Contacts of the helix formed by residues 735 - 748 (chain A) in PDB entry 3L7A
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 ILE 735 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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731A TYR* 3.0 38.0 + - + +
732A TYR 3.8 4.9 - - - +
733A ASP 3.6 0.8 - - - -
734A ARG* 1.3 86.9 - - + +
736A PRO* 1.3 66.8 - - + +
737A GLU* 4.2 5.4 - - + +
738A LEU* 3.1 34.1 + - + +
739A ARG* 3.1 19.9 + - - -
774A PHE 5.0 2.9 - - - +
777A TYR* 3.9 18.2 - - + -
778A GLU* 3.7 40.4 - - + +
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Residues in contact with PRO 736 (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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734A ARG 3.6 9.9 - - - +
735A ILE* 1.3 85.4 - - + +
737A GLU* 1.3 59.6 + - + +
739A ARG* 3.3 29.7 + - - +
740A GLN* 3.1 28.1 + - - +
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Residues in contact with GLU 737 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
585A THR* 4.1 10.1 - - + +
588A ASN* 5.2 1.9 + - - +
589A ARG* 3.0 53.5 + - - +
735A ILE* 3.3 7.7 - - + +
736A PRO* 1.3 80.7 - - + +
738A LEU* 1.3 61.6 + - - +
740A GLN* 3.7 16.1 + - - +
741A ILE* 3.4 26.9 + - - +
777A TYR* 3.9 14.8 + - + +
781A VAL* 5.4 0.5 - - - +
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Residues in contact with LEU 738 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581A LEU* 4.1 22.7 - - + -
731A TYR* 3.9 27.4 - - + +
732A TYR* 4.1 2.9 - - - +
735A ILE* 3.1 28.0 + - + +
737A GLU* 1.3 77.2 - - - +
739A ARG* 1.3 63.7 + - - +
741A ILE* 3.2 7.3 + - + +
742A ILE* 3.1 25.6 + - + +
774A PHE* 3.9 52.0 - - + -
777A TYR* 4.1 24.8 + - + -
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Residues in contact with ARG 739 (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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732A TYR* 3.1 55.1 + - + +
733A ASP* 2.8 33.9 + - - +
734A ARG 4.4 0.4 - - - -
735A ILE 3.1 6.0 + - - +
736A PRO* 3.3 45.0 + - - +
738A LEU* 1.3 76.5 - - - +
740A GLN* 1.3 57.4 + - - +
742A ILE* 3.3 2.3 + - - +
743A GLU* 2.9 50.0 + - - +
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Residues in contact with GLN 740 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588A ASN* 3.7 36.7 + - - +
736A PRO 3.1 12.8 + - - +
737A GLU* 3.7 20.0 - - - +
739A ARG* 1.3 75.7 - - - +
741A ILE* 1.3 56.3 + - - +
743A GLU* 3.3 12.4 + - - +
744A GLN* 2.9 39.5 + - + +
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Residues in contact with ILE 741 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581A LEU* 3.4 41.3 - - + +
584A ILE* 3.7 33.0 - - + -
585A THR* 3.2 32.3 - - - +
588A ASN* 4.0 8.5 - - - +
737A GLU 3.4 16.1 + - - +
738A LEU* 3.2 9.5 + - + +
740A GLN* 1.3 76.4 - - - +
742A ILE* 1.3 59.6 + - - +
744A GLN* 3.1 11.5 + - + +
745A LEU* 2.9 32.3 + - + +
777A TYR* 4.0 9.4 - - + +
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Residues in contact with ILE 742 (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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581A LEU* 5.0 8.1 - - + -
732A TYR* 3.7 28.7 - - + +
738A LEU* 3.1 15.8 + - + +
739A ARG 3.8 6.1 - - - +
741A ILE* 1.3 76.0 - - - +
743A GLU* 1.3 58.6 + - + +
745A LEU* 3.4 20.9 + - + +
746A SER* 3.0 35.9 + - - +
762A VAL* 4.0 24.5 - - + -
765A LEU* 4.5 11.2 - - + -
766A MET* 4.4 7.2 - - + -
774A PHE* 3.6 35.4 - - + -
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Residues in contact with GLU 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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732A TYR* 3.5 21.5 + - - +
739A ARG* 2.9 41.1 + - - +
740A GLN* 3.6 9.2 + - - +
742A ILE* 1.3 78.1 - - + +
744A GLN* 1.3 56.6 + - - +
746A SER* 3.9 4.9 - - - -
747A SER* 2.9 34.7 + - - -
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Residues in contact with GLN 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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584A ILE* 3.5 13.0 - - - +
588A ASN* 2.9 42.7 + - - +
740A GLN* 2.9 25.3 + - + +
741A ILE* 3.1 11.6 + - - +
743A GLU* 1.3 77.2 - - - +
745A LEU* 1.3 61.7 + - - +
747A SER* 3.4 5.9 + - - -
748A GLY 3.4 3.5 + - - -
749A PHE* 3.0 68.3 + - + +
750A PHE* 4.1 11.0 + - + -
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Residues in contact with LEU 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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581A LEU* 5.0 7.2 - - + -
584A ILE* 4.5 7.6 - - + -
622A LEU* 3.8 33.4 - - + -
741A ILE* 2.9 29.3 + - + +
742A ILE* 3.8 19.5 - - + +
744A GLN* 1.3 77.5 - - - +
746A SER* 1.3 63.7 + - - +
748A GLY* 3.6 8.7 + - - -
750A PHE* 4.0 19.4 + - + +
751A SER* 5.2 0.2 + - - -
755A PRO 4.3 3.5 - - - +
758A PHE* 4.5 28.3 + - + +
761A ILE* 5.0 14.6 - - + -
762A VAL* 3.8 21.9 - - + +
765A LEU* 5.1 3.1 - - + -
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Residues in contact with SER 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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742A ILE* 3.0 20.5 + - - +
743A GLU* 3.9 6.3 - - - -
745A LEU* 1.3 77.3 - - - +
747A SER* 1.3 59.5 + - - +
748A GLY 3.4 0.7 + - - -
755A PRO 3.5 11.8 - - - +
756A ASP* 5.0 2.9 - - - +
758A PHE 6.3 0.2 - - - -
759A LYS* 6.2 2.0 - - - +
762A VAL* 3.6 26.0 - - - +
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Residues in contact with SER 747 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
743A GLU 2.9 21.1 + - - -
744A GLN* 3.4 11.4 + - - -
746A SER* 1.3 76.6 - - - +
748A GLY* 1.3 57.6 + - - +
749A PHE* 3.9 6.1 + - - +
755A PRO* 4.1 11.7 - - - +
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Residues in contact with GLY 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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744A GLN 3.4 2.6 + - - -
745A LEU 3.6 3.9 + - - -
746A SER 3.3 4.2 - - - -
747A SER* 1.3 80.0 - - - +
749A PHE* 1.3 66.6 + - - +
750A PHE 3.2 3.1 - - - -
751A SER* 3.1 26.2 + - - -
752A PRO* 3.2 9.4 - - - +
755A PRO* 3.5 25.4 - - - -
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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