Contacts of the helix formed by residues 606 - 615 (chain B) in PDB entry 2HX4
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 ILE 606 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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516B ARG* 4.5 8.7 - - - +
557B LEU* 6.4 0.7 - - + -
559B LEU* 3.5 40.4 - - + -
598B TYR* 3.0 42.9 + - + +
599B CYS* 4.3 0.6 - - - +
604B TYR* 3.6 23.1 - - + +
605B ASN* 1.3 71.0 - - - +
607B LEU* 1.3 67.8 + - - +
608B GLU 3.2 3.4 + - - -
609B GLU* 3.3 14.8 + - + +
610B VAL* 3.0 30.1 + - + +
633B ILE* 3.8 25.1 - - + -
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Residues in contact with LEU 607 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
687A ILE* 4.0 25.6 - - + -
599B CYS* 3.7 36.8 - - + +
601B ASN* 5.5 4.5 - - - +
605B ASN* 3.5 7.8 - - - +
606B ILE* 1.3 79.3 - - - +
608B GLU* 1.3 57.2 + - - +
610B VAL* 3.7 1.6 - - - +
611B ALA* 2.8 31.3 + - - +
625B TRP* 3.9 10.6 - - + -
626B LYS* 3.6 51.8 - - + +
629B ALA* 3.8 18.4 - - + +
630B LEU* 3.8 8.1 - - + +
633B ILE* 4.2 4.3 - - + -
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Residues in contact with GLU 608 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605B ASN* 4.8 7.1 + - - +
606B ILE 3.3 0.6 - - - -
607B LEU* 1.3 76.2 - - - +
609B GLU* 1.3 68.1 + - - +
611B ALA* 2.7 19.1 + - - +
612B LYS* 2.9 41.7 + - - +
618B MET* 3.7 20.6 - - + +
625B TRP* 3.8 12.1 - - + -
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Residues in contact with GLU 609 (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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516B ARG* 5.0 11.6 + - - -
556B ASP 5.3 0.3 - - - +
557B LEU* 2.8 36.9 - - + +
605B ASN 5.5 0.4 + - - -
606B ILE* 3.3 16.8 + - + +
608B GLU* 1.3 79.5 - - - +
610B VAL* 1.3 61.1 + - + +
612B LYS* 3.6 14.9 + - + +
613B LYS* 3.3 39.0 + - - +
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Residues in contact with VAL 610 (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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553B TRP* 4.1 12.6 - - + -
554B PHE* 4.4 3.8 - - + -
557B LEU* 3.7 25.8 - - + -
606B ILE* 3.0 26.9 + - + +
607B LEU 3.8 2.7 - - - +
609B GLU* 1.3 74.9 - - + +
611B ALA* 1.3 66.2 + - - +
613B LYS* 3.6 6.6 + - - +
614B MET* 3.2 38.5 + - - +
629B ALA* 4.1 5.6 - - + +
632B GLU* 5.4 1.3 - - + -
633B ILE* 3.7 37.5 - - + -
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Residues in contact with ALA 611 (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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607B LEU 2.8 16.0 + - - +
608B GLU 2.7 12.4 + - - +
610B VAL* 1.3 74.4 - - - +
612B LYS* 1.3 64.0 - - - +
614B MET* 3.2 10.7 + - - +
615B ASP 3.2 7.4 + - - -
616B LEU* 3.4 23.4 + - + +
618B MET* 3.3 15.0 - - + -
625B TRP* 3.3 31.2 - - + -
629B ALA* 4.4 2.5 - - + -
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Residues in contact with LYS 612 (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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608B GLU* 2.9 43.2 + - - +
609B GLU* 3.8 12.8 - - + +
611B ALA* 1.3 74.1 - - - +
613B LYS* 1.3 58.8 + - + +
615B ASP* 2.5 33.3 + - - +
616B LEU 5.2 0.7 - - - +
618B MET* 4.2 17.7 - - - +
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Residues in contact with LYS 613 (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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553B TRP* 3.3 65.8 + - + -
556B ASP* 6.1 4.7 - - - -
557B LEU* 4.5 7.6 - - + -
609B GLU* 3.3 37.9 + - - +
610B VAL 3.7 2.7 - - - +
612B LYS* 1.3 83.2 - - + +
614B MET* 1.3 58.8 + - - +
615B ASP* 3.6 1.7 + - - +
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Residues in contact with MET 614 (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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551B PHE* 4.0 14.6 - - + -
553B TRP* 3.6 19.7 - - + -
610B VAL* 3.2 22.2 + - - +
611B ALA 3.2 7.8 + - - +
612B LYS 2.8 1.2 + - - -
613B LYS* 1.3 75.2 - - - +
615B ASP* 1.3 71.9 + - - +
616B LEU* 3.7 35.5 - - + +
628B GLN* 4.3 8.5 - - + +
629B ALA* 3.9 16.2 - - - -
632B GLU* 3.4 32.3 - - + +
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Residues in contact with ASP 615 (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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611B ALA 3.2 0.2 + - - -
612B LYS* 2.5 23.5 + - - +
613B LYS 3.3 1.5 - - - +
614B MET* 1.3 76.9 - - - +
616B LEU* 1.3 64.6 + - - +
617B ASP 4.1 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
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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