Contacts of the helix formed by residues 780 - 798 (chain S) in PDB entry 4US1
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 HIS 780 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
762S GLU* 3.7 43.5 + - + +
763S TRP* 3.4 25.4 - - - +
764S HIS* 3.8 8.4 - - + +
779S LEU* 1.3 73.2 - - - +
781S PRO* 1.4 70.0 - - + +
782S ILE* 3.0 45.0 + - + +
783S GLU* 3.0 4.7 + - + +
784S ILE* 2.9 23.0 + - - +
1038S PRO* 3.5 27.2 + - + +
1039S GLY 3.4 24.7 - - - -
1041S ARG 5.1 2.3 + - - -
1043S SER* 4.2 7.3 + - - -
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Residues in contact with PRO 781 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
779S LEU 3.6 5.8 - - - +
780S HIS* 1.4 89.3 - - - +
782S ILE* 1.4 59.2 + - - +
784S ILE* 4.4 5.2 - - + -
785S ALA* 3.3 23.0 + - - +
854S ARG* 3.8 29.6 - - - +
857S GLU* 3.9 19.3 - - + +
858S ILE* 3.7 25.1 - - + +
861S VAL* 4.6 2.4 - - - +
1037S SER* 4.2 2.9 - - - +
1038S PRO* 3.7 16.8 - - + -
1039S GLY 3.7 21.3 - - - +
1040S VAL* 4.8 2.2 - - + -
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Residues in contact with ILE 782 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
762S GLU* 4.2 6.5 - - + -
780S HIS* 3.0 29.2 + - + +
781S PRO* 1.4 74.5 - - - +
783S GLU* 1.3 58.7 + - - +
785S ALA* 3.5 3.3 + - - +
786S ARG* 2.9 63.5 + - + +
861S VAL* 4.2 19.2 - - + +
1040S VAL* 3.3 44.4 - - - +
1041S ARG 3.6 14.8 - - - +
1042S PRO* 3.6 12.1 - - + -
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Residues in contact with GLU 783 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
761S VAL* 3.6 16.9 - - + +
762S GLU* 2.9 42.0 + - + +
779S LEU* 5.9 0.4 - - + -
780S HIS* 3.0 12.5 + - + +
782S ILE* 1.3 78.6 - - - +
784S ILE* 1.3 59.7 + - - +
786S ARG* 3.2 32.6 + - - +
787S GLN* 2.8 61.8 + - + +
982S ARG 4.4 2.4 - - - +
987S ILE* 3.5 30.7 - - + -
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Residues in contact with ILE 784 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
775S ASP 4.3 0.9 - - - +
776S LEU* 3.2 35.0 - - + +
779S LEU* 3.6 30.7 - - + +
780S HIS 2.9 18.0 + - - +
781S PRO* 3.9 5.8 - - + +
782S ILE 3.4 0.2 - - - -
783S GLU* 1.3 75.2 - - - +
785S ALA* 1.3 54.6 + - - +
787S GLN* 3.8 0.9 - - - +
788S LEU* 2.8 51.4 + - + +
834S TRP* 5.2 3.8 - - + -
835S PHE* 5.5 0.2 - - + -
858S ILE* 3.8 30.3 - - + -
987S ILE* 5.1 0.4 - - - -
991S PHE* 3.5 32.5 - - + -
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Residues in contact with ALA 785 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
781S PRO 3.3 15.8 + - - +
782S ILE 3.8 0.2 - - - +
784S ILE* 1.3 79.7 - - - +
786S ARG* 1.3 53.3 + - - +
789S THR* 2.7 36.9 + - - -
858S ILE* 3.6 18.6 - - + +
861S VAL* 3.5 31.9 - - + -
862S PHE* 3.4 18.0 - - + -
865S LEU* 4.2 2.0 - - - -
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Residues in contact with ARG 786 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
759S PRO* 3.6 31.3 + - - +
760S THR 3.2 26.1 + - - -
761S VAL* 4.6 0.4 - - - +
762S GLU* 3.8 7.3 + - - +
782S ILE* 2.9 39.9 + - + +
783S GLU* 3.2 34.0 + - - +
785S ALA* 1.3 73.4 - - - +
787S GLN* 1.3 64.0 + - - +
789S THR* 3.2 3.6 + - - -
790S LEU* 2.9 32.3 + - - +
861S VAL* 5.1 0.9 - - + +
865S LEU* 4.0 16.2 - - + +
981S LEU* 4.0 32.1 - - + +
1042S PRO* 4.3 19.2 - - - +
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Residues in contact with GLN 787 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
761S VAL* 5.1 0.2 - - - +
783S GLU* 2.8 47.8 + - + +
784S ILE 4.2 0.7 - - - +
786S ARG* 1.3 69.7 - - - +
788S LEU* 1.4 65.3 + - - +
790S LEU* 3.3 14.9 + - - +
791S LEU* 3.2 27.8 + - - +
982S ARG 2.8 27.3 + - - -
983S VAL* 3.7 8.3 - - - +
984S GLU* 3.0 34.1 + - - +
987S ILE* 3.5 32.1 - - + -
988S LYS* 4.4 10.7 - - - +
991S PHE* 4.8 2.9 - - + -
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Residues in contact with LEU 788 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
784S ILE* 2.8 41.5 + - + +
787S GLN* 1.4 73.9 - - - +
789S THR* 1.3 55.8 + - - +
791S LEU* 3.4 3.7 + - + +
792S GLU* 3.0 44.4 + - - +
827S HIS* 3.7 20.4 - - + +
831S LEU* 3.5 33.2 - - + -
835S PHE* 4.5 7.2 - - + -
862S PHE* 3.9 23.6 - - + -
873S GLU* 4.9 0.2 - - - +
991S PHE* 3.6 36.1 - - + -
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Residues in contact with THR 789 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
785S ALA 2.7 24.2 + - - -
786S ARG 3.5 4.7 - - - -
788S LEU* 1.3 72.3 - - - +
790S LEU* 1.3 58.7 + - - +
792S GLU* 4.0 0.2 - - - +
793S SER* 2.8 32.4 + - - -
862S PHE* 3.3 8.5 - - - -
865S LEU* 3.7 14.0 - - + +
867S ASN* 3.0 30.7 + - + +
927S VAL* 4.1 0.9 - - + +
979S TYR* 3.4 44.9 - - + +
981S LEU* 5.0 1.1 - - + -
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Residues in contact with LEU 790 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
786S ARG 2.9 14.9 + - - +
787S GLN* 3.3 19.7 + - - +
789S THR* 1.3 76.6 - - - +
791S LEU* 1.3 56.5 + - - +
793S SER* 3.3 4.8 + - - -
794S ASP* 3.0 39.7 + - - +
979S TYR* 4.0 28.7 - - + +
981S LEU* 3.8 35.9 - - + +
982S ARG 3.8 13.0 - - - +
983S VAL* 3.8 30.1 - - + -
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Residues in contact with LEU 791 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
787S GLN 3.2 16.1 + - - +
788S LEU* 3.7 9.0 - - + +
789S THR 3.4 0.2 - - - -
790S LEU* 1.3 75.3 - - - +
792S GLU* 1.3 54.4 + - - +
794S ASP* 3.4 8.0 + - + +
795S LEU* 2.9 44.9 + - + +
827S HIS* 4.1 20.6 - - + +
988S LYS* 3.4 39.7 - - + +
991S PHE* 3.7 30.1 - - + -
992S GLU* 3.4 31.0 - - + +
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Residues in contact with GLU 792 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
788S LEU* 3.0 29.2 + - - +
789S THR 4.0 2.7 - - - +
791S LEU* 1.3 78.4 - - - +
793S SER* 1.4 57.6 + - - +
795S LEU* 3.9 8.0 - - + +
796S TYR* 3.0 29.3 + - - +
824S MET* 5.2 2.1 - - - +
827S HIS* 2.9 30.6 + - + +
867S ASN* 2.9 25.0 + - - +
869S ASN* 2.8 22.1 + - - +
870S GLY* 3.3 6.1 + - - -
873S GLU* 2.8 29.4 - - - +
927S VAL* 3.6 10.0 - - + +
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Residues in contact with SER 793 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
789S THR 2.8 19.9 + - - -
790S LEU* 3.6 7.0 - - - -
791S LEU 3.2 0.2 - - - -
792S GLU* 1.4 72.7 - - - +
794S ASP* 1.3 61.2 + - - +
796S TYR* 3.3 4.6 + - - +
797S ARG* 2.9 44.6 + - - +
926S CYS 5.0 1.9 + - - -
927S VAL* 3.7 18.6 - - - +
977S GLN 5.0 3.1 + - - -
978S PRO* 5.3 0.5 - - - +
979S TYR* 3.6 25.7 + - - -
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Residues in contact with ASP 794 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
790S LEU* 3.0 22.9 + - - +
791S LEU* 3.6 8.2 - - + +
793S SER* 1.3 75.1 + - - +
795S LEU* 1.3 65.3 + - + +
797S ARG* 3.2 21.6 + - - +
798S ALA* 3.0 25.3 + - - +
988S LYS* 4.5 14.0 + - - +
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Residues in contact with LEU 795 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
791S LEU* 2.9 29.5 + - + +
792S GLU* 3.9 5.8 - - - +
794S ASP* 1.3 76.5 - - + +
796S TYR* 1.4 62.6 + - - +
798S ALA* 3.5 12.6 + - - +
799S VAL* 3.5 15.2 - - - +
820S ASN* 4.7 2.7 - - + +
823S LYS* 4.2 16.4 - - + -
824S MET* 3.9 35.3 - - + +
827S HIS* 3.6 42.6 - - + +
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Residues in contact with TYR 796 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
792S GLU 3.0 20.5 + - - +
793S SER* 3.5 7.0 - - - +
795S LEU* 1.4 76.6 - - - +
797S ARG* 1.3 63.8 + - + +
798S ALA 3.3 1.2 + - - -
799S VAL* 3.4 11.0 + - - +
824S MET* 4.2 9.8 - - + +
926S CYS 4.9 3.1 - - - -
927S VAL* 4.0 8.5 - - + -
928S PRO* 3.6 51.7 - - + +
930S PHE* 3.6 34.5 - + - -
933S TYR* 4.2 5.7 - + - -
970S GLU 4.4 0.2 + - - -
971S ILE* 2.6 37.1 + - + -
974S TYR* 3.8 16.7 - - - +
975S GLN* 2.9 41.4 + - + -
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Residues in contact with ARG 797 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
754S PHE* 6.0 2.0 - - - -
793S SER* 2.9 34.5 + - - +
794S ASP* 3.2 18.8 + - - +
796S TYR* 1.3 78.4 - - + +
798S ALA* 1.3 58.7 + - - +
799S VAL 3.3 0.4 - - - -
800S GLN* 3.9 9.5 + - - -
974S TYR 5.2 0.7 - - - +
975S GLN* 3.1 54.0 + - - +
976S ASN 3.7 17.1 + - - -
977S GLN 4.6 6.4 + - - -
978S PRO* 3.7 29.2 - - - +
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Residues in contact with ALA 798 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
794S ASP 3.0 16.2 + - - +
795S LEU* 3.8 9.2 - - + +
796S TYR 3.3 0.6 - - - -
797S ARG* 1.3 75.1 - - - +
799S VAL* 1.4 61.8 + - - +
800S GLN* 3.7 13.4 + - - +
803S GLU* 3.8 0.5 - - - +
820S ASN* 3.6 32.9 + - + +
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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) + - + + + + + -
------------------------------------------------------------
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