Contacts of the helix formed by residues 602 - 615 (chain B) in PDB entry 2XPH
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 602 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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462B HIS 4.6 2.3 - - - +
599B ASN* 2.7 41.4 + - - +
601B SER* 1.3 77.0 + - - +
603B CYS* 1.3 59.0 + - - +
604B GLY 3.4 0.9 - - - -
605B MET* 2.9 22.5 + - - +
606B PHE* 3.0 32.0 + - + -
624B GLN* 2.7 14.4 + - - +
627B MET* 3.6 16.8 - - + +
631B ARG* 2.7 40.2 + - - +
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Residues in contact with CYS 603 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465B TRP* 4.7 5.8 - - - -
532B VAL 4.1 9.9 - - - -
533B HIS* 3.5 27.6 - - + -
534B TRP* 3.8 29.1 - - - +
551B SER* 4.4 4.9 + - - +
597B GLN* 3.4 23.1 - - - +
599B ASN 4.1 1.2 + - - -
600B GLY 3.0 22.6 + - - +
601B SER 3.2 5.1 - - - -
602B ASP* 1.3 77.7 - - - +
604B GLY* 1.3 72.5 + - - +
606B PHE* 3.5 4.4 + - - +
607B ALA* 3.2 21.1 + - - +
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Residues in contact with GLY 604 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466B LEU* 4.0 18.3 - - - +
471B ILE* 4.3 10.7 - - - +
534B TRP* 3.9 23.3 - - - -
601B SER 4.1 3.0 + - - -
602B ASP 3.4 0.6 - - - -
603B CYS* 1.3 85.6 - - - +
605B MET* 1.3 54.5 + - - +
607B ALA* 3.2 4.9 + - - +
608B CYS* 3.0 30.8 + - - -
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Residues in contact with MET 605 (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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460B LEU* 3.7 17.5 - - - -
466B LEU* 3.5 34.0 - - + +
602B ASP* 2.9 11.4 + - - +
604B GLY* 1.3 71.9 - - - +
606B PHE* 1.3 58.4 + - - +
608B CYS* 3.3 2.3 + - - +
609B LYS* 2.5 48.8 + - + +
627B MET* 3.4 16.6 - - - -
630B PHE* 3.6 37.7 - - + +
631B ARG* 4.2 22.9 - - + +
634B MET* 3.3 26.7 - - + -
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Residues in contact with PHE 606 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551B SER* 3.6 20.6 - - - +
595B PRO* 3.4 30.1 - - + -
596B GLN 3.7 5.8 - - - -
597B GLN* 3.5 35.2 - - + -
602B ASP* 3.0 35.9 + - + -
603B CYS 3.8 4.0 - - - +
605B MET* 1.3 75.8 - - - +
607B ALA* 1.3 53.9 + - - +
609B LYS* 4.3 2.2 - - - -
610B TYR* 2.6 64.5 + + + -
622B PHE* 4.2 7.6 - + - -
624B GLN* 3.7 24.7 - - - -
627B MET* 3.6 27.3 - - + +
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Residues in contact with ALA 607 (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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471B ILE* 6.0 2.7 - - + -
475B MET* 4.1 8.9 - - + +
527B PRO* 6.1 1.1 - - + -
534B TRP* 4.3 19.1 - - + +
535B CYS* 4.3 19.1 - - - +
536B LEU* 3.7 13.8 - - + +
603B CYS 3.2 14.4 + - - +
604B GLY 3.4 8.7 - - - +
605B MET 3.2 0.2 - - - -
606B PHE* 1.3 78.0 - - - +
608B CYS* 1.3 62.7 + - - +
610B TYR* 3.8 8.4 - - - +
611B ALA* 3.2 20.1 + - - +
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Residues in contact with CYS 608 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466B LEU* 4.6 2.0 - - - -
471B ILE* 4.0 22.4 - - - -
474B TYR* 3.4 42.0 - - + -
475B MET* 4.0 17.0 - - - +
604B GLY 3.0 19.2 + - - -
605B MET 3.7 4.9 - - - +
607B ALA* 1.3 74.2 - - - +
609B LYS* 1.3 60.7 + - - +
611B ALA* 3.1 4.0 + - - +
612B ASP* 2.9 27.2 + - - +
634B MET* 4.0 19.3 - - + -
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Residues in contact with LYS 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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474B TYR* 3.3 23.1 + - - -
605B MET* 2.5 51.5 + - + +
606B PHE 3.9 0.7 - - - +
608B CYS* 1.3 71.6 - - - +
610B TYR* 1.3 67.5 + - - +
612B ASP* 3.4 23.7 + - - +
613B CYS* 3.3 15.6 + - - -
622B PHE* 3.4 33.1 - - + -
627B MET* 4.1 2.2 - - + -
630B PHE* 3.6 48.8 + - + +
633B ARG* 4.7 12.3 - - - +
634B MET* 4.2 7.5 - - + +
637B GLU* 4.9 2.2 + - - -
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Residues in contact with TYR 610 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536B LEU* 4.0 5.6 - - + -
549B TYR* 3.9 31.2 - + + -
551B SER* 3.1 24.1 - - - -
594B ILE* 3.8 27.8 - - + +
595B PRO* 2.7 35.0 + - + -
606B PHE* 2.6 48.4 + + + +
607B ALA* 3.8 8.3 - - - +
609B LYS* 1.3 70.5 - - - +
611B ALA* 1.3 53.3 + - - +
613B CYS* 3.1 5.4 + - - +
614B ILE* 2.8 51.0 + - + +
620B ILE* 4.3 15.7 - - + +
622B PHE* 4.1 14.1 - + - -
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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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475B MET* 3.9 17.3 - - - -
478B LEU* 3.4 18.4 - - + -
525B LEU* 4.2 9.9 - - + -
536B LEU* 3.9 15.2 - - + +
607B ALA 3.2 11.0 + - - +
608B CYS 3.1 9.3 + - - +
610B TYR* 1.3 79.7 - - - +
612B ASP* 1.3 62.1 + - - +
614B ILE* 3.8 4.7 - - - +
615B THR* 3.0 31.4 + - - +
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Residues in contact with ASP 612 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474B TYR* 3.4 21.2 + - - +
478B LEU* 3.5 11.0 - - - +
481B ARG* 3.1 47.0 + - - -
608B CYS 2.9 11.7 + - - +
609B LYS* 3.4 33.0 + - - +
611B ALA* 1.3 72.1 - - - +
613B CYS* 1.3 68.5 + - - +
615B THR* 3.3 1.9 + - - -
616B LYS* 3.8 8.0 - - - +
630B PHE* 6.0 0.2 - - - -
633B ARG* 4.2 12.8 + - - -
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Residues in contact with CYS 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 LYS 3.3 11.1 + - - +
610B TYR 3.1 7.4 + - - +
612B ASP* 1.3 79.5 - - - +
614B ILE* 1.3 68.3 + - - +
616B LYS* 2.7 21.8 + - - +
617B ASP 3.7 0.9 + - - -
618B ARG* 3.6 29.8 - - - +
619B PRO 3.7 16.8 - - - +
620B ILE* 4.0 14.8 - - + -
621B ASN* 4.1 7.4 - - - -
622B PHE* 3.8 24.7 - - - -
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Residues in contact with ILE 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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488B PRO* 5.2 0.3 - - - +
523B ILE* 4.0 19.2 - - + +
525B LEU* 4.8 3.6 - - + -
536B LEU* 3.9 4.9 - - + -
538B VAL* 3.8 37.7 - - + -
542B ARG* 5.9 0.2 + - - -
549B TYR* 3.7 35.4 - - + +
610B TYR* 2.8 43.5 + - + +
611B ALA* 3.8 4.3 - - - +
613B CYS* 1.3 73.4 - - - +
615B THR* 1.3 63.0 + - + +
616B LYS 3.3 2.8 + - - -
617B ASP* 3.6 11.8 + - - +
618B ARG 4.3 4.0 + - - +
620B ILE* 4.7 10.3 - - + -
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Residues in contact with THR 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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478B LEU* 4.5 10.7 + - + +
481B ARG* 3.1 21.7 + - - -
482B SER* 5.9 1.8 - - - -
487B LEU* 4.5 6.8 - - - +
488B PRO* 3.6 21.5 - - - +
490B VAL* 3.9 26.9 - - + -
523B ILE* 4.5 11.9 - - + -
525B LEU* 4.0 30.3 - - + -
611B ALA 3.0 18.7 + - - +
612B ASP* 3.3 0.9 + - - -
613B CYS 2.8 4.2 + - - -
614B ILE* 1.3 72.5 - - - +
616B LYS* 1.3 59.3 + - - +
617B ASP 3.6 1.1 - - - -
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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