Contacts of the helix formed by residues 148 - 159 (chain A) 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 LEU 148 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115A CYS* 6.1 0.9 - - + +
119A SER* 5.3 1.1 - - - +
141A SER* 5.1 3.1 - - - +
142A LEU* 5.5 4.4 - - - +
145A ASN* 3.8 25.6 + - + +
146A PRO 3.1 7.7 - - - +
147A PHE* 1.3 76.2 - - - +
149A TRP* 1.3 63.5 + - - +
150A SER 3.4 0.2 - - - -
151A PRO* 3.5 28.8 - - + +
152A PHE* 4.3 8.3 + - - +
23B ASP* 3.8 17.0 - - + +
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Residues in contact with TRP 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A PHE 3.3 6.9 + - - +
148A LEU* 1.3 73.8 - - - +
150A SER* 1.3 64.2 + - - +
152A PHE* 3.2 40.5 + + + +
153A GLU* 2.3 58.9 + - + +
472A LEU* 4.3 14.8 - - + -
475A MET* 4.1 11.9 - - + -
476A GLY* 4.0 20.0 - - - -
479A TYR* 4.1 16.4 - + + -
506A TRP* 3.5 27.0 - + - -
22B ARG 5.4 2.0 - - - -
23B ASP* 4.5 5.6 + - - +
26B PHE* 3.4 60.6 - + + -
27B LEU* 6.0 0.9 - - + -
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Residues in contact with SER 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A SER* 6.4 0.4 - - - -
138A TYR* 5.6 0.2 - - - -
149A TRP* 1.3 76.1 - - - +
151A PRO* 1.4 63.8 - - - +
153A GLU* 3.1 9.1 + - - +
154A SER* 2.8 35.9 + - - -
22B ARG* 3.6 12.8 + - - +
23B ASP* 2.8 45.4 + - - -
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Residues in contact with PRO 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A SER* 3.3 24.9 - - - +
138A TYR* 3.8 45.1 - - + +
141A SER* 3.9 6.1 - - - +
142A LEU* 5.0 6.1 - - + +
148A LEU* 3.5 31.9 - - + +
150A SER* 1.4 94.5 - - - +
152A PHE* 1.3 60.9 + - - +
154A SER* 3.3 2.4 + - - -
155A LEU* 3.1 27.6 + - - +
23B ASP* 3.7 2.7 - - - +
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Residues in contact with PHE 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A LEU* 5.7 6.4 - - + +
148A LEU 4.3 6.4 + - - +
149A TRP* 3.2 37.5 + + + +
151A PRO* 1.3 80.0 - - - +
153A GLU* 1.3 64.2 + - - +
155A LEU* 3.3 11.9 + - + +
156A CYS* 3.2 46.6 + - - -
162A PRO* 4.5 21.1 - - + -
164A PRO* 4.4 23.1 - - + -
167A THR* 4.4 16.8 - - - -
476A GLY* 3.4 43.3 - - - -
479A TYR* 4.9 1.8 - - + -
480A LEU* 4.8 1.8 - - + -
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Residues in contact with GLU 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A TRP* 2.3 59.1 + - + +
150A SER* 3.5 8.0 - - - +
152A PHE* 1.3 83.0 - - - +
154A SER* 1.3 60.9 + - - +
156A CYS* 3.8 2.8 + - - +
157A GLU* 3.2 39.6 + - - +
479A TYR* 3.9 27.2 + - + -
506A TRP* 4.9 8.4 + - - -
26B PHE* 4.9 0.3 - - - -
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Residues in contact with SER 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A TYR* 3.5 37.6 + - - -
150A SER* 2.8 15.6 + - - -
151A PRO 3.5 4.7 - - - -
153A GLU* 1.3 75.8 - - - +
155A LEU* 1.3 64.9 + - - +
157A GLU* 3.2 14.4 + - - +
158A ILE* 3.1 30.7 + - - +
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Residues in contact with LEU 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A SER* 3.7 43.5 - - - +
138A TYR* 3.7 22.4 - - + +
139A GLN* 4.0 16.6 - - + +
142A LEU* 5.9 2.7 - - + -
151A PRO 3.1 17.7 + - - +
152A PHE* 3.3 11.4 + - + +
154A SER* 1.3 75.8 - - - +
156A CYS* 1.3 62.0 + - - +
158A ILE* 3.4 8.6 + - + +
160A GLU* 3.1 43.3 + - + +
162A PRO* 4.3 24.7 - - + -
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Residues in contact with CYS 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A PHE* 3.2 48.4 + - - +
153A GLU 4.0 5.4 - - - +
154A SER 3.3 0.2 - - - -
155A LEU* 1.3 78.7 - - - +
157A GLU* 1.3 63.3 + - - +
159A GLY* 3.2 13.3 + - - -
160A GLU 3.8 9.2 - - - +
162A PRO* 5.8 2.2 - - - -
479A TYR* 4.2 15.7 - - + -
480A LEU* 3.9 28.9 - - - +
483A CYS* 3.0 25.7 - - + +
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Residues in contact with GLU 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A GLU* 3.2 31.3 + - - +
154A SER* 3.2 15.5 + - - +
156A CYS* 1.3 78.7 - - - +
158A ILE* 1.3 62.9 + - + +
159A GLY 3.5 0.2 + - - -
479A TYR* 3.3 25.8 + - + +
483A CYS* 3.5 15.8 - - - -
637A ASN* 4.3 15.2 + - - +
639A ARG* 4.1 15.8 - - - +
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Residues in contact with ILE 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A CYS* 4.0 26.9 - - + -
131A LEU* 4.3 22.2 - - + +
135A SER* 3.7 22.7 - - - +
138A TYR* 4.3 8.1 - - + -
154A SER* 3.1 23.2 + - - +
155A LEU* 3.7 10.1 - - - +
156A CYS 3.2 0.6 - - - -
157A GLU* 1.3 78.0 - - + +
159A GLY* 1.3 58.3 + - - +
160A GLU* 4.2 7.0 - - + +
637A ASN* 5.7 1.3 - - - -
638A PRO* 6.1 0.7 - - - +
639A ARG* 4.4 10.2 - - - +
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Residues in contact with GLY 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A CYS 3.2 11.3 + - - -
157A GLU 3.3 0.4 - - - -
158A ILE* 1.3 80.3 - - - +
160A GLU* 1.3 65.7 + - - +
161A LYS* 3.7 3.5 + - - +
639A ARG* 5.7 2.7 - - - -
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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