Contacts of the helix formed by residues 740 - 759 (chain Z) in PDB entry 5WTI
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 740 (chain Z).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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621Z PRO 3.4 1.9 + - - -
622Z GLY 4.0 14.0 + - - -
623Z GLU* 3.9 21.5 - - - -
633Z ARG* 4.4 0.5 + - - -
737Z TYR* 2.6 24.1 + - - -
738Z GLY 3.3 0.4 - - - -
739Z ILE* 1.3 82.2 - - - +
741Z LEU* 1.3 63.9 + - - +
742Z LYS* 3.5 14.6 + - - +
743Z ASN* 3.1 26.9 + - - +
744Z ILE* 3.6 7.3 + - - +
791Z ARG* 4.0 8.7 - - - +
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Residues in contact with LEU 741 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576Z GLY 5.6 0.7 - - - +
577Z GLN* 4.1 22.2 - - - +
623Z GLU* 5.1 1.0 + - - +
740Z SER* 1.3 71.6 - - - +
742Z LYS* 1.3 61.8 + - + +
744Z ILE* 3.0 21.1 + - + +
745Z ASP* 2.8 30.0 + - - +
788Z LYS* 4.5 2.0 - - - +
791Z ARG* 3.5 41.0 - - - +
849Z LYS* 3.6 28.0 - - + +
850Z TRP* 4.9 17.5 - - + +
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Residues in contact with LYS 742 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
622Z GLY 5.7 0.2 - - - +
625Z LEU* 6.3 1.0 - - - +
630Z GLU* 4.4 8.3 + - - -
633Z ARG* 3.7 28.6 - - - +
737Z TYR* 3.9 18.3 - - + -
740Z SER* 3.2 13.4 - - - +
741Z LEU* 1.3 79.1 - - + +
743Z ASN* 1.3 62.7 + - - +
745Z ASP* 4.1 10.0 - - + +
746Z GLU* 3.2 25.5 + - - +
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Residues in contact with ASN 743 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B U 3.1 23.2 + - - -
47B G 4.8 1.2 + - - -
733Z ARG* 2.6 39.1 + - - +
737Z TYR* 3.5 23.1 - - + +
738Z GLY 2.5 28.2 + - - +
740Z SER* 3.1 16.2 + - - +
742Z LYS* 1.3 79.7 - - - +
744Z ILE* 1.3 61.6 + - - +
747Z ILE* 3.1 28.6 + - - +
787Z LEU* 3.5 14.3 - - + +
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Residues in contact with ILE 744 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
740Z SER 3.6 4.5 + - - +
741Z LEU* 3.0 27.2 + - + +
743Z ASN* 1.3 76.2 - - - +
745Z ASP* 1.3 53.0 + - - +
747Z ILE* 3.3 6.1 + - - +
748Z ASP* 2.7 35.5 + - - +
784Z LEU* 3.7 25.2 - - + +
787Z LEU* 3.8 26.7 - - + -
788Z LYS* 3.7 40.8 - - + +
791Z ARG* 4.3 11.2 - - - -
849Z LYS* 4.1 24.9 - - + +
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Residues in contact with ASP 745 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
741Z LEU 2.8 19.4 + - - +
742Z LYS* 4.1 11.6 - - + +
743Z ASN 3.4 0.2 - - - -
744Z ILE* 1.3 73.0 - - - +
746Z GLU* 1.3 58.2 + - - +
748Z ASP* 3.1 5.6 + - - +
749Z ARG* 2.7 65.5 + - - +
849Z LYS* 3.7 27.3 + - - +
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Residues in contact with GLU 746 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B C 3.3 16.5 + - - -
636Z ARG* 3.1 34.9 + - + +
637Z GLU* 6.3 1.6 - - - -
640Z LEU* 5.2 4.2 - - + +
729Z LEU* 4.9 1.0 - - - +
733Z ARG* 2.6 39.0 + - - -
737Z TYR* 3.3 22.5 - - + +
742Z LYS 3.2 17.0 + - - +
743Z ASN 4.3 0.2 - - - +
745Z ASP* 1.3 73.7 - - - +
747Z ILE* 1.3 61.0 + - - +
749Z ARG* 4.0 23.0 - - - +
750Z THR* 2.8 39.3 + - - +
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Residues in contact with ILE 747 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B C 3.9 35.9 - - + +
733Z ARG* 3.5 14.4 - - - +
743Z ASN* 3.1 32.9 + - - +
744Z ILE* 3.3 4.6 + - - +
746Z GLU* 1.3 75.8 - - - +
748Z ASP* 1.3 62.5 + - - +
750Z THR* 3.9 1.0 - - - -
751Z ARG* 3.0 23.2 + - - +
780Z GLN* 4.1 13.5 + - + +
783Z HIS* 3.6 30.3 - - + +
784Z LEU* 4.0 23.5 - - + +
787Z LEU* 3.9 11.0 - - + -
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Residues in contact with ASP 748 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
744Z ILE* 2.7 24.1 + - + +
745Z ASP* 3.1 9.1 + - - +
747Z ILE* 1.3 73.0 - - - +
749Z ARG* 1.3 65.0 + - - +
751Z ARG* 3.4 6.0 + - - +
752Z LYS* 3.1 45.8 + - - +
784Z LEU* 3.8 18.7 - - + +
848Z MET* 5.6 4.7 - - - +
849Z LYS* 3.9 29.4 + - + +
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Residues in contact with ARG 749 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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637Z GLU* 4.0 26.7 - - - +
640Z LEU* 4.2 19.3 - - + +
745Z ASP* 2.7 55.7 + - - +
746Z GLU* 4.0 24.9 - - - +
748Z ASP* 1.3 80.0 - - - +
750Z THR* 1.3 61.6 + - - +
751Z ARG 3.1 1.1 - - - -
752Z LYS* 3.7 19.1 - - + +
753Z PHE* 3.0 30.8 + - - +
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Residues in contact with THR 750 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B C 3.2 20.5 + - - +
640Z LEU* 4.3 9.8 - - - +
725Z TRP* 3.6 32.7 - - + -
729Z LEU* 3.7 28.0 - - + +
746Z GLU* 2.8 30.8 + - - +
747Z ILE 3.9 3.4 - - - -
749Z ARG* 1.3 76.4 - - - +
751Z ARG* 1.3 61.3 + - - +
753Z PHE* 3.8 1.7 + - - +
754Z LEU* 3.3 25.6 + - + +
780Z GLN* 4.0 5.2 - - - +
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Residues in contact with ARG 751 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9E A 5.8 3.6 - - - +
10E C 5.2 7.5 + - - -
747Z ILE 3.0 17.0 + - - +
748Z ASP* 3.4 7.0 - - - +
749Z ARG 3.1 0.2 - - - -
750Z THR* 1.3 77.2 - - - +
752Z LYS* 1.3 60.2 + - - +
754Z LEU* 3.1 7.5 + - - +
755Z LEU* 2.9 39.2 + - + +
776Z PHE* 2.5 44.6 + - + +
777Z ALA* 3.0 26.7 + - - +
780Z GLN* 3.1 25.7 + - - +
781Z LEU* 3.9 34.1 - - - +
784Z LEU* 4.5 17.5 - - - -
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Residues in contact with LYS 752 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B U 5.3 0.4 + - - -
114B C 3.6 54.3 - - - +
115B A 4.1 10.2 - - - +
748Z ASP* 3.1 36.6 + - - +
749Z ARG* 3.3 20.6 + - + +
751Z ARG* 1.3 74.3 - - + +
753Z PHE* 1.3 67.2 + - + +
755Z LEU* 3.4 15.1 + - + +
756Z ARG* 3.1 35.1 + - - +
849Z LYS* 5.5 3.4 - - - +
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Residues in contact with PHE 753 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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640Z LEU* 3.9 11.0 - - + -
643Z MET* 3.1 42.8 - - + -
644Z ASN* 3.1 25.6 - - - +
647Z LEU* 3.8 22.7 - - + -
718Z ILE* 6.1 0.7 - - + -
722Z VAL* 4.3 19.1 - - + -
725Z TRP* 3.7 36.1 - + - -
749Z ARG 3.0 16.9 + - - +
750Z THR 4.1 1.1 - - - +
752Z LYS* 1.3 75.6 - - + +
754Z LEU* 1.3 64.4 + - + +
755Z LEU 3.1 0.2 - - - -
756Z ARG* 3.1 10.3 + - - +
757Z TRP* 2.8 41.5 + + + +
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Residues in contact with LEU 754 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B A 3.3 39.4 + - - +
61B A 4.1 13.2 - - - +
722Z VAL* 6.3 1.6 - - + -
725Z TRP* 4.4 17.9 - - + -
726Z ARG* 4.7 14.6 - - + +
750Z THR* 3.3 21.9 + - + +
751Z ARG 3.1 8.6 + - - +
753Z PHE* 1.3 81.2 - - + +
755Z LEU* 1.3 61.8 + - - +
757Z TRP* 3.6 6.6 + - + -
758Z SER* 3.1 18.9 + - - -
776Z PHE* 3.3 26.3 - - + -
777Z ALA* 5.5 1.1 - - + -
780Z GLN* 4.0 24.2 - - - +
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Residues in contact with LEU 755 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B C 4.2 17.5 - - - +
115B A 4.3 15.5 - - - +
8E G 6.1 1.6 - - - +
751Z ARG* 2.9 29.2 + - + +
752Z LYS* 3.4 20.0 - - + +
753Z PHE 3.1 0.4 - - - -
754Z LEU* 1.3 74.1 - - - +
756Z ARG* 1.3 58.9 + - - +
758Z SER* 3.1 1.4 + - - -
759Z LEU* 2.9 50.2 + - + +
770Z LEU* 4.8 6.7 - - + -
776Z PHE* 3.4 43.1 - - + -
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Residues in contact with ARG 756 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B A 3.2 50.3 + - - +
116B U 3.2 16.6 + - - +
644Z ASN* 3.4 39.6 + - - +
647Z LEU* 3.7 18.8 - - + +
648Z ASN* 3.2 28.7 + - - +
651Z ARG* 4.8 3.5 + - - +
752Z LYS* 3.1 22.9 + - - +
753Z PHE* 3.1 12.4 + - - +
755Z LEU* 1.3 76.2 - - - +
757Z TRP* 1.3 63.0 + - - +
759Z LEU 3.9 0.3 - - - -
760Z ARG* 3.3 24.6 + - - +
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Residues in contact with TRP 757 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B G 2.9 47.2 + - - +
60B A 3.0 43.0 + - - -
647Z LEU* 3.5 34.3 - - + +
650Z LEU* 4.1 7.9 - - + -
715Z GLU* 3.7 19.3 - - - -
718Z ILE* 3.7 28.9 - - + -
719Z GLY* 3.6 21.8 - - - -
722Z VAL* 3.8 14.9 - - + +
753Z PHE* 2.8 28.4 + + + +
754Z LEU* 4.0 8.1 - - + +
756Z ARG* 1.3 76.9 - - - +
758Z SER* 1.3 57.8 + - - +
760Z ARG* 3.3 36.0 + - - +
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Residues in contact with SER 758 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B G 4.1 2.6 + - - +
60B A 2.7 61.2 + - - +
754Z LEU 3.1 11.2 + - - -
755Z LEU 3.1 3.4 + - - -
757Z TRP* 1.3 78.8 - - - +
759Z LEU* 1.3 63.7 + - - +
760Z ARG* 3.4 4.9 + - - +
768Z ARG* 3.5 19.2 + - - -
776Z PHE* 3.4 19.2 - - - -
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Residues in contact with LEU 759 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B A 3.5 28.9 - - + +
116B U 3.3 17.0 - - - +
8E G 6.0 1.1 - - - +
755Z LEU* 2.9 28.8 + - + +
756Z ARG 3.9 2.7 - - - -
758Z SER* 1.3 85.2 - - - +
760Z ARG* 1.3 63.4 + - - +
768Z ARG* 3.2 35.4 - - + +
769Z ARG* 4.3 15.5 - - - +
770Z LEU* 3.9 45.3 - - + +
776Z PHE* 5.9 1.6 - - + -
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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
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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