Contacts of the helix formed by residues 143 - 149 (chain A) in PDB entry 4M8J
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 GLY 143 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139A LEU 3.2 16.2 + - - -
140A PHE 3.7 3.4 + - - -
141A HIS 3.7 1.6 - - - -
142A TRP* 1.3 78.3 - - - +
144A PRO* 1.3 69.0 - - - +
145A LEU 3.0 10.9 + - - -
146A PRO* 3.1 9.0 - - - +
147A TRP* 2.9 24.3 - - - -
356A THR* 3.7 2.5 - - - -
360A TRP* 3.5 6.3 - - - -
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Residues in contact with PRO 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A PHE* 4.7 2.0 - - - -
139A LEU 4.2 2.7 - - - +
143A GLY* 1.3 82.9 - - - +
145A LEU* 1.3 59.8 + - + +
146A PRO 3.7 0.2 - - - -
147A TRP* 4.4 1.6 - - + -
148A ALA* 3.2 28.5 + - - +
293A LEU* 5.8 0.9 - - + -
297A MET* 5.1 10.3 - - + -
352A VAL* 3.6 25.4 - - + +
356A THR* 3.3 26.8 - - + +
360A TRP* 3.8 18.2 - - + -
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Residues in contact with LEU 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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59A MET* 4.7 9.9 - - + +
63A PHE* 3.9 27.4 - - + -
140A PHE* 4.0 20.6 - - + +
143A GLY 3.0 1.4 - - - -
144A PRO* 1.3 79.9 - - + +
146A PRO* 1.3 71.7 - - + +
148A ALA* 3.6 8.3 + - - +
149A THR* 3.2 19.8 - - - +
297A MET* 3.7 38.1 - - + -
301A LEU* 3.6 43.7 - - + -
321A TRP* 4.1 13.9 - - + -
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Residues in contact with PRO 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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59A MET* 3.7 10.3 - - + -
140A PHE 3.4 17.3 - - - +
141A HIS 3.1 24.9 - - - +
143A GLY 3.1 18.8 - - - +
145A LEU* 1.3 83.6 - - + +
147A TRP* 1.3 62.0 + - - +
149A THR* 2.7 21.3 + - - -
150A TYR* 3.8 3.3 + - - -
321A TRP* 3.5 20.9 - - + -
324A TRP* 3.4 40.1 - - + -
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Residues in contact with TRP 147 (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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99A CYS* 4.5 6.3 - - - -
142A TRP 4.3 1.4 + - - -
143A GLY 2.9 25.9 + - - +
144A PRO* 4.2 6.1 - - + +
145A LEU 3.3 0.4 - - - -
146A PRO* 1.3 78.4 - - - +
148A ALA* 1.3 62.0 + - - +
150A TYR* 3.2 22.3 + + + +
324A TRP* 3.6 24.4 - + - -
331A MET* 4.5 10.8 - - + -
335A LEU* 5.4 0.2 - - + -
351A MET* 3.2 27.3 - - + +
352A VAL* 4.2 15.9 - - + -
355A LEU* 3.5 42.7 - - + +
356A THR* 3.6 19.1 - - - -
359A THR* 3.2 40.2 + - + +
601A NM2 3.4 36.3 - - + -
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Residues in contact with ALA 148 (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 MET 4.0 3.9 - - - +
63A PHE* 3.6 30.3 - - + -
66A TRP* 3.4 44.0 - - + +
144A PRO 3.2 21.7 + - - +
145A LEU 3.8 2.0 - - - +
146A PRO 3.2 0.8 - - - -
147A TRP* 1.3 76.7 - - - +
149A THR* 1.3 58.2 + - - +
150A TYR 3.1 4.0 + - - -
151A SER* 3.4 9.9 + - - -
152A PHE 4.5 1.7 + - - -
352A VAL* 4.0 3.3 - - + +
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Residues in contact with THR 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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58A TYR* 5.0 4.5 + - - -
59A MET* 3.2 52.3 - - + +
62A MET* 3.6 27.9 - - + +
63A PHE* 3.9 12.6 - - - +
145A LEU 3.2 18.6 - - - +
146A PRO 2.7 15.9 + - - -
148A ALA* 1.3 76.4 - - - +
150A TYR* 1.3 68.2 + - - +
151A SER 3.6 0.2 - - - -
152A PHE* 4.9 2.5 - - - -
153A LEU* 4.1 13.5 - - - +
328A ALA* 5.7 0.2 - - - +
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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