Contacts of the helix formed by residues 760 - 778 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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657A SER 2.5 27.7 + - - -
658A TYR* 3.4 18.8 - - - +
659A ASP 4.8 1.1 - - - +
712A GLY* 3.2 7.6 + - - -
758A VAL* 3.2 5.7 - - - -
759A THR* 1.3 82.7 - - - +
761A PHE* 1.3 63.9 + - - +
762A THR 3.2 2.1 + - - -
763A GLU* 3.0 24.7 + - - +
764A LEU* 3.3 23.6 + - - +
807A PHE* 5.3 2.7 - - - -
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Residues in contact with PHE 761 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
729A LEU* 4.0 17.7 - - + -
730A GLY 5.1 2.0 - - - -
731A SER* 4.4 6.7 - - - -
758A VAL* 3.6 41.7 + - + +
760A SER* 1.3 72.2 - - - +
762A THR* 1.3 57.1 + - - +
764A LEU* 3.5 3.7 + - + -
765A ALA* 2.9 24.8 + - - +
788A ILE* 5.4 1.1 - - + -
799A ALA* 4.2 7.2 - - + -
800A SER 5.4 0.7 - - - -
801A THR* 3.6 18.4 - - - -
807A PHE* 3.1 51.7 - + + +
808A ALA* 3.6 21.1 - - + -
810A GLN* 3.5 3.3 + - - +
811A VAL* 3.3 28.8 - - + +
820A TYR* 3.4 21.8 - - - -
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Residues in contact with THR 762 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
646A HIS* 4.4 4.3 + - - -
650A LEU* 3.6 34.8 - - + +
657A SER* 4.7 14.5 - - - +
760A SER* 3.1 5.3 - - - +
761A PHE* 1.3 76.0 - - - +
763A GLU* 1.3 68.7 + - - +
764A LEU 3.1 1.1 - - - -
765A ALA* 3.1 2.4 + - - +
766A ARG* 2.9 46.0 + - + +
807A PHE* 3.7 12.9 - - - -
810A GLN* 3.1 23.6 + - - +
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Residues in contact with GLU 763 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
656A ILE* 3.7 40.5 - - + +
657A SER 4.3 3.7 + - - +
658A TYR* 4.5 7.9 - - - +
676A ARG* 5.0 6.1 + - - -
710A ARG 5.1 0.9 - - - +
711A LYS 3.8 18.8 - - - +
760A SER* 3.0 26.6 + - - +
762A THR* 1.3 77.5 - - - +
764A LEU* 1.3 57.1 + - - +
766A ARG* 3.5 34.8 + - - +
767A ASP* 3.0 28.4 + - - +
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Residues in contact with LEU 764 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
711A LYS 3.3 20.6 - - - +
712A GLY* 3.6 9.2 - - - +
713A ILE* 3.5 43.1 - - + -
758A VAL* 3.7 15.7 - - + -
760A SER 3.3 9.3 + - - +
761A PHE* 3.5 9.0 - - + +
762A THR 3.1 0.4 - - - -
763A GLU* 1.3 74.6 - - - +
765A ALA* 1.3 59.7 + - - +
767A ASP* 3.3 8.0 + - + +
768A GLY* 2.9 25.1 + - - -
787A TYR* 4.2 13.9 - - + -
788A ILE* 3.9 35.3 + - + +
811A VAL* 4.0 9.2 - - + -
814A TYR* 4.7 2.4 - - - -
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Residues in contact with ALA 765 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
761A PHE 2.9 12.7 + - - +
762A THR 3.1 3.1 + - - +
764A LEU* 1.3 74.9 - - - +
766A ARG* 1.3 59.3 + - + +
768A GLY* 3.1 2.3 + - - -
769A GLN* 2.8 41.7 + - - +
810A GLN* 3.2 45.5 - - + +
811A VAL* 3.8 7.2 - - + +
814A TYR* 3.8 9.0 - - + -
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Residues in contact with ARG 766 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
650A LEU* 3.0 29.1 + - - +
652A ILE 2.8 26.4 + - - -
653A PRO* 3.3 17.9 + - - +
655A CYS 2.9 23.2 + - - -
656A ILE* 4.2 4.4 - - - +
762A THR* 2.9 31.3 + - + +
763A GLU* 3.5 31.0 + - - +
765A ALA* 1.3 78.7 - - + +
767A ASP* 1.3 56.3 + - - +
769A GLN* 3.3 15.2 + - - +
770A ASP* 2.9 36.8 + - - +
884B ARG* 3.9 37.9 - - - +
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Residues in contact with ASP 767 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
711A LYS* 5.6 4.3 + - - +
763A GLU 3.0 18.1 + - - +
764A LEU* 3.5 8.8 - - + +
765A ALA 3.3 0.2 - - - -
766A ARG* 1.3 75.0 - - - +
768A GLY* 1.3 64.0 + - - +
770A ASP* 3.3 10.2 + - - +
771A CYS* 3.0 29.6 + - - -
786A PRO* 3.3 6.8 - - - +
787A TYR* 2.8 43.1 + - + +
788A ILE 4.5 0.9 + - - -
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Residues in contact with GLY 768 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
764A LEU 2.9 12.9 + - - -
765A ALA 3.1 2.7 + - - -
767A ASP* 1.3 78.2 + - - +
769A GLN* 1.3 60.8 + - - +
771A CYS* 3.2 3.6 + - - +
772A GLU* 3.0 27.7 + - - +
786A PRO* 3.8 13.0 - - - -
814A TYR* 3.2 30.7 - - - -
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Residues in contact with GLN 769 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
765A ALA* 2.8 20.0 + - - +
766A ARG* 3.5 26.8 + - - +
768A GLY* 1.3 75.0 - - - +
770A ASP* 1.3 61.4 + - - +
772A GLU* 3.8 3.9 - - - +
773A ARG* 2.9 31.6 + - - +
814A TYR* 3.1 21.5 - - + +
805B LYS* 3.4 46.1 + - + +
806B LEU* 4.3 9.3 - - - +
809B GLU* 3.4 14.1 + - - +
826B ASP* 4.0 12.8 + - - +
882B ASN* 5.2 0.7 - - - +
884B ARG* 4.6 5.1 + - - +
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Residues in contact with ASP 770 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
766A ARG 2.9 17.7 + - - +
767A ASP* 3.5 9.2 - - - +
768A GLY 3.2 0.2 - - - -
769A GLN* 1.3 77.8 - - - +
771A CYS* 1.3 58.4 + - - +
773A ARG* 3.4 4.1 + - - +
774A TRP* 3.0 30.0 + - - +
882B ASN* 2.7 21.6 + - - +
884B ARG* 2.7 43.7 + - - -
885B LEU* 5.1 4.5 - - - +
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Residues in contact with CYS 771 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
767A ASP* 3.0 25.1 + - - +
768A GLY 3.6 7.4 - - - +
770A ASP* 1.3 75.6 - - - +
772A GLU* 1.3 55.7 + - - +
774A TRP* 3.2 6.3 + - - +
775A ASN* 2.8 41.1 + - - +
784A ARG* 4.1 30.5 - - + +
785A VAL 3.9 9.9 - - - -
786A PRO* 3.9 28.0 - - + -
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Residues in contact with GLU 772 (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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768A GLY 3.0 17.2 + - - +
769A GLN* 3.9 4.3 - - - +
771A CYS* 1.3 75.1 - - - +
773A ARG* 1.3 57.5 + - - +
775A ASN* 3.3 19.0 + - - +
776A MET* 2.9 30.3 + - - +
786A PRO* 4.1 11.8 - - - +
813A THR* 4.4 14.4 - - + +
814A TYR* 3.2 29.4 - - + +
821B ARG* 5.4 0.7 + - - -
858B LYS* 5.9 1.4 + - - -
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Residues in contact with ARG 773 (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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769A GLN 2.9 20.2 + - - +
770A ASP 3.6 4.8 + - - +
772A GLU* 1.3 77.8 - - - +
774A TRP* 1.3 69.0 + - - +
776A MET* 3.4 9.6 + - - +
777A LEU* 3.1 42.8 + - + +
805B LYS* 4.3 15.9 - - - +
842B GLU* 2.6 43.8 + - - +
878B ALA 5.0 2.8 + - - -
880B LYS* 3.0 29.1 + - - +
881B VAL 3.6 7.1 + - - -
882B ASN* 3.5 41.8 - - - +
883B PRO* 3.6 3.8 - - - +
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Residues in contact with TRP 774 (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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770A ASP 3.0 17.2 + - - +
771A CYS* 3.2 5.8 + - - +
773A ARG* 1.3 82.4 - - + +
775A ASN* 1.3 90.1 + - - +
777A LEU* 3.2 3.2 + - - -
778A HIS* 2.8 72.1 + + + -
781A GLU* 3.4 33.9 - - + -
782A THR 3.6 21.5 - - - -
784A ARG* 3.3 58.5 - - + +
878B ALA 5.3 0.2 - - - -
879B ASP* 4.7 2.0 + - - -
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Residues in contact with ASN 775 (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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771A CYS 2.8 21.9 + - - +
772A GLU* 3.6 23.1 + - - +
773A ARG 3.3 0.2 - - - -
774A TRP* 1.3 92.0 - - - +
776A MET* 1.3 62.4 + - - +
778A HIS 3.2 22.4 + - - +
779A PRO* 3.7 4.2 - - - +
783A PRO* 3.4 18.5 - - + +
784A ARG* 2.7 44.6 + - - +
821B ARG* 4.8 7.3 + - - +
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Residues in contact with MET 776 (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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772A GLU 2.9 16.8 + - - +
773A ARG* 3.7 9.4 - - - +
774A TRP 3.3 0.2 - - - -
775A ASN* 1.3 77.4 - - - +
777A LEU* 1.3 66.7 + - + +
778A HIS 3.3 0.6 + - - -
779A PRO* 3.9 9.2 - - - +
821B ARG* 3.4 36.3 + - - +
823B LEU* 4.0 19.1 - - + -
847B TYR* 3.2 51.6 - - + +
850B VAL* 3.9 24.2 - - + +
851B ALA* 3.8 19.5 - - + +
854B GLY* 5.8 0.6 - - - -
867B VAL* 4.7 2.9 - - - +
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Residues in contact with LEU 777 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
773A ARG* 3.1 51.3 + - + +
774A TRP* 3.2 1.5 + - - -
776A MET* 1.3 86.9 - - + +
778A HIS* 1.3 64.8 + - - +
779A PRO* 3.3 10.8 - - - +
842B GLU* 4.4 6.1 - - - +
847B TYR* 4.0 17.7 - - + -
850B VAL* 5.1 2.0 - - + -
871B ILE* 3.6 10.5 - - + +
876B ILE* 3.8 27.4 - - + -
877B ASP 4.5 1.8 - - - +
878B ALA* 3.1 50.6 - - + +
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Residues in contact with HIS 778 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
774A TRP* 2.8 79.9 + + + +
775A ASN* 3.3 8.9 - - - +
777A LEU* 1.3 82.9 - - + +
779A PRO* 1.3 64.8 - - - +
780A LEU 3.2 3.1 - - - -
781A GLU* 3.2 28.2 + - + +
878B ALA* 3.1 31.6 + - + +
879B ASP* 2.8 27.6 + - - -
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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