Contacts of the helix formed by residues 756 - 775 (chain T) in PDB entry 1BGX
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 THR 756 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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618T VAL* 4.0 16.6 - - + +
622T LEU* 4.8 2.5 - - + +
722T THR* 3.4 21.6 - - - +
723T LEU* 4.0 30.4 + - + +
724T PHE* 4.3 15.3 - - + -
751T MET 4.1 0.8 + - - -
752T PRO 3.0 22.7 + - - -
753T VAL 3.9 1.2 + - - -
755T GLY* 1.3 71.7 - - - +
757T ALA* 1.3 65.5 + - - +
759T ASP* 3.1 7.8 + - - -
760T LEU* 3.0 33.7 + - + +
813T LEU* 6.4 0.2 - - + -
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Residues in contact with ALA 757 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573T ARG* 5.1 0.2 - - - +
611T TYR* 4.9 0.2 - - - -
614T ILE* 3.8 45.5 - - + +
615T GLU* 4.6 7.9 - - + -
618T VAL* 4.5 7.9 - - + +
753T VAL 3.3 19.0 + - - +
754T GLN* 4.1 7.9 - - - +
755T GLY 3.2 0.4 - - - -
756T THR* 1.3 78.7 - - - +
758T ALA* 1.3 58.1 + - - +
760T LEU 4.0 0.2 + - - -
761T MET* 3.9 12.3 + - - +
785T ASP* 3.3 18.7 - - - +
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Residues in contact with ALA 758 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572T GLY 3.3 27.8 - - - +
573T ARG* 3.8 19.7 - - + +
754T GLN 3.5 16.2 + - - +
755T GLY 3.5 4.3 - - - +
756T THR 3.1 0.6 - - - -
757T ALA* 1.3 80.0 - - - +
759T ASP* 1.3 58.8 + - - +
760T LEU 3.3 0.7 - - - -
761T MET* 3.3 8.8 + - - +
762T LYS* 3.0 29.5 + - - +
782T GLN* 6.3 0.4 - - - +
784T HIS 5.6 0.4 - - - +
785T ASP* 4.7 3.4 - - - -
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Residues in contact with ASP 759 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429T LEU* 4.4 7.3 - - + +
433T VAL* 4.7 5.7 - - + +
572T GLY 5.2 1.6 - - - -
722T THR* 4.6 4.5 + - - -
724T PHE* 3.8 26.4 - - + -
726T ARG* 2.9 49.5 + - - +
755T GLY 2.8 25.9 + - - +
756T THR* 3.1 8.2 + - - +
758T ALA* 1.3 74.9 - - - +
760T LEU* 1.3 58.6 + - - +
761T MET 3.1 2.0 - - - -
762T LYS* 3.7 13.5 - - - +
763T LEU* 3.0 29.1 + - - +
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Residues in contact with LEU 760 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611T TYR* 3.6 9.2 + - + +
614T ILE* 4.0 26.7 - - + -
618T VAL* 4.6 11.2 - - + -
723T LEU* 5.6 0.4 - - + -
724T PHE* 3.9 25.6 - - + -
756T THR* 3.0 25.5 + - + +
757T ALA 4.2 4.9 - - - +
759T ASP* 1.3 75.6 - - - +
761T MET* 1.3 58.1 + - - +
763T LEU* 4.0 3.8 - - - +
764T ALA* 3.3 22.9 + - - +
810T VAL* 3.7 28.4 - - + +
811T TYR* 4.1 12.1 - - + -
813T LEU* 4.2 29.8 - - + -
817T LEU* 5.1 5.6 - - + -
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Residues in contact with MET 761 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574T LEU* 5.9 0.2 - - + -
611T TYR* 3.6 28.5 + - + -
757T ALA 3.9 6.1 + - - +
758T ALA* 3.3 15.4 + - - +
760T LEU* 1.3 78.2 - - - +
762T LYS* 1.3 59.3 + - + +
763T LEU 3.3 0.2 - - - -
764T ALA* 3.1 5.0 + - - +
765T MET* 3.0 37.6 + - - +
782T GLN* 3.5 37.5 - - + +
785T ASP* 3.7 30.3 - - - +
786T GLU 3.7 0.4 - - - -
787T LEU* 3.7 37.0 - - + +
807T MET* 4.0 11.4 - - + -
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Residues in contact with LYS 762 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378T TYR* 4.4 6.9 - - - -
433T VAL* 3.9 16.1 - - + +
434T GLU* 3.4 21.2 + - - +
437T LEU* 3.7 32.5 - - + +
566T GLN 3.5 17.8 + - - -
572T GLY* 3.3 29.9 + - - +
573T ARG* 4.5 0.9 - - - -
574T LEU* 3.9 30.5 - - + -
726T ARG* 4.3 7.3 - - - +
758T ALA 3.0 17.0 + - - +
759T ASP* 3.4 19.9 + - - +
761T MET* 1.3 79.0 - - + +
763T LEU* 1.3 57.4 + - - +
765T MET* 3.8 3.8 + - - -
766T VAL* 3.2 22.7 - - - +
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Residues in contact with LEU 763 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428T TRP* 4.4 18.6 - - + -
432T GLU* 4.1 15.5 - - + +
433T VAL* 3.9 25.6 - - + -
724T PHE* 4.0 30.5 - - + -
759T ASP 3.0 16.2 + - - +
760T LEU* 4.4 1.6 - - + +
762T LYS* 1.3 74.1 - - - +
764T ALA* 1.3 62.8 + - - +
765T MET 3.5 0.2 - - - -
766T VAL* 3.7 8.6 + - + +
767T LYS* 3.6 39.9 + - - +
810T VAL* 4.0 29.6 - - + +
811T TYR* 4.8 5.4 - - + -
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Residues in contact with ALA 764 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611T TYR* 3.9 13.7 - - - +
760T LEU 3.3 18.1 + - - +
761T MET* 3.1 9.5 + - - +
763T LEU* 1.3 76.9 - - - +
765T MET* 1.3 59.0 + - - +
766T VAL 3.1 2.2 + - - -
767T LYS* 3.3 2.0 + - - -
768T LEU* 2.9 33.4 + - + +
787T LEU* 6.1 1.6 - - + -
806T VAL* 3.9 10.5 - - + +
807T MET* 4.4 20.0 - - + -
810T VAL* 4.1 11.0 - - + -
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Residues in contact with MET 765 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437T LEU* 3.9 19.1 - - + -
440T VAL* 3.7 16.5 - - + +
441T LEU* 4.3 6.5 - - + -
444T MET* 3.8 22.2 - - + -
574T LEU* 3.8 28.9 - - + -
761T MET* 3.0 27.8 + - + +
762T LYS* 4.0 0.7 - - - +
763T LEU 3.5 0.4 - - - -
764T ALA* 1.3 76.0 - - - +
766T VAL* 1.3 61.5 + - - +
768T LEU* 4.0 0.9 - - - -
769T PHE* 3.5 21.8 + - - +
779T MET* 3.6 41.4 - - + +
782T GLN* 4.1 16.6 - - + -
787T LEU* 4.2 12.6 - - + -
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Residues in contact with VAL 766 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432T GLU 3.9 24.7 - - - +
433T VAL* 4.0 14.1 - - - +
436T PRO* 4.0 21.3 - - + +
437T LEU* 4.3 13.2 - - + +
440T VAL* 4.7 5.2 - - - -
762T LYS 3.2 19.7 - - - +
763T LEU* 3.7 11.0 + - + +
764T ALA 3.1 0.4 - - - -
765T MET* 1.3 78.7 - - - +
767T LYS* 1.3 62.4 + - + +
769T PHE* 3.7 4.4 + - - +
770T PRO* 3.3 21.1 - - - +
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Residues in contact with LYS 767 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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763T LEU* 3.6 34.6 + - + +
764T ALA 3.3 6.7 + - - +
766T VAL* 1.3 80.3 - - + +
768T LEU* 1.3 59.9 + - - +
769T PHE 3.4 0.2 - - - -
770T PRO* 3.4 8.0 - - - +
771T ARG* 2.8 41.2 + - - +
806T VAL* 4.0 9.2 - - + -
809T GLY 5.0 3.2 + - - +
810T VAL* 2.9 38.0 + - + +
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Residues in contact with LEU 768 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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764T ALA 2.9 18.5 + - - +
765T MET* 4.5 2.7 - - - +
767T LYS* 1.3 75.8 - - - +
769T PHE* 1.3 65.2 + - - +
770T PRO 3.3 0.9 - - - -
771T ARG* 3.1 21.2 + - + +
772T LEU* 3.2 34.3 + - + +
779T MET* 4.0 9.6 - - + -
787T LEU* 4.0 27.1 - - + -
789T LEU* 4.4 10.1 - - + -
799T VAL* 6.2 0.7 - - + -
802T LEU* 4.9 3.8 - - + -
803T ALA* 4.0 39.0 - - + +
806T VAL* 4.0 20.2 - - + +
807T MET* 5.3 6.1 - - + -
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Residues in contact with PHE 769 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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436T PRO 5.7 0.7 - - - -
439T ALA* 3.6 29.4 - - + -
440T VAL* 3.9 35.2 - - + -
443T HIS* 3.6 33.0 - + + -
765T MET 3.5 16.2 + - - +
766T VAL 3.9 5.2 - - - +
768T LEU* 1.3 78.1 - - - +
770T PRO* 1.4 69.5 - - + +
771T ARG 3.4 0.2 + - - -
772T LEU* 3.6 20.9 + - + +
773T GLU* 3.5 38.5 + - + +
779T MET* 5.2 3.8 - - + +
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Residues in contact with PRO 770 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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766T VAL 3.3 17.9 - - - +
767T LYS* 3.4 14.8 - - - +
769T PHE* 1.4 94.1 - - + +
771T ARG* 1.3 67.5 + - - +
772T LEU 3.3 0.7 + - - -
773T GLU* 3.8 12.7 + - + +
774T GLU* 3.5 17.5 + - - +
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Residues in contact with ARG 771 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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767T LYS* 2.8 39.4 + - - +
768T LEU* 3.1 14.9 + - + +
770T PRO* 1.3 88.5 - - - +
772T LEU* 1.3 61.4 + - - +
773T GLU 3.5 0.2 - - - -
774T GLU* 3.5 21.4 - - - +
775T MET* 3.4 26.0 - - - +
802T LEU* 4.0 36.2 - - + +
805T GLU* 5.4 6.1 + - - -
806T VAL* 3.6 30.1 - - - +
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Residues in contact with LEU 772 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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768T LEU* 3.2 33.1 + - + +
769T PHE* 4.1 13.9 - - + +
770T PRO 3.3 0.4 - - - -
771T ARG* 1.3 77.6 - - - +
773T GLU* 1.3 63.8 + - - +
774T GLU 3.3 0.4 - - - -
775T MET* 4.8 0.7 - - + -
776T GLY* 3.1 10.4 + - - -
777T ALA* 3.0 57.7 + - + +
778T ARG* 4.3 1.1 - - - +
779T MET* 4.1 47.6 - - + +
789T LEU* 4.3 12.6 - - + -
799T VAL* 4.3 15.5 - - + -
802T LEU* 6.4 1.1 - - + -
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Residues in contact with GLU 773 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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443T HIS* 5.3 9.4 + - - -
769T PHE* 3.5 40.4 - - + +
770T PRO* 4.1 9.0 - - + +
771T ARG 3.5 0.4 - - - -
772T LEU* 1.3 80.3 - - - +
774T GLU* 1.3 58.8 + - - +
776T GLY* 4.2 6.2 + - - -
777T ALA 4.5 6.6 - - - +
778T ARG* 6.0 0.3 - - - -
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Residues in contact with GLU 774 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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770T PRO* 3.5 17.1 + - - +
771T ARG* 3.5 28.1 - - - +
773T GLU* 1.3 76.8 - - - +
775T MET* 1.3 89.2 + - + +
776T GLY* 3.3 0.8 + - - -
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Residues in contact with MET 775 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
771T ARG 3.4 18.8 + - - +
772T LEU* 3.5 4.5 + - - +
774T GLU* 1.3 102.6 - - + +
776T GLY* 1.3 60.4 + - - +
777T ALA* 4.7 2.0 - - + +
798T ALA* 5.3 14.1 - - - +
799T VAL* 4.4 24.3 - - + +
802T LEU* 4.0 20.9 - - + -
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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
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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