Contacts of the helix formed by residues 149 - 158 (chain B) in PDB entry 4RG7
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 TRP 149 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A ARG* 5.4 4.9 - - + -
23A ASP* 4.5 6.7 - - - +
26A PHE* 3.5 61.6 - + + -
147B PHE 3.4 5.2 + - - +
148B LEU* 1.3 73.8 - - - +
150B SER* 1.3 63.9 + - - +
151B PRO* 3.4 1.3 - - - -
152B PHE* 3.2 23.5 + + - +
153B GLU* 2.9 56.7 + - + +
168B PHE* 4.4 8.3 - + - -
472B LEU* 4.2 16.2 - - + -
475B MET* 4.0 4.5 - - + -
476B GLY* 3.6 37.9 - - - -
479B TYR* 3.9 24.5 - + + -
506B TRP* 3.6 24.8 - + - -
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Residues in contact with SER 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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20A ALA* 6.1 0.2 - - - +
22A ARG* 4.4 27.8 - - - -
23A ASP* 4.5 14.7 - - - +
119B SER* 4.2 9.0 + - - -
148B LEU* 4.6 0.2 - - - +
149B TRP* 1.3 82.2 - - - +
151B PRO* 1.4 72.7 - - - +
153B GLU* 3.4 10.6 - - - +
154B SER* 2.8 30.3 + - - -
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Residues in contact with PRO 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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119B SER* 4.0 15.3 - - - +
138B TYR* 4.0 40.1 - - + +
141B SER* 4.4 12.6 - - - -
142B LEU* 5.0 7.9 - - + +
148B LEU* 3.8 26.2 - - + +
149B TRP 3.4 4.7 - - - -
150B SER* 1.4 98.1 - - - +
152B PHE* 1.3 55.8 + - - +
154B SER* 3.2 6.3 + - - +
155B LEU* 2.9 35.1 + - + +
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Residues in contact with PHE 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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142B LEU* 5.5 5.3 - - + +
148B LEU 5.0 0.4 - - - +
149B TRP* 3.2 25.6 + + - +
151B PRO* 1.3 76.9 - - - +
153B GLU* 1.3 68.2 + - - +
155B LEU* 3.3 10.5 + - + +
156B CYS* 3.1 40.0 + - - -
162B PRO* 3.6 34.5 - - + -
164B PRO* 4.7 3.8 - - + -
167B THR* 4.0 16.2 - - + +
168B PHE* 3.3 40.8 - + + -
476B GLY* 3.3 44.2 - - - -
479B TYR* 4.8 1.6 - + - -
480B LEU* 4.6 5.6 - - + -
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Residues in contact with GLU 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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22A ARG* 3.4 38.5 + - - +
149B TRP* 2.9 40.3 + - + +
150B SER* 3.4 11.0 - - - +
152B PHE* 1.3 80.6 - - - +
154B SER* 1.3 62.8 + - - +
156B CYS* 3.4 3.1 + - - +
157B GLU* 3.2 45.6 + - - +
479B TYR* 3.5 25.6 + - + -
506B TRP* 4.6 10.0 + - - -
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Residues in contact with SER 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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126B CYS* 5.8 0.7 - - - -
138B TYR* 3.5 33.0 + - - -
150B SER* 2.8 16.2 + - - -
151B PRO* 3.4 8.0 - - - +
153B GLU* 1.3 75.8 + - - +
155B LEU* 1.3 59.4 + - - +
157B GLU* 3.1 10.0 + - - +
158B ILE* 2.8 34.6 + - - +
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Residues in contact with LEU 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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135B SER* 3.9 24.0 - - - +
138B TYR* 3.4 42.4 - - + +
139B GLN* 4.5 15.3 - - + +
142B LEU* 5.7 3.1 - - + -
151B PRO 2.9 14.5 + - - +
152B PHE* 3.3 17.0 + - + +
154B SER* 1.3 76.5 - - - +
156B CYS* 1.3 60.9 + - - +
158B ILE* 3.7 4.0 + - + -
159B GLY 3.5 2.4 + - - -
160B GLU* 3.0 35.7 + - + +
162B PRO* 4.1 30.7 - - + -
167B THR* 5.6 3.6 - - - +
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Residues in contact with CYS 156 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152B PHE* 3.1 48.6 + - - -
153B GLU 3.7 6.1 - - - +
154B SER 3.2 0.4 - - - -
155B LEU* 1.3 78.8 - - - +
157B GLU* 1.3 63.1 + - - +
159B GLY* 3.2 13.3 + - - -
160B GLU 3.7 7.4 - - - +
162B PRO* 4.6 3.8 - - - -
479B TYR* 4.1 4.7 - - + -
480B LEU* 3.9 25.6 - - + -
483B CYS* 3.6 36.6 - - + +
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Residues in contact with GLU 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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22A ARG* 5.8 0.7 + - - -
153B GLU* 3.2 32.3 + - - +
154B SER* 3.1 9.6 + - - +
156B CYS* 1.3 73.3 - - - +
158B ILE* 1.3 56.1 + - - +
159B GLY 3.1 8.5 + - - -
479B TYR* 3.1 26.8 + - - +
483B CYS* 4.3 9.4 - - - -
639B ARG* 3.6 20.3 - - - +
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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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126B CYS* 5.3 13.5 - - - -
131B LEU* 5.7 9.4 - - + +
135B SER* 6.3 2.9 - - - -
138B TYR* 6.4 0.4 - - + -
154B SER 2.8 20.7 + - - +
155B LEU* 3.9 3.6 - - - +
156B CYS 3.4 0.4 - - - -
157B GLU* 1.3 71.1 - - - +
159B GLY* 1.3 57.2 + - - +
160B GLU* 3.3 7.8 + - + +
638B PRO* 6.5 1.6 - - - -
639B ARG* 5.2 4.0 - - - -
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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