Contacts of the helix formed by residues 760 - 778 (chain B) in PDB entry 1L8A
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 760 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
657B SER 2.5 26.9 + - - -
658B TYR* 3.5 18.6 - - - +
659B ASP 4.9 0.7 - - - +
712B GLY* 3.2 10.1 + - - -
758B VAL* 3.2 4.7 - - - -
759B THR* 1.3 82.9 + - - +
761B PHE* 1.3 64.4 + - - +
762B THR 3.9 1.6 + - - +
763B GLU* 3.0 26.7 + - - +
764B LEU* 3.2 23.0 + - - +
807B PHE* 5.4 2.5 - - - -
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Residues in contact with PHE 761 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
729B LEU* 4.3 9.0 - - + -
730B GLY 5.2 0.9 - - - -
731B SER* 4.6 3.6 - - - -
758B VAL* 3.3 45.1 - - + +
760B SER* 1.3 71.7 - - - +
762B THR* 1.3 57.9 + - - +
764B LEU* 3.3 5.6 + - + -
765B ALA* 2.9 25.3 + - - +
788B ILE* 5.2 2.2 - - + -
799B ALA* 4.2 10.1 - - + -
801B THR* 3.7 22.9 - - + -
807B PHE* 3.2 49.8 - + + +
808B ALA* 3.7 18.2 - - + -
810B GLN* 3.6 3.4 - - - +
811B VAL* 3.4 33.5 - - + +
820B TYR* 3.4 21.8 - - - -
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Residues in contact with THR 762 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
646B HIS 4.3 2.6 + - - -
650B LEU* 3.5 35.9 - - + +
655B CYS 5.9 0.2 - - - +
657B SER* 4.7 17.6 - - - +
760B SER* 3.1 4.8 - - - -
761B PHE* 1.3 76.5 - - - +
763B GLU* 1.3 61.1 + - - +
765B ALA* 3.2 2.4 + - - +
766B ARG* 3.0 51.0 + - + +
807B PHE* 3.7 12.5 - - - -
810B GLN* 3.1 23.8 + - - +
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Residues in contact with GLU 763 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
656B ILE* 3.7 38.2 - - + +
657B SER 4.3 3.1 + - - +
658B TYR* 4.6 6.7 - - - +
676B ARG* 5.1 5.4 + - - -
710B ARG 5.2 1.3 - - - +
711B LYS 4.1 14.2 - - - +
760B SER* 3.0 33.4 + - - +
762B THR* 1.3 78.5 - - - +
764B LEU* 1.3 57.7 + - - +
766B ARG* 3.2 37.3 + - - +
767B ASP* 3.0 28.6 + - - +
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Residues in contact with LEU 764 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
711B LYS 3.5 18.8 - - - +
712B GLY* 3.5 20.2 - - - +
713B ILE* 3.6 31.9 - - + -
758B VAL* 4.4 10.1 - - + -
760B SER 3.2 14.6 + - - +
761B PHE* 3.5 10.8 - - + +
762B THR 3.2 0.2 - - - -
763B GLU* 1.3 77.0 - - - +
765B ALA* 1.3 57.1 + - - +
767B ASP* 3.4 6.5 + - + +
768B GLY* 3.0 24.6 + - - -
787B TYR* 3.8 17.0 - - + -
788B ILE* 4.2 34.6 + - + +
811B VAL* 4.0 9.5 - - + +
814B TYR* 4.7 2.4 - - - -
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Residues in contact with ALA 765 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
761B PHE 2.9 12.6 + - - +
762B THR* 3.2 3.1 + - + +
764B LEU* 1.3 73.8 - - - +
766B ARG* 1.3 60.8 + - + +
768B GLY* 3.2 1.4 + - - -
769B GLN* 2.8 42.2 + - - +
810B GLN* 3.4 45.5 - - + +
811B VAL* 3.7 6.9 - - + +
814B TYR* 3.8 7.9 - - + -
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Residues in contact with ARG 766 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
884A ARG* 3.7 40.3 - - - +
650B LEU* 3.2 27.7 + - - +
652B ILE 2.8 28.1 + - - -
653B PRO* 3.5 17.6 + - - +
655B CYS 2.9 23.2 + - - -
656B ILE* 4.0 5.3 - - - +
762B THR* 3.0 29.3 + - + +
763B GLU* 3.2 30.7 + - - +
765B ALA* 1.3 73.3 - - + +
767B ASP* 1.3 61.5 + - - +
769B GLN* 3.2 13.9 + - - +
770B ASP* 2.8 37.2 + - - +
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Residues in contact with ASP 767 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
711B LYS* 5.9 2.4 - - - +
763B GLU 3.0 18.8 + - - +
764B LEU* 3.6 7.9 - - + +
766B ARG* 1.3 77.1 - - - +
768B GLY* 1.3 59.8 + - - +
770B ASP* 3.2 9.8 + - - +
771B CYS* 2.9 35.6 + - - -
786B PRO* 3.4 5.7 - - - +
787B TYR* 2.7 42.9 + - + +
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Residues in contact with GLY 768 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
764B LEU 3.0 15.9 + - - -
765B ALA 3.6 2.7 - - - -
767B ASP* 1.3 73.9 + - - +
769B GLN* 1.3 64.2 + - - +
771B CYS* 3.2 2.3 + - - +
772B GLU* 3.1 20.6 + - - +
786B PRO* 3.9 15.0 - - - -
814B TYR* 3.3 33.6 - - - -
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Residues in contact with GLN 769 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
805A LYS* 3.5 34.6 + - + +
806A LEU* 4.2 10.3 - - - +
809A GLU* 3.0 25.9 + - - +
826A ASP* 4.0 12.3 + - - +
884A ARG* 5.0 3.7 - - - +
765B ALA* 2.8 25.1 + - - +
766B ARG* 3.6 25.2 + - - +
768B GLY* 1.3 72.3 - - - +
770B ASP* 1.3 60.3 + - - +
772B GLU* 4.0 2.1 - - - +
773B ARG* 2.9 32.4 + - - +
814B TYR* 3.0 23.8 + - + +
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Residues in contact with ASP 770 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
882A ASN* 2.9 27.2 - - - +
884A ARG* 2.5 34.1 + - - -
885A LEU* 4.9 3.5 - - - +
766B ARG 2.8 24.1 + - - +
767B ASP* 3.4 8.9 - - - +
769B GLN* 1.3 79.4 - - - +
771B CYS* 1.3 58.1 + - - +
773B ARG* 3.7 4.0 + - - +
774B TRP* 3.1 29.1 + - - +
784B ARG* 5.3 1.9 + - - -
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Residues in contact with CYS 771 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
767B ASP* 2.9 29.0 + - - +
768B GLY 3.2 4.9 + - - +
770B ASP* 1.3 75.4 - - - +
772B GLU* 1.3 61.0 + - - +
774B TRP* 3.3 4.1 + - - +
775B ASN* 2.8 35.7 + - - +
784B ARG* 3.8 33.4 - - + +
785B VAL 3.8 23.6 - - - -
786B PRO* 3.8 16.8 - - + -
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Residues in contact with GLU 772 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
821A ARG* 5.8 4.6 + - + -
768B GLY 3.1 17.3 + - - +
769B GLN* 4.1 2.9 - - - +
771B CYS* 1.3 73.8 - - - +
773B ARG* 1.3 67.2 + - - +
775B ASN* 3.3 23.7 + - - +
776B MET* 2.9 27.2 + - - +
784B ARG 4.4 0.2 - - - +
786B PRO* 3.9 21.8 - - - +
813B THR* 5.2 6.1 - - + -
814B TYR* 3.9 19.4 - - + -
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Residues in contact with ARG 773 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
805A LYS* 4.3 16.2 - - - +
842A GLU* 2.8 41.2 + - - +
878A ALA 4.7 3.6 + - - -
880A LYS* 2.9 33.5 + - - +
881A VAL 3.7 3.2 + - - -
882A ASN* 3.4 41.5 + - - +
883A PRO* 3.9 2.4 - - - +
769B GLN 2.9 19.0 + - - +
770B ASP* 3.7 5.0 + - - +
772B GLU* 1.3 78.4 - - - +
774B TRP* 1.3 73.5 + - - +
776B MET* 3.3 17.7 - - + +
777B LEU* 3.1 41.9 + - + +
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Residues in contact with TRP 774 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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878A ALA 5.2 0.2 - - - -
879A ASP* 4.7 1.8 + - - -
770B ASP 3.1 15.9 + - - +
771B CYS 3.6 2.7 - - - +
773B ARG* 1.3 90.5 - - - +
775B ASN* 1.3 84.6 + - - +
777B LEU* 3.0 4.2 + - - -
778B HIS* 2.7 78.2 + + + -
781B GLU* 3.6 33.7 - - + -
782B THR 3.4 23.6 - - - -
783B PRO* 4.5 0.7 - - + -
784B ARG* 3.3 54.8 - - + +
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Residues in contact with ASN 775 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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821A ARG* 5.3 1.6 - - - +
858A LYS* 5.5 2.8 + - - -
771B CYS 2.8 22.3 + - - +
772B GLU* 3.3 29.0 + - - +
773B ARG 3.3 0.2 - - - -
774B TRP* 1.3 90.3 - - - +
776B MET* 1.3 58.8 + - - +
778B HIS 2.9 29.8 + - - +
779B PRO* 3.3 3.8 - - - +
783B PRO* 3.3 17.9 - - + +
784B ARG* 2.6 47.0 + - - +
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Residues in contact with MET 776 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
821A ARG* 3.3 49.7 + - + +
823A LEU* 3.6 31.0 - - + -
842A GLU* 5.9 2.0 - - + +
847A TYR* 4.7 12.6 - - + +
850A VAL* 4.1 17.9 - - - +
851A ALA* 3.9 17.9 - - + -
854A GLY* 5.8 0.2 - - - -
858A LYS* 5.4 2.8 + - - +
867A VAL* 4.4 3.5 - - - +
871A ILE* 4.0 6.8 - - - +
772B GLU 2.9 15.7 + - - +
773B ARG* 3.3 21.5 - - + +
775B ASN* 1.3 75.0 - - - +
777B LEU* 1.3 72.8 + - + +
778B HIS 3.3 0.2 - - - -
779B PRO* 3.6 13.0 - - - +
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Residues in contact with LEU 777 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
842A GLU* 4.6 7.0 - - - +
847A TYR* 4.5 9.2 - - + -
850A VAL* 4.8 4.3 - - + -
871A ILE* 3.5 13.6 - - + +
876A ILE* 4.2 20.9 - - + -
877A ASP 4.8 2.2 - - - +
878A ALA* 3.2 42.5 - - - +
773B ARG* 3.1 55.5 + - + +
774B TRP* 3.0 7.2 + - - +
776B MET* 1.3 94.4 - - + +
778B HIS* 1.3 68.9 + - + +
779B PRO* 3.3 8.3 - - - +
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Residues in contact with HIS 778 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
878A ALA* 3.1 29.1 + - + +
879A ASP* 2.6 28.5 + - - -
774B TRP* 2.7 75.8 + + + +
775B ASN* 3.1 7.7 - - - +
777B LEU* 1.3 85.5 - - + +
779B PRO* 1.3 59.2 - - - +
780B LEU 3.3 3.1 - - - -
781B GLU* 3.0 50.4 + - - +
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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
------------------------------------------------------------
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