Contacts of the helix formed by residues 566 - 576 (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 THR 566 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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233B ARG* 5.2 1.9 + - - -
264B VAL* 5.1 5.2 - - + -
564B HIS* 3.7 29.1 + - + +
565B LEU* 1.3 79.9 - - - +
567B TYR* 1.3 61.3 + - - +
568B ASN* 3.4 8.1 + - - +
569B MET* 2.9 31.9 + - + +
570B VAL* 2.9 23.6 + - - +
854B ARG* 4.4 5.4 - - - +
885B GLU* 5.4 2.7 - - - -
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Residues in contact with TYR 567 (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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566B THR* 1.3 72.8 - - - +
568B ASN* 1.3 58.5 + - - +
570B VAL* 3.6 4.6 - - + +
571B LEU* 2.7 36.7 + - + +
854B ARG* 3.6 59.7 + - + +
857B VAL* 3.9 22.4 - - + +
858B LEU* 3.8 24.5 - - + -
884B ASP* 5.4 1.3 - - - -
885B GLU* 3.6 26.2 + - + +
886B LEU* 3.8 34.6 - - + +
946B SER* 4.6 3.3 + - - -
951B LEU* 4.2 7.1 - - - +
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Residues in contact with ASN 568 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B ARG* 1.8 42.0 + - - +
566B THR* 3.2 6.0 + - - +
567B TYR* 1.3 75.8 - - - +
569B MET* 1.3 65.3 + - - +
571B LEU* 4.4 4.5 - - - +
572B ASN* 3.1 30.6 + - - +
877B ALA 4.1 0.6 + - - -
878B CYS* 2.7 36.0 + - - +
880B ILE 3.9 7.2 + - - +
881B SER* 4.1 14.1 + - - +
885B GLU* 3.2 23.8 + - - +
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Residues in contact with MET 569 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B ARG* 3.9 6.5 - - - +
237B TYR* 4.2 2.4 + - - +
264B VAL* 4.4 4.0 - - + -
268B GLU* 3.3 34.3 - - - +
563B PHE* 4.0 15.3 - - + -
564B HIS 3.8 20.9 - - - +
565B LEU* 3.6 25.8 - - + -
566B THR* 2.9 23.8 + - + +
568B ASN* 1.3 76.8 + - - +
570B VAL* 1.3 67.1 + - + +
572B ASN* 4.1 0.5 - - - +
573B LEU* 3.1 40.1 + - + +
581B PRO* 5.0 3.1 - - + +
584B MET* 3.8 24.7 - - + -
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Residues in contact with VAL 570 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565B LEU* 4.6 8.7 - - + -
566B THR 2.9 16.2 + - - +
567B TYR* 3.6 8.7 - - + +
569B MET* 1.3 76.6 - - + +
571B LEU* 1.3 66.5 + - - +
573B LEU* 3.5 0.6 + - - -
574B LEU* 3.1 24.5 + - + +
581B PRO* 3.9 23.5 - - + +
851B LEU* 4.0 24.7 - - + -
854B ARG* 4.5 16.8 - - + -
855B LYS* 4.9 5.6 - - + -
858B LEU* 3.9 25.6 - - + -
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Residues in contact with LEU 571 (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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567B TYR* 2.7 26.0 + - + +
568B ASN* 4.3 4.0 - - - +
570B VAL* 1.3 75.4 - - - +
572B ASN* 1.3 65.2 + - - +
574B LEU* 3.1 9.6 + - + +
575B ARG* 3.0 21.0 + - - +
858B LEU* 3.7 39.7 - - + -
863B PHE* 4.6 6.1 - - + -
864B ALA* 5.0 1.3 - - + -
870B ILE* 3.9 20.2 - - + +
874B GLY* 3.4 30.3 - - - +
877B ALA* 3.7 20.0 - - + +
878B CYS* 4.0 11.7 - - - -
885B GLU* 5.7 1.3 - - + -
886B LEU* 5.6 1.8 - - + -
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Residues in contact with ASN 572 (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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233B ARG* 4.6 0.2 - - - +
237B TYR* 3.7 33.1 - - + +
568B ASN* 3.1 41.3 + - - +
571B LEU* 1.3 80.8 - - - +
573B LEU* 1.3 59.7 + - - +
575B ARG* 3.0 37.7 + - - +
576B VAL* 2.7 31.4 + - - +
878B CYS* 3.8 20.2 + - - +
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Residues in contact with LEU 573 (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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237B TYR* 4.0 20.2 - - + +
272B LEU* 4.9 3.8 - - + -
569B MET* 3.1 34.4 + - + +
570B VAL 4.0 1.6 - - - +
572B ASN* 1.3 78.2 - - - +
574B LEU* 1.3 61.6 + - - +
576B VAL* 3.3 11.0 + - + +
579B ILE* 3.2 55.5 - - + +
580B ASN* 3.6 8.6 - - - +
581B PRO* 3.8 19.1 - - + -
584B MET* 3.7 40.6 - - + -
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Residues in contact with LEU 574 (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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570B VAL* 3.1 24.4 + - + +
571B LEU* 3.5 14.1 - - + +
573B LEU* 1.3 77.8 - - - +
575B ARG* 1.3 61.1 + - - +
576B VAL 3.8 4.7 - - - +
579B ILE 5.1 0.8 - - - +
580B ASN* 5.1 2.0 - - + -
581B PRO* 3.3 30.1 - - + -
855B LYS* 4.8 4.0 - - + -
858B LEU* 4.6 5.2 - - + -
864B ALA* 4.3 22.0 - - + -
868B ASP* 4.1 53.1 - - + +
869B VAL* 5.5 0.2 - - - -
870B ILE* 4.7 14.5 + - + +
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Residues in contact with ARG 575 (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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237B TYR* 2.3 39.0 + - - +
238B ARG* 4.5 6.0 + - - +
571B LEU 3.0 11.6 + - - +
572B ASN* 3.0 32.4 + - - +
574B LEU* 1.3 76.2 - - - +
576B VAL* 1.3 74.4 + - - +
577B GLU* 3.5 4.3 + - - +
870B ILE* 3.9 31.9 - - + +
875B ARG* 4.2 25.7 + - + +
878B CYS* 4.5 13.1 - - - +
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Residues in contact with VAL 576 (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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236B LEU 6.0 0.2 - - - +
237B TYR* 4.0 23.8 - - + +
272B LEU* 5.7 4.5 - - + -
572B ASN 2.7 22.2 + - - +
573B LEU* 3.3 10.0 - - + +
574B LEU 3.4 4.4 - - - +
575B ARG* 1.3 91.8 - - - +
577B GLU* 1.3 61.4 + - - +
578B GLU 4.3 1.3 - - - +
579B ILE* 3.2 51.3 - - + +
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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
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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