Contacts of the helix formed by residues 605 - 625 (chain B) in PDB entry 5XA0
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 LEU 605 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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571B GLN* 5.3 13.0 - - + -
602B ASN* 3.8 8.9 + - + +
603B ARG 3.4 3.2 - - - +
604B LYS* 1.3 79.1 - - - +
606B LEU* 1.3 71.9 + - - +
607B GLU 3.2 2.3 + - - +
608B LYS* 3.5 13.3 + - - +
609B HIS* 3.9 6.9 + - - +
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Residues in contact with LEU 606 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
595B ILE* 6.4 2.2 - - + -
598B LEU* 6.3 3.1 - - + -
602B ASN 4.5 6.6 + - - +
604B LYS 4.9 0.4 - - - +
605B LEU* 1.3 76.0 - - - +
607B GLU* 1.3 58.1 + - - +
609B HIS* 2.8 27.7 + - - +
610B ILE* 2.9 19.8 + - + +
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Residues in contact with GLU 607 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
604B LYS* 5.7 4.9 - - - +
605B LEU 3.2 3.7 + - - +
606B LEU* 1.3 76.9 - - - +
608B LYS* 1.3 58.1 + - - +
610B ILE* 3.7 7.6 - - - -
611B THR* 2.9 31.2 + - - -
643B LYS* 5.8 8.7 - - + -
646B PRO* 5.8 7.9 - - + -
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Residues in contact with LYS 608 (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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604B LYS 5.7 2.2 + - - +
605B LEU* 3.5 9.3 + - - +
606B LEU 2.9 0.6 + - - -
607B GLU* 1.3 80.8 - - - +
609B HIS* 1.3 62.0 + - - +
610B ILE 3.2 0.7 + - - -
611B THR* 3.8 8.5 + - - -
612B ALA 5.4 0.2 + - - -
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Residues in contact with HIS 609 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578B PHE* 6.2 4.0 - - + -
605B LEU 3.9 3.9 + - - +
606B LEU* 2.8 14.0 + - - +
608B LYS* 1.3 76.5 - - - +
610B ILE* 1.3 59.4 + - + +
612B ALA 5.4 0.4 + - - -
613B ALA* 3.7 16.8 + - - +
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Residues in contact with ILE 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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606B LEU* 2.9 26.4 + - + +
607B GLU* 4.1 3.8 - - - -
608B LYS 3.1 0.2 - - - -
609B HIS* 1.3 78.4 - - + +
611B THR* 1.3 56.6 + - - +
612B ALA 3.7 0.2 - - - -
613B ALA* 4.6 2.0 - - - -
614B GLU* 2.0 52.1 + - + +
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Residues in contact with THR 611 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
607B GLU 2.9 17.0 + - - -
608B LYS* 3.8 6.5 + - - -
609B HIS 3.6 1.2 - - - -
610B ILE* 1.3 83.7 - - - +
612B ALA* 1.3 58.0 + - - +
614B GLU* 2.6 22.0 + - - +
615B ILE* 3.0 5.4 + - - +
646B PRO* 5.4 14.4 - - - -
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Residues in contact with ALA 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 LYS 5.4 0.4 + - - -
609B HIS 5.4 0.4 + - - -
611B THR* 1.3 73.9 - - - +
613B ALA* 1.3 56.4 + - - +
614B GLU 2.7 4.3 - - - -
615B ILE* 2.5 37.6 + - - +
616B ASP* 3.4 3.2 + - - +
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Residues in contact with ALA 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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609B HIS 3.7 21.5 + - - +
610B ILE* 4.3 2.5 - - - +
612B ALA* 1.3 75.0 - - - +
614B GLU* 1.3 58.2 + - - +
616B ASP* 2.9 26.6 + - - +
617B THR* 3.0 15.4 + - - -
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Residues in contact with GLU 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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610B ILE* 2.0 39.4 + - + +
611B THR* 2.6 8.7 + - - +
612B ALA 2.6 1.0 + - - -
613B ALA* 1.3 76.3 - - - +
615B ILE* 1.3 64.5 + - - -
617B THR* 4.3 6.5 - - - +
618B PHE* 2.8 29.0 + - + +
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Residues in contact with ILE 615 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611B THR 3.0 6.1 + - - +
612B ALA* 2.5 25.8 + - - +
614B GLU* 1.3 72.8 - - - +
616B ASP* 1.3 62.0 + - - +
618B PHE* 4.3 2.1 - - - +
619B VAL* 3.2 23.9 + - - +
649B GLN* 6.3 2.5 - - + -
650B GLU* 5.6 11.9 - - - +
653B CYS* 4.7 15.2 - - + +
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Residues in contact with ASP 616 (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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612B ALA 3.4 2.5 + - - +
613B ALA* 2.9 12.7 + - - +
615B ILE* 1.3 79.1 - - - +
617B THR* 1.3 50.9 + - - +
619B VAL* 4.3 2.8 - - - +
620B SER* 2.4 40.2 + - - +
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Residues in contact with THR 617 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
582B GLN* 5.9 6.3 - - - -
613B ALA* 3.0 15.1 + - - -
614B GLU* 3.2 7.6 + - - -
615B ILE 3.1 0.2 - - - -
616B ASP* 1.3 76.6 - - - +
618B PHE* 1.3 51.5 + - - +
620B SER* 4.0 2.5 - - - -
621B LEU* 1.9 53.0 - - - +
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Residues in contact with PHE 618 (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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614B GLU* 2.8 19.8 + - + +
615B ILE* 4.3 2.0 - - - +
617B THR* 1.3 72.8 - - - +
619B VAL* 1.3 61.0 + - - +
622B VAL* 2.6 39.6 - - + +
634B LEU* 6.1 5.8 - - + -
650B GLU* 5.8 8.5 - - + -
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Residues in contact with VAL 619 (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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615B ILE 3.2 16.6 + - - +
616B ASP* 4.3 2.9 - - - +
618B PHE* 1.3 73.3 - - - +
620B SER* 1.3 66.0 + - - +
622B VAL* 4.3 0.2 - - - +
623B ARG* 3.1 26.5 + - - +
653B CYS* 4.4 19.4 - - + +
657B LEU* 4.7 21.1 - - + +
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Residues in contact with SER 620 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
616B ASP 2.4 28.2 + - - -
617B THR* 4.0 2.7 - - - -
619B VAL* 1.3 76.7 - - - +
621B LEU* 1.4 51.3 + - - +
623B ARG* 3.6 4.0 - - - +
624B LYS* 2.7 38.6 + - - +
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Residues in contact with LEU 621 (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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582B GLN* 5.8 9.2 - - + -
617B THR* 1.9 44.1 + - - +
618B PHE* 4.1 0.4 - - - -
620B SER* 1.4 74.0 - - - +
622B VAL* 1.3 57.9 + - - +
623B ARG 3.1 1.1 - - - -
624B LYS* 4.1 6.5 - - - -
625B ASN* 2.6 37.0 + - + +
630B PHE* 5.5 4.9 - - + +
631B LEU* 5.1 1.3 - - - -
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Residues in contact with VAL 622 (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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618B PHE* 2.6 31.1 + - + +
619B VAL 4.3 0.4 - - - +
621B LEU* 1.3 71.4 - - - +
623B ARG* 1.3 58.1 + - - +
625B ASN 2.7 27.9 - - - +
626B ARG* 4.0 1.0 - - - -
631B LEU* 3.4 29.0 - - + +
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Residues in contact with ARG 623 (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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619B VAL 3.1 20.2 + - - +
620B SER* 3.6 4.3 - - - +
622B VAL* 1.3 76.9 - - - +
624B LYS* 1.3 53.7 + - - +
626B ARG* 2.6 38.8 + - - +
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Residues in contact with LYS 624 (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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582B GLN* 5.5 9.6 - - + +
586B GLY* 4.5 13.0 - - - -
620B SER* 2.7 25.6 + - - +
621B LEU* 4.1 4.3 - - - -
623B ARG* 1.3 68.4 - - - +
625B ASN* 1.3 57.9 + - - +
626B ARG* 2.8 13.4 + - - +
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Residues in contact with ASN 625 (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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585B ILE* 5.2 6.3 - - + +
586B GLY* 5.3 2.5 - - - -
621B LEU 2.6 23.5 + - - +
622B VAL 2.7 12.8 - - - +
624B LYS* 1.3 69.3 - - - +
626B ARG* 1.3 54.8 + - - +
627B GLU 2.6 23.1 - - - +
629B ARG* 6.0 0.2 - - - -
630B PHE* 2.9 39.5 - - + +
631B LEU* 3.1 15.4 - - - +
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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