Contacts of the helix formed by residues 599 - 618 (chain B) in PDB entry 2X04
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 SER 599 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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595B HIS* 2.9 24.2 + - - -
596B MET 3.1 7.5 + - - +
597B LEU 3.4 0.2 - - - -
598B GLU* 1.3 81.3 - - - +
600B PRO* 1.3 61.2 - - - +
601B GLU* 3.8 8.0 + - - +
602B SER* 2.8 42.8 + - - -
603B LEU 3.1 9.7 + - - -
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Residues in contact with PRO 600 (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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573B MET* 5.6 1.7 - - - +
596B MET 4.6 0.7 - - - +
597B LEU 5.2 2.7 - - - +
598B GLU 3.8 6.7 - - - +
599B SER* 1.3 85.6 - - - +
601B GLU* 1.3 56.3 + - - +
603B LEU* 3.4 8.9 + - + +
604B ARG* 3.0 30.8 + - - +
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Residues in contact with GLU 601 (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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599B SER* 3.1 8.0 + - - +
600B PRO* 1.3 78.7 - - - +
602B SER* 1.3 65.1 + - - +
604B ARG* 3.6 5.1 + - - +
605B SER* 3.2 23.9 + - - -
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Residues in contact with SER 602 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
595B HIS* 3.0 28.6 + - - -
596B MET* 4.2 8.5 - - - -
599B SER* 2.8 26.9 + - - -
601B GLU* 1.3 82.0 - - - +
603B LEU* 1.3 57.1 - - - +
605B SER* 3.5 1.2 - - - -
606B LYS* 2.7 53.1 + - - -
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Residues in contact with LEU 603 (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 LEU* 3.6 32.3 - - + -
569B LEU* 4.0 37.0 - - + -
570B ILE* 4.4 6.1 - - + -
573B MET* 4.1 12.1 - - + -
585B LEU* 3.9 11.2 - - + -
596B MET* 3.5 40.7 + - + +
597B LEU* 5.1 0.4 - - + -
599B SER 3.1 5.8 + - - +
600B PRO* 3.9 9.0 - - + +
602B SER* 1.3 75.4 + - - +
604B ARG* 1.3 59.3 + - - +
606B LYS* 3.2 1.7 + - - +
607B VAL* 2.8 42.8 + - + +
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Residues in contact with ARG 604 (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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573B MET* 4.0 31.1 - - + +
574B HIS* 5.8 2.9 - - - -
600B PRO 3.0 18.7 + - - +
601B GLU* 3.8 6.5 - - - +
603B LEU* 1.3 75.5 - - - +
605B SER* 1.3 58.1 + - - +
607B VAL* 3.2 4.7 + - - +
608B ASP* 2.8 61.6 + - - +
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Residues in contact with SER 605 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601B GLU* 3.2 16.4 + - - -
602B SER* 3.7 4.9 - - - -
603B LEU 3.3 0.2 - - - -
604B ARG* 1.3 79.5 - - - +
606B LYS* 1.3 73.4 + - - +
608B ASP* 3.3 9.2 + - - +
609B GLU* 3.2 35.0 + - - +
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Residues in contact with LYS 606 (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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587A GLU* 4.9 13.7 - - - +
585B LEU* 4.2 10.8 - - + -
588B ILE* 5.2 1.6 - - + -
592B GLU* 3.5 18.3 + - - +
595B HIS* 5.7 0.6 - - - -
596B MET* 3.7 35.9 - - + -
602B SER* 2.7 43.7 + - - -
603B LEU 3.2 1.9 + - - +
605B SER* 1.3 86.7 + - - +
607B VAL* 1.3 65.2 - - - +
609B GLU* 3.3 16.4 - - - +
610B ALA* 3.0 23.4 - - - -
1385C TRP* 4.5 16.1 - - + -
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Residues in contact with VAL 607 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570B ILE* 3.9 29.6 - - + -
573B MET* 4.0 18.6 - - - -
574B HIS* 3.7 31.0 - - + +
581B ILE* 4.3 16.2 - - + -
585B LEU* 4.1 6.7 - - + -
603B LEU* 2.8 33.5 + - + +
604B ARG 3.6 3.6 - - - +
606B LYS* 1.3 76.0 + - - +
608B ASP* 1.3 66.6 + - - +
610B ALA* 3.2 2.3 + - - +
611B VAL* 2.9 24.9 + - + +
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Residues in contact with ASP 608 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574B HIS* 4.7 7.4 - - - -
604B ARG* 2.8 53.8 + - - +
605B SER* 3.6 7.9 - - - +
606B LYS 3.2 0.2 - - - +
607B VAL* 1.3 81.1 - - - +
609B GLU* 1.3 61.8 + - + +
611B VAL* 3.8 5.4 - - - +
612B ALA* 3.1 24.5 + - - +
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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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587A GLU* 4.7 7.0 - - - +
605B SER* 3.2 25.8 + - - +
606B LYS* 3.6 15.4 - - - +
607B VAL 3.3 0.2 - - - -
608B ASP* 1.3 74.6 - - + +
610B ALA* 1.3 65.5 + - - +
612B ALA* 3.4 6.1 + - - +
613B VAL* 3.0 29.2 + - - +
1385C TRP* 2.9 35.0 + - + +
1387C PRO* 5.3 0.3 - - - +
1397C GLY* 4.1 20.6 - - - +
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Residues in contact with ALA 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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581B ILE* 4.0 13.9 - - + -
584B MET* 3.9 24.9 - - + +
585B LEU* 3.8 21.5 - - + -
606B LYS 3.0 16.3 - - - -
607B VAL 3.2 4.0 + - - +
609B GLU* 1.3 76.0 - - - +
611B VAL* 1.3 58.3 + - - +
613B VAL* 3.3 4.9 + - - +
614B LEU* 2.9 33.6 + - - +
1385C TRP* 4.5 5.6 - - + +
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Residues in contact with VAL 611 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574B HIS* 3.5 31.9 - - + +
577B LEU* 4.6 7.9 - - + -
581B ILE* 3.5 27.6 - - + -
607B VAL 2.9 20.7 + - - +
608B ASP* 3.8 5.8 - - - +
609B GLU 3.3 0.2 - - - -
610B ALA* 1.3 73.8 - - - +
612B ALA* 1.3 57.9 + - - +
614B LEU* 3.1 7.5 + - - -
615B GLN* 2.7 65.6 + - + +
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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 ASP 3.1 17.6 + - - +
609B GLU* 3.7 7.6 - - - +
611B VAL* 1.3 76.5 - - - +
613B VAL* 1.3 61.9 + - + +
615B GLN* 3.9 10.4 - - - +
616B ALA* 3.1 25.1 + - - +
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Residues in contact with VAL 613 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
584B MET* 4.0 17.0 - - + -
609B GLU* 3.0 15.0 + - + +
610B ALA 3.5 7.6 - - - +
612B ALA* 1.3 75.6 - - + +
614B LEU* 1.3 63.4 + - + +
616B ALA* 3.4 5.6 + - - +
617B HIS* 3.2 38.5 + - + +
1385C TRP* 3.6 36.6 - - + +
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Residues in contact with LEU 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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577B LEU* 4.4 17.5 - - + -
580B LYS* 4.1 23.1 - - + -
581B ILE* 3.7 27.1 - - + -
584B MET* 3.5 34.5 - - + -
610B ALA 2.9 14.4 + - - +
611B VAL* 3.6 4.0 - - - +
613B VAL* 1.3 77.5 - - + +
615B GLN* 1.3 58.0 + - - +
617B HIS* 3.3 7.5 + - + +
618B GLN* 3.0 55.1 + - + +
1385D TRP 5.7 6.5 - - - +
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Residues in contact with GLN 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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574B HIS* 5.6 2.6 + - - -
577B LEU* 4.8 12.5 - - + +
611B VAL* 2.7 48.9 + - + +
612B ALA* 3.9 8.1 - - - +
614B LEU* 1.3 72.6 - - - +
616B ALA* 1.3 56.8 - - - +
618B GLN* 3.0 30.6 - - - +
1620B SO4 5.8 1.8 + - - -
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Residues in contact with ALA 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 3.1 17.9 + - - +
613B VAL* 3.7 6.7 - - - +
615B GLN* 1.3 78.9 - - - +
617B HIS* 1.3 63.0 + - + +
618B GLN 3.5 4.0 + - - +
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Residues in contact with HIS 617 (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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613B VAL* 3.2 33.9 + - + +
614B LEU* 3.3 11.9 + - + +
616B ALA* 1.3 81.7 - - + +
618B GLN* 1.3 62.0 + - + +
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Residues in contact with GLN 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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577B LEU* 3.8 22.3 - - - +
580B LYS* 3.1 39.2 - - - +
614B LEU* 3.0 31.2 + - + +
615B GLN* 3.0 19.2 + - - +
616B ALA 3.9 3.8 - - - +
617B HIS* 1.3 83.2 - - + +
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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