.3 61.6 + - - +
158D HIS* 3.3 5.5 + - + +
159D ILE* 3.0 34.5 + - - +
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Residues in contact with ILE 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D ILE* 5.1 11.4 - - + -
152D LEU* 2.9 13.8 + - + +
155D TYR* 1.3 75.2 - - + +
157D LEU* 1.3 67.4 - - - +
159D ILE* 3.2 8.5 + - + +
160D MET* 2.9 43.3 + - + +
193D VAL* 4.6 6.1 - - + +
196D THR* 3.3 36.1 - - + -
197D LEU* 3.7 32.8 - - + -
200D MET* 3.5 25.8 - - + -
218D VAL* 4.8 9.0 - - + -
222D LEU* 6.1 2.5 - - + -
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Residues in contact with LEU 157 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153D ILE* 3.2 21.9 + - + +
154D CYS* 4.0 0.7 - - - +
156D ILE* 1.3 79.6 - - - +
158D HIS* 1.3 62.6 + - - +
160D MET* 3.3 8.6 + - - -
162D ALA* 3.0 35.0 + - + +
167D TYR* 3.4 57.0 - - + +
170D ILE* 3.9 22.0 - - + -
200D MET* 3.3 22.7 - - + -
204D MET* 3.7 26.7 - - + -
210D TYR* 4.4 1.3 - - + -
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Residues in contact with HIS 158 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D SER* 4.3 15.6 + - - +
13D SER* 5.8 1.8 - - - -
14D LEU 5.6 0.4 - - - -
15D LEU* 2.7 36.8 + - + -
16D ASN* 3.8 10.8 - - - -
17D GLU 4.6 0.9 + - - -
20D CYS* 3.4 26.2 - - - -
154D CYS 3.2 11.2 + - - +
155D TYR* 3.5 8.7 - - + +
156D ILE 3.1 0.8 - - - -
157D LEU* 1.3 73.2 - - - +
159D ILE* 1.3 60.0 + - - +
160D MET 3.0 1.3 - - - -
161D HIS* 2.7 35.2 + + - -
162D ALA 4.9 0.7 - - - +
167D TYR* 3.1 20.6 + - + +
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Residues in contact with ILE 159 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D GLU* 3.6 34.3 - - + +
20D CYS* 3.5 26.0 - - + -
21D ARG* 3.9 28.5 - - + +
24D ILE* 3.8 24.0 - - + -
155D TYR 3.0 13.7 + - - +
156D ILE* 3.6 9.6 - - + +
158D HIS* 1.3 77.4 - - - +
160D MET* 1.3 57.3 + - + +
161D HIS* 3.1 19.1 + - - -
214D ARG* 4.2 7.9 + - - -
218D VAL* 4.6 20.0 - - + -
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Residues in contact with MET 160 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156D ILE* 2.9 35.1 + - + +
157D LEU* 3.3 5.8 - - - +
158D HIS 3.0 0.4 - - - -
159D ILE* 1.3 76.9 - - + +
161D HIS* 1.3 71.8 - - - +
162D ALA* 2.8 6.2 + - - -
200D MET* 4.9 2.5 - - - -
204D MET* 4.9 4.7 - - - -
210D TYR* 3.5 25.2 - - + +
211D TYR* 3.9 36.8 - - + +
214D ARG* 3.8 26.4 + - + +
215D ILE* 3.5 41.3 - - + +
218D VAL* 3.9 15.7 - - + -
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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