Contacts of the helix formed by residues 776 - 792 (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 ASP 776 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575A ARG* 2.8 43.9 + - - +
578A LEU* 4.3 5.4 - - + -
668A THR* 5.1 1.4 - - - -
669A ALA 5.5 1.0 + - - -
691A THR* 4.6 2.4 - - - +
711A PHE* 4.2 9.3 - - + -
712A GLY* 3.2 9.1 - - - -
713A MET* 2.8 50.3 + - - +
772A LYS 3.8 1.0 + - - -
773A VAL 3.4 3.7 + - - +
774A PHE 3.2 0.2 - - - -
775A ALA* 1.3 79.0 - - - +
777A TYR* 1.3 63.6 + - - +
778A GLU 3.5 1.8 - - - -
779A GLU* 3.6 7.1 + - - +
780A TYR* 3.0 24.4 + - - +
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Residues in contact with TYR 777 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578A LEU* 3.9 12.1 - - + -
581A LEU* 4.1 29.8 - - + -
582A HIS 5.2 0.7 - - - -
585A THR* 2.7 38.7 + - - +
735A ILE* 3.9 31.2 - - + -
737A GLU* 3.9 17.1 + - + +
738A LEU* 4.1 26.5 - - + -
741A ILE* 4.0 5.0 - - + +
773A VAL 3.5 8.9 + - - +
774A PHE* 3.2 20.3 + - - +
775A ALA 3.5 0.2 - - - -
776A ASP* 1.3 78.0 - - - +
778A GLU* 1.3 72.7 + - + +
780A TYR* 3.3 2.6 + + - +
781A VAL* 3.0 44.4 + - + +
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Residues in contact with GLU 778 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
731A TYR* 6.1 0.2 - - - -
735A ILE* 3.7 42.3 - - + +
774A PHE 4.6 1.6 + - - -
775A ALA 5.3 1.2 + - - -
776A ASP 3.5 0.2 - - - -
777A TYR* 1.3 86.9 - - + +
779A GLU* 1.3 63.2 + - + +
781A VAL* 3.4 4.0 + - - +
782A LYS* 3.1 51.9 + - - +
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Residues in contact with GLU 779 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
710A ILE 5.1 0.2 - - - +
711A PHE* 3.7 11.4 - - - +
712A GLY* 2.9 46.1 + - - +
714A ARG* 5.1 2.1 + - - -
776A ASP* 3.6 8.6 + - - +
777A TYR 3.4 0.6 - - - -
778A GLU* 1.3 78.0 - - + +
780A TYR* 1.3 57.1 + - - +
782A LYS* 3.5 8.8 + - + +
783A CYS* 3.0 30.3 + - - +
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Residues in contact with TYR 780 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578A LEU* 3.5 40.8 - - + -
579A ASN* 3.7 15.1 + - - -
582A HIS* 3.5 21.3 - + + -
664A GLU* 2.8 31.1 + - - -
666A ILE* 3.7 16.5 - - + +
689A ILE* 3.9 10.8 - - + -
711A PHE* 3.5 32.9 - + + -
776A ASP 3.0 20.7 + - - +
777A TYR* 3.5 5.4 - + - +
779A GLU* 1.3 74.2 - - - +
781A VAL* 1.3 62.4 + - + +
783A CYS* 3.3 2.3 + - - +
784A GLN* 3.0 54.1 + - - +
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Residues in contact with VAL 781 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
582A HIS* 4.3 22.3 + - + -
585A THR* 4.4 9.4 - - + +
586A LEU* 6.1 0.2 - - + -
589A ARG* 3.6 37.0 - - - +
737A GLU* 5.4 0.2 - - - +
777A TYR* 3.0 53.1 + - + +
778A GLU* 3.9 4.9 - - - +
780A TYR* 1.3 75.5 - - + +
782A LYS* 1.3 64.9 + - + +
784A GLN* 3.3 9.0 + - - +
785A GLU* 3.1 24.3 + - - +
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Residues in contact with LYS 782 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
778A GLU* 3.1 44.1 + - - +
779A GLU* 3.9 8.3 - - + +
781A VAL* 1.3 78.4 - - + +
783A CYS* 1.3 61.2 + - - +
785A GLU* 3.2 29.3 + - - +
786A ARG* 3.3 17.1 + - - +
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Residues in contact with CYS 783 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
689A ILE* 3.7 20.4 - - + -
709A PHE* 3.8 33.9 - - - -
710A ILE 4.1 0.7 - - - -
711A PHE* 3.9 17.3 - - + -
779A GLU 3.0 19.6 + - - +
780A TYR 3.6 4.7 - - - +
782A LYS* 1.3 75.6 - - - +
784A GLN* 1.3 58.1 + - - +
786A ARG* 3.0 41.5 + - - +
787A VAL* 3.1 15.2 + - - +
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Residues in contact with GLN 784 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564A ASP* 3.9 0.2 + - - -
582A HIS* 3.3 46.6 + - + +
601A ARG* 2.7 47.7 + - - +
662A LEU* 3.7 9.2 - - - +
664A GLU* 3.1 26.5 + - - -
689A ILE* 3.7 15.0 - - + +
780A TYR* 3.0 38.0 + - + +
781A VAL 3.5 7.6 - - - +
783A CYS* 1.3 72.6 - - - +
785A GLU* 1.3 65.4 + - + +
787A VAL* 3.3 5.9 + - - +
788A SER* 3.1 10.8 + - - -
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Residues in contact with GLU 785 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586A LEU* 6.5 0.7 - - + -
589A ARG* 2.8 38.6 + - - +
781A VAL* 3.1 15.9 + - + +
782A LYS* 3.2 21.7 + - - +
784A GLN* 1.3 75.6 - - - +
786A ARG* 1.3 58.4 + - + +
788A SER* 3.3 8.2 + - - +
789A ALA* 3.0 28.1 + - - +
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Residues in contact with ARG 786 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
708A PHE 5.0 3.6 + - - -
709A PHE* 3.9 29.5 - - + +
710A ILE 4.1 12.5 + - - +
782A LYS 3.6 11.1 + - - +
783A CYS* 3.0 34.2 + - - +
785A GLU* 1.3 74.3 - - + +
787A VAL* 1.3 63.3 + - - +
789A ALA* 3.5 8.8 + - - +
790A LEU* 3.2 22.5 + - - +
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Residues in contact with VAL 787 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
562A LEU* 3.9 17.9 - - + -
601A ARG* 4.1 7.4 - - - +
662A LEU* 3.9 28.3 - - + -
689A ILE* 4.5 6.5 - - + -
709A PHE* 3.7 38.1 - - + -
783A CYS 3.1 13.4 + - - +
784A GLN* 3.4 16.8 - - - +
785A GLU 3.3 0.2 - - - -
786A ARG* 1.3 75.3 - - - +
788A SER* 1.3 65.1 + - - +
790A LEU* 3.3 1.9 + - - -
791A TYR* 3.0 21.5 + - - +
797A TRP* 3.7 13.8 - - + -
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Residues in contact with SER 788 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
562A LEU* 5.0 1.1 - - - +
599A VAL* 3.4 35.8 + - - +
601A ARG* 2.9 31.3 + - - +
784A GLN 3.1 6.1 + - - -
785A GLU* 3.3 10.5 + - - -
787A VAL* 1.3 76.1 - - - +
789A ALA* 1.3 62.0 + - - +
791A TYR* 3.4 6.0 + - - +
792A LYS* 3.3 19.4 + - - +
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Residues in contact with ALA 789 (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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785A GLU 3.0 13.5 + - - +
786A ARG* 3.5 13.7 - - - +
787A VAL 3.2 0.2 - - - -
788A SER* 1.3 76.7 - - - +
790A LEU* 1.3 61.2 + - - +
792A LYS* 3.4 29.3 + - - +
793A ASN* 4.1 4.2 + - - +
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Residues in contact with LEU 790 (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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687A LEU* 4.0 2.9 - - + -
709A PHE* 3.8 14.8 - - + -
786A ARG 3.2 14.1 + - - +
787A VAL 3.3 4.0 + - - +
789A ALA* 1.3 76.6 - - - +
791A TYR* 1.3 60.3 + - - +
793A ASN* 3.0 31.7 + - + +
796A GLU* 3.9 26.7 - - + +
797A TRP* 3.8 27.1 - - + +
800A MET* 3.6 40.2 - - + -
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Residues in contact with TYR 791 (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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542A LYS* 3.1 26.5 + - - -
560A ASN 4.0 12.1 + - - -
561A SER 3.6 3.1 + - - -
562A LEU* 3.7 39.7 - - + -
599A VAL* 3.8 20.4 - - + -
600A PRO* 6.1 0.9 - - + -
661A ASP* 3.5 21.2 + - - -
787A VAL 3.0 16.8 + - - +
788A SER 3.8 5.4 - - - +
789A ALA 3.3 0.4 - - - -
790A LEU* 1.3 76.6 - - - +
792A LYS* 1.3 62.1 + - - +
793A ASN 3.1 1.5 + - - -
794A PRO* 4.0 13.0 - - - +
797A TRP* 3.6 36.7 - + + +
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Residues in contact with LYS 792 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597A PHE* 4.6 19.4 - - + -
599A VAL* 3.6 28.7 - - + +
788A SER 3.3 9.9 + - - +
789A ALA* 3.4 19.5 - - - +
790A LEU 3.2 0.4 - - - -
791A TYR* 1.3 75.9 - - - +
793A ASN* 1.3 55.2 + - - +
794A PRO* 3.2 10.5 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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