Contacts of the helix formed by residues 743 - 747 (chain A) in PDB entry 4L01
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 PRO 743 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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634A ALA* 3.2 41.1 - - + +
638A ALA* 4.1 3.6 - - + -
712A HIS 5.6 1.3 - - - +
740A PRO* 5.5 4.0 - - + +
741A GLY 3.3 6.5 - - - +
742A ILE* 1.4 87.0 - - - +
744A ILE* 1.3 65.8 + - - +
745A THR* 3.0 9.4 + - - +
746A VAL* 3.1 16.6 + - - +
747A LEU* 3.7 3.2 + - - +
568B TYR* 3.7 48.7 - - + +
571B SER* 3.9 9.2 - - - +
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Residues in contact with ILE 744 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
712A HIS 5.8 0.8 + - - -
713A GLY* 3.3 33.3 - - - +
742A ILE 3.5 1.6 + - - -
743A PRO* 1.3 71.1 - - - +
745A THR* 1.3 65.1 + - - +
746A VAL 3.0 1.6 + - - -
747A LEU* 3.0 26.1 + - + +
752A CYS* 4.3 7.4 - - - -
755A ARG* 3.8 17.0 - - - +
759A ILE* 3.8 28.7 - - + -
763A CYS* 4.2 22.2 - - + -
767A SER* 3.5 24.6 - - - +
770A LEU* 4.0 25.5 - - + +
774A ALA* 5.8 1.6 - - + -
568B TYR* 5.6 0.2 - - - -
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Residues in contact with THR 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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743A PRO* 4.1 3.3 - - - +
744A ILE* 1.3 77.1 - - - +
746A VAL* 1.3 57.1 + - - +
747A LEU 4.8 0.3 - - - +
767A SER* 3.3 22.0 + - - +
768A LYS* 6.2 1.1 - - - -
770A LEU* 3.6 18.7 - - - +
567B VAL* 4.6 2.6 + - - +
568B TYR* 3.8 16.5 - - - +
571B SER* 3.8 34.5 - - - +
572B GLN* 4.1 13.0 - - + +
575B PHE* 3.3 38.2 - - + -
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Residues in contact with VAL 746 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
594A ARG* 4.3 3.1 + - - -
630A ASP* 4.5 6.7 - - - +
631A ILE* 3.7 29.2 - - + +
634A ALA* 3.6 24.5 - - + -
742A ILE* 3.5 29.6 - - + -
743A PRO 3.6 3.4 - - - +
744A ILE 3.1 0.4 - - - -
745A THR* 1.3 80.6 - - + +
747A LEU* 1.3 65.4 + - - +
748A SER 3.8 0.5 + - - -
571B SER* 3.6 27.1 - - - +
574B SER* 4.0 16.8 - - - +
575B PHE* 5.2 2.9 - - + -
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Residues in contact with LEU 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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593A THR* 3.8 19.1 - - + -
594A ARG* 4.6 2.0 - - - +
742A ILE* 3.8 31.0 - - + +
743A PRO 3.7 10.3 + - - +
744A ILE* 3.0 29.8 + - + +
745A THR 4.8 0.2 - - - +
746A VAL* 1.3 81.2 - - - +
748A SER* 1.3 68.9 + - - +
751A GLU* 3.5 27.6 - - + +
752A CYS* 4.2 12.1 - - - -
755A ARG* 3.8 32.5 - - - +
767A SER* 4.6 8.0 + - - -
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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