Contacts of the helix formed by residues 133 - 146 (chain A) in PDB entry 4M92
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 ALA 133 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67A GLU* 3.6 10.3 - - - +
130A ILE 6.1 0.2 - - - +
131A GLY 3.7 1.6 + - - -
132A PHE* 1.3 79.3 - - - +
134A ALA* 1.3 66.9 + - - +
135A GLU* 4.0 15.0 - - + +
136A GLN* 2.9 28.0 + - + +
137A LEU* 3.1 10.4 + - - +
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Residues in contact with ALA 134 (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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67A GLU* 2.9 38.9 + - - +
70A ILE* 4.0 19.1 - - + -
71A LEU* 3.8 8.4 - - + +
132A PHE 3.3 2.1 + - - -
133A ALA* 1.3 71.6 - - - +
135A GLU* 1.3 59.8 + - - +
137A LEU* 3.2 12.7 + - - +
138A ALA* 2.9 30.3 + - - +
151A VAL* 3.8 15.1 - - + +
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Residues in contact with GLU 135 (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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67A GLU* 4.7 1.6 - - - +
133A ALA* 3.1 10.8 - - + +
134A ALA* 1.3 82.1 + - - +
136A GLN* 1.3 64.0 + - + +
138A ALA* 3.4 3.1 + - - +
139A LYS* 3.0 42.7 + - - +
151A VAL* 3.9 35.5 - - + +
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Residues in contact with GLN 136 (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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125A PHE* 3.9 8.4 - - + -
130A ILE* 3.5 41.3 - - + +
131A GLY 4.6 2.2 - - - +
133A ALA* 2.9 21.3 + - + +
135A GLU* 1.3 80.5 - - + +
137A LEU* 1.3 64.7 + - - +
139A LYS* 3.2 17.7 + - - +
140A TRP* 3.1 22.5 + - - +
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Residues in contact with LEU 137 (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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67A GLU* 4.5 0.2 - - + -
68A TYR* 4.5 12.1 - - - +
71A LEU* 3.9 24.0 - - + -
110A PHE* 3.9 42.0 - - + -
125A PHE* 3.6 39.7 - - + -
132A PHE* 3.7 19.7 - - - +
133A ALA 3.1 11.9 + - - +
134A ALA* 3.5 12.6 - - - +
136A GLN* 1.3 77.2 - - - +
138A ALA* 1.4 56.4 + - - +
140A TRP* 3.3 10.2 + - + +
141A ILE* 2.9 33.1 + - - +
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Residues in contact with ALA 138 (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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71A LEU* 3.9 16.3 - - + +
134A ALA 2.9 17.4 + - - +
135A GLU* 3.6 6.5 - - - +
137A LEU* 1.4 72.7 - - - +
139A LYS* 1.3 63.3 + - + +
141A ILE* 3.3 7.0 + - - +
142A ALA* 2.9 30.0 + - - +
147A VAL 4.7 1.2 - - - +
149A ILE* 3.4 32.2 + - + +
151A VAL* 4.0 6.5 - - + -
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Residues in contact with LYS 139 (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 GLU* 3.0 33.4 + - - +
136A GLN* 3.4 23.8 - - - +
138A ALA* 1.3 78.3 - - + +
140A TRP* 1.3 55.9 + - - +
142A ALA* 3.3 7.4 + - - +
143A ASP* 3.0 38.1 + - - +
150A ARG* 4.6 15.6 - - - +
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Residues in contact with TRP 140 (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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46A ILE* 4.1 11.7 - - + -
110A PHE* 3.8 24.2 - - + -
111A MET 3.6 22.9 - - - -
112A HIS* 3.7 12.6 - - + -
122A ALA 2.9 26.6 + - - -
123A ASP 3.5 22.2 - - - -
124A THR 5.1 0.2 - - - -
125A PHE* 3.7 44.8 - + + +
130A ILE* 6.2 0.2 - - + -
136A GLN 3.1 9.6 + - - +
137A LEU* 3.5 22.0 - - + +
139A LYS* 1.3 76.0 - - - +
141A ILE* 1.3 83.7 + - + +
143A ASP* 3.1 10.6 + - + +
144A ARG* 3.0 38.6 + - + +
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Residues in contact with ILE 141 (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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46A ILE* 4.0 19.3 - - + -
71A LEU* 3.6 22.2 - - + -
85A LEU* 4.1 20.2 - - + -
87A PHE* 3.6 31.9 - - + -
137A LEU* 2.9 20.7 + - + +
138A ALA* 3.7 5.4 - - - +
140A TRP* 1.3 92.0 - - + +
142A ALA* 1.3 55.9 + - - +
144A ARG* 3.2 4.1 + - - +
145A THR* 2.8 52.4 + - + +
147A VAL 4.1 7.2 - - - +
149A ILE* 4.4 6.3 - - + -
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Residues in contact with ALA 142 (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 ALA 2.9 13.1 + - - +
139A LYS* 3.5 11.2 - - - +
141A ILE* 1.3 75.2 - - - +
143A ASP* 1.3 62.3 + - - +
146A ASP* 2.8 30.6 + - - +
147A VAL 3.2 20.7 + - - +
148A HIS* 3.6 31.6 - - + +
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Residues in contact with ASP 143 (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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139A LYS* 3.0 23.3 + - - +
140A TRP* 3.1 11.8 + - + +
142A ALA* 1.3 77.3 - - - +
144A ARG* 1.3 77.2 + - - +
146A ASP 4.9 0.5 + - - -
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Residues in contact with ARG 144 (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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112A HIS* 3.8 22.3 - - + +
120A LYS* 4.1 18.0 - - - +
122A ALA* 3.5 36.3 + - - +
123A ASP* 2.9 38.4 + - - +
140A TRP* 3.0 42.5 + - + +
141A ILE* 4.0 3.1 - - - +
143A ASP* 1.3 93.3 + - - +
145A THR* 1.3 64.0 + - + +
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Residues in contact with THR 145 (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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44A SER* 3.9 14.1 - - - +
46A ILE* 4.9 2.0 - - + -
85A LEU* 4.3 10.2 - - + +
112A HIS* 3.5 30.5 - - + +
141A ILE* 2.8 25.5 + - + +
144A ARG* 1.3 83.3 - - + +
146A ASP* 1.3 67.6 + - - +
147A VAL* 3.0 32.6 + - - +
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Residues in contact with ASP 146 (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 ALA 2.8 17.8 + - - +
143A ASP 4.7 0.4 + - - -
144A ARG 3.9 0.2 - - - -
145A THR* 1.3 78.9 - - - +
147A VAL* 1.3 60.7 + - - +
148A HIS* 3.3 29.5 + - - -
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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