Contacts of the helix formed by residues 742 - 755 (chain A) in PDB entry 4C48
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 742 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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740A GLY 4.2 1.2 + - - -
741A VAL* 1.3 76.0 - - - +
743A ILE* 1.3 66.6 + - - +
744A ASN* 3.6 7.7 + - - +
745A ASP* 2.8 40.0 + - - +
746A ILE* 3.0 20.8 + - - +
792A ARG 5.2 0.4 + - - -
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Residues in contact with ILE 743 (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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731A ILE* 5.0 9.9 - - + -
733A GLN* 3.5 41.5 - - - +
736A ALA* 5.0 8.1 - - + -
737A GLN* 5.7 9.6 - - + +
741A VAL 4.9 4.0 - - - +
742A SER* 1.3 73.9 - - - +
744A ASN* 1.3 69.8 + - - +
746A ILE* 3.5 7.8 - - + +
747A ASN* 3.0 41.4 + - - +
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Residues in contact with ASN 744 (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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742A SER* 3.6 6.9 + - - +
743A ILE* 1.3 84.4 - - - +
745A ASP* 1.3 65.3 + - - +
747A ASN* 3.9 3.5 - - - +
748A THR* 3.0 31.6 + - - +
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Residues in contact with ASP 745 (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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199A THR* 5.9 1.6 - - + +
201A VAL* 3.7 32.2 - - + +
742A SER* 2.8 35.8 + - - +
744A ASN* 1.3 78.3 - - - +
746A ILE* 1.3 61.8 + - - +
748A THR* 3.8 0.9 - - - -
749A THR* 2.8 29.3 + - - -
791A VAL* 3.8 19.5 - - + -
792A ARG 4.4 8.9 - - - +
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Residues in contact with ILE 746 (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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731A ILE* 4.0 33.2 - - + -
736A ALA* 4.1 18.6 - - + -
741A VAL* 3.9 15.5 - - + +
742A SER 3.0 17.7 + - - +
743A ILE* 3.5 12.1 - - + +
745A ASP* 1.3 79.3 - - - +
747A ASN* 1.3 69.1 + - - +
749A THR* 3.1 10.0 + - - -
750A LEU* 3.1 11.0 + - + -
791A VAL* 4.2 8.9 - - + +
801A PHE* 3.7 20.2 - - + -
804A PHE* 3.6 39.0 - - + -
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Residues in contact with ASN 747 (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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731A ILE* 4.4 10.8 - - - +
743A ILE* 3.0 34.5 + - - +
744A ASN* 4.1 3.3 - - - +
746A ILE* 1.3 86.7 - - - +
748A THR* 1.3 55.9 + - - +
750A LEU* 3.5 14.1 + - - +
751A GLY* 3.0 24.9 + - - -
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Residues in contact with THR 748 (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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201A VAL* 3.7 23.8 - - + +
204A ILE* 4.3 22.7 - - + -
744A ASN* 3.0 22.4 + - - +
745A ASP 3.8 2.9 - - - -
747A ASN* 1.3 73.8 - - - +
749A THR* 1.3 57.2 + - - +
751A GLY* 3.1 1.4 + - - -
752A ALA* 2.8 35.0 + - + +
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Residues in contact with THR 749 (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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199A THR* 4.2 6.8 - - - -
200A PRO* 3.7 37.0 - - + +
201A VAL* 4.3 3.1 - - - +
745A ASP 2.8 21.8 + - - -
746A ILE 3.3 4.5 - - - -
748A THR* 1.3 72.4 - - - +
750A LEU* 1.3 65.4 - - - +
753A ALA* 3.1 28.4 + - - +
789A TRP* 4.4 16.6 - - + -
790A TYR 4.5 3.1 - - - +
791A VAL* 3.7 27.3 - - + +
801A PHE* 4.0 9.6 - - + -
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Residues in contact with LEU 750 (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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729A ILE* 4.1 35.2 - - + -
731A ILE* 5.2 4.5 - - + -
746A ILE* 3.1 7.8 + - + +
747A ASN* 3.6 18.8 - - - +
749A THR* 1.3 75.7 - - - +
751A GLY* 1.3 63.8 + - - +
754A TRP* 3.0 57.9 + - + +
786A ILE* 4.6 3.1 - - + -
801A PHE* 3.8 28.2 - - + -
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Residues in contact with GLY 751 (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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747A ASN 3.0 15.7 + - - -
748A THR* 3.1 2.2 + - - -
750A LEU* 1.3 79.4 - - - +
752A ALA* 1.3 57.0 + - - +
755A GLY* 2.7 29.0 + - - -
756A GLY 2.9 11.2 + - - +
757A SER* 5.4 0.4 - - - -
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Residues in contact with ALA 752 (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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188A MET* 4.2 2.5 - - + -
200A PRO* 4.2 13.9 - - + -
204A ILE* 4.1 17.9 - - + -
748A THR* 2.8 21.6 + - + +
751A GLY* 1.3 70.4 - - - +
753A ALA* 1.3 65.9 + - - +
756A GLY* 3.3 8.6 + - - +
757A SER* 3.9 28.3 - - - -
773A VAL* 3.5 4.9 - - + +
774A MET* 3.2 23.4 - - - -
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Residues in contact with ALA 753 (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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188A MET* 4.2 4.9 - - + +
200A PRO* 4.9 0.6 - - + +
749A THR 3.1 19.9 + - - +
752A ALA* 1.3 78.5 - - - +
754A TRP* 1.3 71.6 + - + +
774A MET* 3.7 1.7 - - - +
775A SER* 3.0 35.4 + - - +
780A ARG* 3.7 5.7 - - - -
789A TRP* 3.5 38.4 - - + -
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Residues in contact with TRP 754 (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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750A LEU* 3.0 45.9 + - + +
753A ALA* 1.3 89.4 - - + +
755A GLY* 1.3 61.6 + - - +
756A GLY 3.6 0.2 - - - -
774A MET* 4.1 7.5 - - - +
780A ARG* 3.1 55.4 - - + +
781A MET 5.0 0.2 - - - -
782A LEU 3.6 25.1 - - - -
783A PRO* 5.5 0.2 - - + -
785A ASP* 3.9 6.5 - - + -
786A ILE* 3.3 43.1 + - + +
789A TRP* 3.7 22.4 - - - +
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Residues in contact with GLY 755 (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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50A PRO* 4.8 2.1 - - - +
51A GLY* 4.0 30.5 + - - -
750A LEU 4.1 0.2 + - - -
751A GLY* 2.7 19.3 + - - -
754A TRP* 1.3 75.9 - - - +
756A GLY* 1.3 61.7 + - - +
774A MET* 3.6 10.0 - - - +
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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