Contacts of the helix formed by residues 786 - 804 (chain B) in PDB entry 2XWU
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 786 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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778B LEU* 3.8 40.0 - - + +
782B GLY 5.0 3.6 - - - -
783B PRO 4.2 3.4 + - - -
784B ARG 3.5 0.8 - - - -
785B ASP* 1.3 103.9 + - + +
787B PRO* 1.3 66.7 - - - +
788B ASP* 3.2 10.1 + - - +
789B ILE* 3.0 35.0 + - + +
790B VAL* 3.0 18.7 + - + +
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Residues in contact with PRO 787 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
784B ARG* 4.1 12.1 - - - +
785B ASP 3.5 7.9 - - - +
786B HIS* 1.3 87.6 - - - +
788B ASP* 1.3 60.0 + - - +
790B VAL* 3.3 6.3 + - + +
791B ASP* 2.8 25.5 + - - +
828B PHE* 5.2 5.6 - - + -
830B GLU* 3.9 33.4 - - + +
833B THR* 3.1 25.5 + - + +
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Residues in contact with ASP 788 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
741B ALA* 4.0 15.0 + - + +
786B HIS* 3.5 14.6 + - - +
787B PRO* 1.3 73.1 - - - +
789B ILE* 1.3 78.5 + - - +
791B ASP* 3.4 7.9 - - - +
792B SER* 3.0 32.4 + - - -
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Residues in contact with ILE 789 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
735B TYR* 3.8 10.3 - - - +
739B PRO* 3.6 31.9 - - + +
740B GLN* 4.0 2.2 - - - +
741B ALA* 3.7 20.0 - - - +
744B LEU* 3.5 18.6 - - + +
775B THR* 4.0 13.7 - - + -
778B LEU* 4.2 19.5 - - + -
786B HIS* 3.0 26.8 + - + +
788B ASP* 1.3 88.6 + - - +
790B VAL* 1.3 58.1 + - + +
792B SER 3.3 0.3 + - - -
793B PHE* 2.7 37.4 + - - +
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Residues in contact with VAL 790 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
775B THR* 5.8 2.7 - - + -
779B PHE* 3.8 33.0 - - + -
783B PRO 4.0 5.4 - - - +
786B HIS* 3.0 19.1 + - + +
787B PRO 3.6 7.2 - - - +
789B ILE* 1.3 76.5 - - + +
791B ASP* 1.3 63.8 + - - +
793B PHE* 3.2 8.2 + - + +
794B MET* 2.9 34.0 + - + +
821B CYS* 5.2 4.9 - - - -
825B ALA* 3.9 14.1 - - + -
828B PHE* 3.7 18.6 - - + -
833B THR* 3.6 22.2 - - + -
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Residues in contact with ASP 791 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
787B PRO 2.8 17.6 + - - +
788B ASP* 3.4 10.3 - - - +
790B VAL* 1.3 76.5 - - - +
792B SER* 1.3 67.3 + - - +
794B MET* 3.0 6.9 + - - +
795B GLN* 2.6 53.7 + - - +
832B PRO* 3.1 38.4 - - + +
833B THR* 4.0 11.9 - - - +
836B ALA* 3.7 9.0 - - - +
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Residues in contact with SER 792 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
741B ALA* 3.5 15.1 - - - +
744B LEU* 3.8 22.9 - - - +
745B ASP* 3.2 25.0 + - - -
748B ARG* 4.8 1.9 + - - -
788B ASP 3.0 15.0 + - - -
789B ILE 3.7 2.9 - - - -
791B ASP* 1.3 83.4 + - - +
793B PHE* 1.3 57.3 - - - +
795B GLN* 3.2 8.1 + - - +
796B LEU* 2.8 30.0 + - - +
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Residues in contact with PHE 793 (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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744B LEU* 3.9 16.1 - - + +
772B THR* 3.5 50.9 - - + -
775B THR* 3.6 32.1 - - + -
776B LEU* 4.0 21.8 - - + -
789B ILE 2.7 22.6 + - - +
790B VAL* 3.5 7.6 - - + +
792B SER* 1.3 73.1 - - - +
794B MET* 1.3 65.4 + - - +
796B LEU* 3.4 9.2 + - + +
797B LEU* 3.0 54.2 + - + +
818B VAL* 4.8 2.5 - - + -
821B CYS* 4.2 20.0 - - + -
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Residues in contact with MET 794 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
790B VAL* 2.9 29.9 + - + +
791B ASP 3.4 7.0 - - - +
793B PHE* 1.3 84.7 - - - +
795B GLN* 1.3 60.8 + - - +
797B LEU* 3.5 14.9 + - - +
798B ALA* 3.0 24.4 + - - +
818B VAL 5.6 0.4 - - - +
821B CYS* 4.9 3.4 - - - -
822B ALA* 3.2 42.0 - - + -
825B ALA* 4.8 3.6 - - - -
833B THR 4.7 1.3 - - - +
836B ALA* 3.4 19.7 - - + +
837B SER* 3.3 33.2 - - - +
840B PHE* 3.3 24.2 - - + +
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Residues in contact with GLN 795 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
745B ASP* 3.9 4.7 - - - +
748B ARG* 3.0 40.1 + - - +
791B ASP* 2.6 41.5 + - - +
792B SER* 3.2 7.8 + - - +
794B MET* 1.3 72.7 - - - +
796B LEU* 1.3 66.3 + - - +
798B ALA* 3.4 6.4 + - - +
799B GLN* 3.0 23.0 + - - +
836B ALA* 4.2 13.5 - - + +
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Residues in contact with LEU 796 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
744B LEU* 4.2 26.0 - - + +
747B THR* 3.8 25.6 - - + +
748B ARG* 3.4 44.5 - - + +
751B VAL* 4.2 11.4 - - + -
768B PHE* 4.1 22.0 - - + -
771B VAL* 4.6 7.0 - - + -
772B THR* 5.2 2.2 - - - +
792B SER 2.8 16.7 + - - +
793B PHE* 3.7 11.2 - - + +
795B GLN* 1.3 75.5 - - - +
797B LEU* 1.3 65.1 + - - +
799B GLN* 2.9 6.0 + - + +
800B ALA* 2.9 19.9 + - - +
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Residues in contact with LEU 797 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
768B PHE* 4.0 23.3 - - + -
772B THR* 4.8 2.2 - - + -
793B PHE* 3.0 57.3 + - + +
794B MET* 3.7 14.6 - - - +
796B LEU* 1.3 77.6 - - - +
798B ALA* 1.3 55.9 + - - +
800B ALA* 3.2 7.6 + - - +
801B LEU* 3.0 32.3 + - - +
808B PHE* 4.1 11.9 - - + -
813B LEU* 5.8 0.7 - - + -
818B VAL* 3.5 38.6 - - + +
840B PHE* 3.8 16.6 - - + -
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Residues in contact with ALA 798 (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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794B MET 3.0 17.9 + - - +
795B GLN* 3.7 6.7 - - - +
797B LEU* 1.3 73.2 - - - +
799B GLN* 1.3 61.0 + - - +
801B LEU* 3.3 12.4 + - - +
802B LYS* 2.9 30.4 + - - +
836B ALA 5.5 0.4 - - - +
839B GLY 3.9 10.1 - - - +
840B PHE* 3.9 21.2 - - - +
843B GLU* 4.0 10.0 - - + +
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Residues in contact with GLN 799 (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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748B ARG* 3.9 34.1 - - + +
751B VAL* 4.2 12.7 - - + +
752B HIS* 2.9 43.1 - - - +
795B GLN 3.0 13.3 + - - +
796B LEU* 2.9 10.9 + - + +
798B ALA* 1.3 73.1 - - - +
800B ALA* 1.3 65.9 + - - +
802B LYS* 3.3 14.7 + - - +
803B ARG* 2.9 30.5 + - + +
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Residues in contact with ALA 800 (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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751B VAL* 4.3 13.2 - - + +
768B PHE* 3.8 33.0 - - + -
796B LEU 2.9 7.3 + - - +
797B LEU 3.5 8.5 - - - +
798B ALA 3.2 0.2 - - - -
799B GLN* 1.3 77.6 - - - +
801B LEU* 1.3 58.3 + - - +
804B LYS 2.7 38.0 + - - +
807B LEU* 4.0 16.4 - - + -
808B PHE* 4.2 7.4 - - + -
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Residues in contact with LEU 801 (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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797B LEU 3.0 17.7 + - - +
798B ALA* 3.3 7.8 + - - +
800B ALA* 1.3 75.3 - - - +
802B LYS* 1.3 59.0 + - - +
805B PRO* 3.2 11.9 - - + +
808B PHE* 3.3 32.5 - - + -
840B PHE* 3.6 34.5 - - + +
843B GLU* 4.0 13.7 - - + +
844B LEU* 3.8 32.3 - - + +
847B ARG* 3.1 49.3 + - + -
851B VAL* 5.9 0.2 - - + -
854B VAL* 4.6 5.2 - - + -
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Residues in contact with LYS 802 (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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798B ALA 2.9 15.0 + - - +
799B GLN* 3.8 16.2 - - - +
800B ALA 3.2 0.2 - - - -
801B LEU* 1.3 79.1 - - - +
803B ARG* 1.3 101.6 + - + +
805B PRO* 4.4 0.5 - - - +
843B GLU* 2.9 43.0 + - - +
847B ARG* 3.3 17.8 + - - +
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Residues in contact with ARG 803 (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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751B VAL* 4.9 4.3 - - + +
752B HIS* 4.9 10.9 + - + +
755B ALA* 3.7 30.6 - - + +
799B GLN* 2.9 34.0 + - - +
802B LYS* 1.3 126.0 + - + +
804B LYS* 1.3 61.6 + - - +
805B PRO* 3.5 7.2 - - - +
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Residues in contact with LYS 804 (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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751B VAL* 4.9 4.3 - - + -
755B ALA* 4.9 10.1 - - + +
761B PHE* 4.4 15.3 - - + -
799B GLN 4.2 0.2 + - - -
800B ALA 2.7 18.7 + - - +
803B ARG* 1.3 76.0 - - - +
805B PRO* 1.3 64.7 - - - +
806B ASP* 3.4 10.8 - - - +
807B LEU* 3.2 41.0 - - + +
808B PHE* 4.9 0.5 - - - -
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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