Contacts of the helix formed by residues 787 - 807 (chain B) in PDB entry 6IEH
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 ASP 787 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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643B TYR* 6.3 2.0 - - + -
649B TYR* 4.4 20.7 + - + +
780B ILE* 6.0 1.2 - - - +
785B ILE* 3.4 5.0 - - + +
786B GLN* 1.3 79.1 - - - +
788B GLN* 1.3 68.2 + - - +
789B GLY* 3.3 5.7 + - - +
790B LEU* 3.5 22.8 + - + +
791B LYS* 3.9 3.8 + - - +
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Residues in contact with GLN 788 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
786B GLN 3.2 5.6 + - - +
787B ASP* 1.3 73.8 + - - +
789B GLY* 1.3 64.7 + - - +
791B LYS* 2.9 26.1 + - - +
792B LYS* 3.5 6.0 + - - +
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Residues in contact with GLY 789 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
787B ASP* 3.2 6.4 - - - +
788B GLN* 1.3 78.1 - - - +
790B LEU* 1.3 59.4 + - - +
792B LYS* 3.3 13.6 - - - +
793B VAL* 3.2 23.6 + - - +
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Residues in contact with LEU 790 (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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639B GLU 5.0 0.9 - - - +
640B ILE* 4.2 34.1 - - + -
643B TYR* 4.5 20.6 - - + -
644B ILE* 6.5 0.2 - - + -
779B PRO* 3.8 27.1 - - + -
780B ILE* 4.3 18.6 - - + -
785B ILE* 4.5 14.6 - - + +
787B ASP* 3.5 18.4 + - + +
788B GLN 3.1 0.8 + - - -
789B GLY* 1.3 73.4 - - - +
791B LYS* 1.3 54.4 + - - +
793B VAL* 2.9 10.2 + - + -
794B ILE* 2.7 48.1 + - + +
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Residues in contact with LYS 791 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
780B ILE* 5.1 12.8 - - + +
787B ASP 3.9 4.1 + - - +
788B GLN* 2.9 15.0 + - - +
790B LEU* 1.3 78.8 - - - +
792B LYS* 1.3 51.9 + - + +
794B ILE* 3.0 10.9 + - - +
795B GLN* 2.6 36.9 + - - +
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Residues in contact with LYS 792 (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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788B GLN 3.5 5.3 + - - +
789B GLY* 3.3 15.7 + - - +
791B LYS* 1.3 78.0 - - + +
793B VAL* 1.3 56.8 - - + +
795B GLN* 3.0 8.2 + - - +
796B LYS* 2.7 32.1 + - - +
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Residues in contact with VAL 793 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
636B LEU* 3.5 44.4 - - + +
639B GLU* 4.1 16.8 - - + +
640B ILE* 3.8 15.0 - - + +
789B GLY 3.2 14.1 + - - +
790B LEU* 2.9 16.2 + - + +
792B LYS* 1.3 76.0 - - + +
794B ILE* 1.3 64.7 + - - +
796B LYS* 3.2 5.6 + - - +
797B VAL* 2.8 22.2 + - + +
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Residues in contact with ILE 794 (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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640B ILE* 4.0 22.0 - - + -
778B ASP* 5.7 4.0 - - - +
779B PRO* 5.1 11.9 - - + -
780B ILE* 5.0 14.1 - - + -
790B LEU* 2.7 33.7 + - + +
791B LYS* 3.3 11.9 - - - +
793B VAL* 1.3 74.6 - - - +
795B GLN* 1.3 63.8 + - - +
797B VAL* 3.3 7.4 + - + +
798B GLU* 2.9 26.2 + - + +
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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
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791B LYS 2.6 16.7 + - - +
792B LYS* 3.5 11.4 - - - +
794B ILE* 1.3 74.7 - - - +
796B LYS* 1.3 58.9 + - - +
798B GLU* 2.9 9.0 + - - +
799B ALA* 2.8 28.5 + - - +
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Residues in contact with LYS 796 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
636B LEU* 4.0 18.4 - - + -
792B LYS 2.7 19.8 + - - +
793B VAL* 3.8 5.4 - - - +
795B GLN* 1.3 72.1 - - - +
797B VAL* 1.3 61.6 + - - +
799B ALA* 3.1 7.2 + - - +
800B PHE* 3.1 37.0 + - + -
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Residues in contact with VAL 797 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
633B LEU* 3.7 18.1 - - + +
636B LEU* 3.6 35.4 - - + -
637B GLY* 4.6 3.6 - - - +
640B ILE* 4.5 16.6 - - + -
793B VAL 2.8 16.3 + - - +
794B ILE* 3.6 7.2 - - + +
796B LYS* 1.3 76.2 - - - +
798B GLU* 1.3 63.1 + - - +
800B PHE 3.5 0.5 + - - -
801B GLU* 2.8 46.2 + - + +
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Residues in contact with GLU 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 ILE* 2.9 17.9 + - + +
795B GLN* 2.9 11.4 + - - +
797B VAL* 1.3 81.1 - - + +
799B ALA* 1.3 60.8 + - - +
801B GLU* 3.3 20.3 + - - +
802B HIS* 3.4 7.6 + - - +
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Residues in contact with ALA 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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795B GLN 2.8 12.9 + - - +
796B LYS* 3.5 11.9 - - - +
798B GLU* 1.3 77.0 - - - +
800B PHE* 1.3 62.4 + - + +
802B HIS* 3.0 28.5 + - - +
803B ARG* 3.1 11.8 + - + +
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Residues in contact with PHE 800 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
629B ILE* 4.1 29.9 - - + +
632B GLN* 3.9 29.6 - - + -
633B LEU* 3.7 24.9 - - + -
636B LEU* 4.8 11.9 - - + -
796B LYS* 3.1 31.5 + - + +
799B ALA* 1.3 81.5 - - + +
801B GLU* 1.3 61.4 + - - +
803B ARG* 3.5 29.6 - - + +
804B MET* 2.7 29.8 + - - +
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Residues in contact with GLU 801 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
633B LEU* 4.1 13.8 - - + +
797B VAL* 2.8 37.6 - - - +
798B GLU* 3.4 10.7 - - - +
800B PHE* 1.3 78.6 - - - +
802B HIS* 1.3 61.4 + - - +
804B MET* 3.4 11.7 + - + +
805B TYR* 3.1 23.9 + - - +
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Residues in contact with HIS 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 GLU 3.4 6.0 + - - +
799B ALA* 3.0 19.3 - - - +
801B GLU* 1.3 74.0 - - - +
803B ARG* 1.3 66.3 + - + +
805B TYR* 3.3 5.4 + - - +
806B SER* 3.0 30.7 + - - -
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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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625B ILE* 4.3 33.6 + - - +
629B ILE* 5.2 11.7 - - + +
799B ALA 3.1 11.5 + - - +
800B PHE* 3.5 35.6 - - + +
802B HIS* 1.3 82.4 + - + +
804B MET* 1.3 63.0 + - - +
806B SER* 3.2 21.0 + - - -
807B HIS* 3.5 13.0 + - - +
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Residues in contact with MET 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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626B TYR* 3.6 21.7 - - + -
629B ILE* 5.1 7.6 - - + +
630B ARG* 4.1 29.6 - - + +
633B LEU* 2.6 41.7 - - + -
800B PHE 2.7 16.7 + - - +
801B GLU* 3.6 9.9 - - + +
802B HIS 3.2 0.2 - - - -
803B ARG* 1.3 75.7 - - - +
805B TYR* 1.3 58.8 + - + +
807B HIS* 3.7 15.5 + - - +
810B HIS* 3.4 35.9 - - + -
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Residues in contact with TYR 805 (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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801B GLU 3.1 13.5 + - - +
802B HIS* 3.3 4.2 + - - +
803B ARG 3.3 0.2 - - - -
804B MET* 1.3 78.0 - - - +
806B SER* 1.3 65.4 + - - +
807B HIS 3.2 6.3 - - - +
810B HIS* 4.6 10.1 - - + +
811B ASN* 6.1 0.5 - - - +
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Residues in contact with SER 806 (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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802B HIS* 3.0 30.2 + - - -
803B ARG* 3.2 12.9 + - - -
805B TYR* 1.3 75.6 - - - +
807B HIS* 1.3 67.3 + - - +
808B PRO* 3.3 6.9 - - - +
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Residues in contact with HIS 807 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
622B SER* 3.4 42.3 + - - -
623B VAL* 4.5 0.7 - - - -
625B ILE* 4.0 15.2 - - + +
626B TYR* 3.5 35.9 + + + +
803B ARG* 3.5 10.5 + - - +
804B MET 3.7 11.4 - - - +
805B TYR 3.6 5.7 - - - +
806B SER* 1.3 81.1 - - - +
808B PRO* 1.3 81.2 - - + +
809B LEU* 3.3 22.4 + - + +
810B HIS* 3.5 17.5 - - - +
811B ASN* 4.3 2.6 + - - +
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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