Contacts of the helix formed by residues 594 - 609 (chain B) in PDB entry 5DO7
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 594 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570B PHE* 3.1 48.9 + - - +
573B ALA* 4.1 8.5 - - - -
590B ILE 3.2 2.5 + - - -
591B SER 3.0 13.9 + - - -
592B LYS 3.5 0.6 + - - -
593B VAL* 1.3 73.1 - - - +
595B PHE* 1.3 64.6 + - - +
596B LEU 3.4 4.3 + - - -
597B ARG* 2.8 32.0 + - - +
598B TRP* 2.8 15.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 595 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460B PRO* 4.5 4.0 - - + -
538B VAL* 3.6 32.1 - - + +
541B CYS* 4.0 29.2 - - + -
542B CYS* 3.4 39.9 - - + -
545B MET* 4.3 13.9 - - - -
567B TYR* 5.3 5.2 - + + -
570B PHE* 3.4 34.3 - + - -
593B VAL 3.3 7.6 + - - -
594B SER* 1.3 70.1 - - - +
596B LEU* 1.3 74.8 + - + +
598B TRP* 4.0 5.5 - - - +
599B CYS* 2.8 34.5 + - - +
647B VAL* 5.1 4.3 - - + -
650B LEU* 3.8 11.4 - - + +
654B PHE* 4.7 5.8 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 596 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453B PHE* 4.7 7.9 - - + +
456B GLY 4.3 2.9 - - - +
457B ALA* 3.5 36.4 + - + +
460B PRO* 3.9 9.4 - - + -
538B VAL* 4.9 2.0 - - + -
567B TYR* 3.8 17.5 - - + -
570B PHE* 3.6 16.8 - - + +
571B TYR* 3.5 39.9 - - + +
574B GLY* 4.8 2.5 - - - -
594B SER* 2.9 6.0 + - - +
595B PHE* 1.3 103.8 - - + +
597B ARG* 1.3 65.1 + - - +
599B CYS* 3.6 5.6 - - - +
600B PHE* 3.4 19.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 597 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573B ALA 4.1 4.7 - - - +
574B GLY* 3.6 19.9 - - - +
575B GLY* 4.0 15.7 - - - +
580B LEU* 3.7 30.1 - - + +
591B SER* 3.3 17.7 + - - +
592B LYS* 3.6 18.2 - - - +
594B SER* 2.8 17.2 + - - +
596B LEU* 1.3 78.8 - - - +
598B TRP* 1.3 100.1 + - - +
600B PHE* 2.8 10.7 + - + +
601B GLU* 2.8 54.7 + - + +
634B GLU 5.9 0.8 + - - -
635B LEU* 5.7 1.8 - - - +
637B SER* 5.4 2.8 - - - -
638B TYR* 4.6 11.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 598 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534B LEU* 4.0 1.3 - - - +
591B SER 4.8 0.2 - - - -
592B LYS* 2.5 44.0 + - + -
594B SER 2.8 21.1 + - - +
595B PHE* 4.0 2.0 - - - +
597B ARG* 1.3 112.2 - - - +
599B CYS* 1.3 57.5 + - - +
601B GLU* 3.4 34.3 - - + +
602B GLY* 2.8 27.5 + - - -
638B TYR* 3.9 22.2 - + + -
643B ILE* 3.5 34.3 - - + +
646B ILE* 3.1 41.8 - - + +
647B VAL* 3.7 12.3 - - + -
650B LEU* 3.8 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 599 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452B LEU 4.5 1.6 - - - -
453B PHE 5.1 0.2 - - - -
456B GLY* 3.5 29.8 - - - -
534B LEU* 3.5 4.8 - - - +
535B VAL* 4.9 7.6 - - - -
538B VAL* 3.5 31.7 - - + +
595B PHE 2.8 22.8 + - - +
596B LEU* 3.6 8.5 - - - +
598B TRP* 1.3 72.3 - - - +
600B PHE* 1.3 58.2 + - - +
603B LEU* 2.8 55.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 600 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449B ALA* 4.0 12.3 - - + -
452B LEU* 4.2 10.0 - - - +
453B PHE* 3.5 36.8 - + + -
575B GLY* 3.9 18.4 - - - -
576B PHE* 3.8 32.3 - + + -
596B LEU 3.4 11.2 + - - +
597B ARG* 2.8 17.2 + - + +
599B CYS* 1.3 72.8 - - - +
601B GLU* 1.3 63.1 + - + +
603B LEU* 4.0 0.9 - - - +
604B MET* 2.8 64.3 + - + +
633B MET* 4.5 11.9 - - + -
635B LEU* 3.3 24.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 601 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597B ARG* 2.8 48.9 + - - +
598B TRP* 3.4 19.6 - - + -
600B PHE* 1.3 74.6 - - + +
602B GLY* 1.3 54.1 + - - +
604B MET* 3.3 0.9 + - - +
605B LYS* 2.7 36.1 + - + +
635B LEU* 2.7 58.8 - - + +
637B SER* 4.3 0.9 + - - -
638B TYR* 3.5 28.3 + - - +
643B ILE* 4.4 6.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 602 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534B LEU* 3.5 13.9 - - - -
598B TRP 2.8 18.6 + - - -
601B GLU* 1.3 72.5 - - - +
603B LEU* 1.3 66.2 + - - +
605B LYS* 2.8 13.7 + - - +
606B ILE* 2.8 21.5 + - - +
643B ILE* 3.5 22.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 603 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452B LEU* 3.5 39.7 - - + +
455B ILE* 3.6 18.6 - - + -
531B HIS* 3.2 61.2 - - + +
534B LEU* 3.5 9.3 - - + +
535B VAL* 4.3 7.0 - - + -
599B CYS* 2.8 33.9 + - - +
600B PHE 4.0 1.8 - - - +
602B GLY* 1.3 70.0 - - - +
604B MET* 1.3 65.3 + - - +
606B ILE* 3.2 3.3 - - + +
607B GLN* 2.8 27.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 604 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448B THR 5.6 0.2 - - - -
449B ALA* 3.5 23.3 - - + +
452B LEU* 3.7 17.2 - - + +
600B PHE* 2.8 73.7 + - + +
601B GLU* 3.4 6.7 - - - +
603B LEU* 1.3 73.5 - - - +
605B LYS* 1.3 57.9 + - - +
608B PHE* 2.8 54.6 + - + -
609B SER 3.4 5.4 + - - -
630B LEU* 3.7 18.6 - - + -
633B MET* 5.6 5.4 - - + -
635B LEU* 4.3 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 605 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601B GLU* 2.7 22.5 + - + +
602B GLY* 2.8 5.8 + - - +
604B MET* 1.3 74.2 - - - +
606B ILE* 1.3 65.1 + - + +
609B SER* 3.7 10.8 - - - +
610B ARG* 3.4 35.4 + - - +
627B ASP* 5.8 1.8 - - - -
630B LEU* 3.9 14.3 - - + +
635B LEU 4.1 12.6 - - - +
636B ASP* 3.9 19.9 + - - +
638B TYR 3.5 19.3 - - - +
639B PRO* 3.7 6.2 - - - +
640B LEU* 3.4 50.3 - - + +
643B ILE* 4.7 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 606 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522B ARG* 5.8 0.2 - - - +
527B PRO* 3.6 38.0 - - + +
530B LEU* 3.4 34.8 - - + -
531B HIS* 3.7 22.9 - - + +
534B LEU* 5.7 0.9 - - + -
602B GLY* 2.8 19.2 + - - +
603B LEU* 3.2 19.3 - - - +
605B LYS* 1.3 80.1 - - + +
607B GLN* 1.3 82.7 + - + +
609B SER 4.5 0.2 - - - +
610B ARG* 3.7 23.0 + - - +
612B THR* 4.9 3.3 + - - -
640B LEU* 4.7 13.7 - - - +
644B TYR* 4.2 7.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 607 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448B THR* 5.7 2.2 - - - +
452B LEU* 3.8 16.2 - - + -
516B TYR* 3.3 19.6 + - - -
521B LEU* 3.1 43.1 - - + +
522B ARG* 2.3 48.6 + - - +
527B PRO* 4.7 0.2 - - - +
531B HIS* 4.1 1.6 + - - -
603B LEU* 2.8 17.5 + - + +
606B ILE* 1.3 92.7 - - + +
608B PHE* 1.3 65.2 + - + +
609B SER 3.6 1.5 + - - +
612B THR* 3.8 19.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 608 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445B PHE* 3.3 27.8 - + + -
448B THR* 4.5 15.9 - - + +
449B ALA* 6.0 0.9 - - + -
452B LEU* 4.7 2.7 - - + -
604B MET* 2.8 44.4 + - + +
607B GLN* 1.3 82.7 - - + +
609B SER* 1.3 62.3 + - - +
612B THR* 4.9 5.8 - - - +
613B TYR* 6.0 0.2 - - - -
614B LYS* 3.3 49.1 - - + +
626B GLY 5.6 0.9 - - - -
629B ILE* 3.3 47.5 - - + +
630B LEU* 5.9 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 609 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
604B MET 3.4 2.8 + - - -
605B LYS* 3.6 10.3 + - - +
607B GLN 3.9 2.1 - - - +
608B PHE* 1.3 78.2 - - - +
610B ARG* 1.3 92.1 + - - +
612B THR* 3.1 20.4 - - - +
627B ASP* 3.9 16.8 + - - +
629B ILE* 4.4 2.5 - - - -
630B LEU* 3.0 54.6 - - - +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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