Contacts of the helix formed by residues 150 - 161 (chain A) in PDB entry 3R7G
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 SER 150 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55A GLU* 2.8 32.4 + - - -
59A TRP* 5.1 2.4 + - - -
148A GLU 4.2 0.2 + - - -
149A LEU* 1.3 74.1 - - - +
151A PRO* 1.3 75.3 - - - +
152A PRO* 3.6 13.2 - - - +
153A LEU* 3.1 7.8 + - - +
154A GLU* 3.0 19.1 + - - +
206A HIS* 6.1 0.7 - - - -
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Residues in contact with PRO 151 (chain A).
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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149A LEU 4.0 4.0 - - - +
150A SER* 1.3 84.9 - - - +
152A PRO* 1.4 67.3 - - + +
154A GLU* 3.8 7.9 - - + +
155A GLN* 2.9 45.1 + - + +
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Residues in contact with PRO 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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59A TRP* 3.7 22.2 - - + -
150A SER* 3.5 13.5 - - - +
151A PRO* 1.4 96.4 - - + +
153A LEU* 1.3 55.7 + - - +
155A GLN* 3.5 11.6 + - + +
156A LEU* 3.0 26.0 + - - +
206A HIS* 5.5 4.3 - - + +
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Residues in contact with LEU 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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55A GLU* 3.8 40.4 - - + +
58A ALA* 4.3 13.7 - - + -
59A TRP* 3.7 28.6 - - + +
133A ILE* 5.9 0.2 - - + -
137A LEU* 4.1 21.5 - - + -
149A LEU* 4.3 11.2 - - + -
150A SER* 3.1 16.6 + - - +
152A PRO* 1.3 79.8 - - - +
154A GLU* 1.3 66.7 + - - +
156A LEU* 3.2 21.3 + - + +
157A ILE* 3.0 31.9 + - + +
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Residues in contact with GLU 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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149A LEU* 4.2 29.1 + - + +
150A SER 3.0 16.0 + - - +
151A PRO* 3.8 8.5 - - + +
153A LEU* 1.3 76.5 - - - +
155A GLN* 1.3 56.4 + - + +
157A ILE* 3.3 5.3 + - - +
158A ASP* 2.9 35.6 + - + +
1714B ILE* 3.8 38.7 + - + +
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Residues in contact with GLN 155 (chain A).
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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151A PRO* 2.9 33.1 + - + +
152A PRO* 3.6 9.6 - - - +
154A GLU* 1.3 74.4 - - + +
156A LEU* 1.3 65.8 + - - +
158A ASP* 4.3 4.3 - - - -
159A HIS* 2.7 46.8 + - + +
202A LEU* 5.9 0.6 - - - +
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Residues in contact with LEU 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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58A ALA 5.7 0.4 - - - +
59A TRP* 3.9 30.1 - - + -
62A CYS* 4.1 23.1 - - + -
152A PRO 3.0 15.2 + - - +
153A LEU* 3.2 21.3 + - + +
155A GLN* 1.3 76.0 - - - +
157A ILE* 1.3 61.4 + - + +
159A HIS* 3.3 3.1 + - - +
160A MET* 2.9 52.0 + - + +
193A ILE* 4.3 0.9 - - + -
199A VAL* 4.3 11.7 - - + +
202A LEU* 4.1 36.3 - - + -
203A CYS* 4.2 3.1 - - - -
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Residues in contact with ILE 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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62A CYS* 6.1 0.2 - - - -
130A GLY* 3.9 20.6 - - - +
133A ILE* 4.3 24.5 - - + -
134A TYR* 4.0 10.1 - - + +
137A LEU* 5.0 3.1 - - + -
149A LEU* 4.7 10.5 - - + -
153A LEU* 3.0 30.5 + - + +
154A GLU 3.8 5.4 - - - +
156A LEU* 1.3 85.0 - - + +
158A ASP* 1.3 56.7 + - - +
160A MET* 3.8 11.7 - - - +
161A ALA* 2.9 29.9 + - + +
1714B ILE* 3.8 8.1 - - + -
1718B ILE* 3.8 28.0 - - + -
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Residues in contact with ASP 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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154A GLU* 2.9 22.9 + - - +
155A GLN* 3.7 8.9 - - - +
156A LEU 3.2 0.2 - - - -
157A ILE* 1.3 76.1 - - - +
159A HIS* 1.3 59.4 + - + +
162A ASN* 3.1 7.1 + - - -
163A THR* 2.6 58.8 + - - -
164A VAL* 3.2 27.5 + - + +
1714B ILE* 4.0 10.8 - - + +
1717B LYS* 2.9 29.4 + - - -
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Residues in contact with HIS 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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155A GLN* 2.7 44.5 + - + +
156A LEU* 5.0 0.7 - - - -
158A ASP* 1.3 76.3 - - + +
160A MET* 1.3 65.6 + - - +
162A ASN* 3.3 17.2 + - - +
164A VAL* 3.7 32.1 - - + +
192A ALA* 4.5 23.5 + - - -
193A ILE* 3.7 32.2 + - + +
202A LEU* 5.4 4.2 - - + +
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Residues in contact with MET 160 (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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62A CYS* 3.6 33.4 - - - -
123A THR 4.8 0.5 - - - +
126A ILE* 3.5 42.0 - - + +
127A GLU* 3.2 24.0 + - - +
129A LEU* 3.9 15.3 - - + -
130A GLY* 3.6 21.5 - - - +
133A ILE* 5.8 1.1 - - + -
156A LEU* 2.9 36.8 + - + +
157A ILE* 3.8 8.7 - - - +
159A HIS* 1.3 77.7 - - - +
161A ALA* 1.3 58.8 + - - +
162A ASN* 3.3 4.7 + - - -
193A ILE* 3.8 17.0 - - + -
199A VAL* 4.1 7.0 - - + -
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Residues in contact with ALA 161 (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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127A GLU* 3.6 12.4 + - - +
130A GLY 5.0 0.2 - - - -
131A ILE* 4.2 26.2 - - + +
157A ILE* 2.9 18.1 + - + +
160A MET* 1.3 75.7 - - - +
162A ASN* 1.3 70.4 + - - +
163A THR* 3.2 17.2 + - + +
1718B ILE* 4.5 10.5 - - + -
1721B LYS* 3.3 22.6 + - + -
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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