Contacts of the helix formed by residues 594 - 609 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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570D PHE* 3.1 46.7 + - - +
573D ALA* 4.1 9.0 - - - -
590D ILE 3.3 0.4 + - - -
591D SER* 2.8 15.5 + - - -
592D LYS 3.5 1.2 + - - -
593D VAL* 1.3 77.0 - - - +
595D PHE* 1.3 57.6 + - - +
596D LEU 3.4 4.5 + - - -
597D ARG* 2.8 25.1 + - - +
598D TRP* 2.8 29.3 + - - +
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Residues in contact with PHE 595 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460D PRO* 4.5 3.6 - - + -
538D VAL* 3.6 30.9 - - + +
541D CYS* 4.0 29.2 - - + -
542D CYS* 3.5 40.6 - - + -
545D MET* 4.2 14.6 - - - -
567D TYR* 5.3 4.7 - + + -
570D PHE* 3.4 36.1 - + - -
593D VAL 3.5 3.8 + - - -
594D SER* 1.3 71.6 - - - +
596D LEU* 1.3 74.4 + - + +
598D TRP* 3.8 5.5 - - - +
599D CYS* 2.8 34.5 + - - +
647D VAL* 5.0 4.7 - - + -
650D LEU* 3.8 13.4 - - + +
654D PHE* 4.6 5.8 - + - -
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Residues in contact with LEU 596 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453D PHE* 4.6 8.5 - - + +
456D GLY 4.3 2.9 - - - +
457D ALA* 3.5 40.3 + - + +
460D PRO* 3.9 10.5 - - + -
538D VAL* 4.9 1.6 - - + -
567D TYR* 3.8 21.3 - - + -
570D PHE* 3.6 15.7 - - + +
571D TYR* 3.5 32.5 - - - +
574D GLY* 4.8 3.1 - - - -
594D SER* 3.0 6.7 - - - +
595D PHE* 1.3 100.7 - - + +
597D ARG* 1.3 63.8 + - - +
599D CYS* 3.6 6.6 - - - +
600D PHE* 3.4 20.1 + - - +
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Residues in contact with ARG 597 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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573D ALA 4.1 5.6 - - - +
574D GLY* 3.6 27.8 - - - +
575D GLY* 4.1 6.5 - - - +
580D LEU* 3.4 26.8 - - + +
591D SER* 3.3 32.3 + - - +
592D LYS* 3.6 11.7 - - - +
594D SER* 2.8 17.4 + - - +
596D LEU* 1.3 79.2 - - - +
598D TRP* 1.3 99.2 + - - +
600D PHE* 2.8 11.1 + - + +
601D GLU* 2.8 53.9 + - + +
634D GLU 5.8 0.2 + - - -
637D SER* 5.3 2.8 - - - -
638D TYR* 4.6 10.5 - - - -
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Residues in contact with TRP 598 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534D LEU* 4.0 0.9 - - - +
591D SER 4.7 0.2 - - - -
592D LYS* 2.5 45.0 + - + -
594D SER 2.8 21.1 + - - +
595D PHE* 4.0 1.8 - - - +
597D ARG* 1.3 112.5 - - - +
599D CYS* 1.3 57.0 + - - +
601D GLU* 3.4 34.8 - - + -
602D GLY* 2.8 28.2 + - - -
638D TYR* 3.9 22.9 - + + -
643D ILE* 3.5 32.8 - - + +
646D ILE* 3.1 40.9 - - + +
647D VAL* 3.7 13.5 - - + -
650D LEU* 3.8 13.5 - - + -
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Residues in contact with CYS 599 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452D LEU 4.5 1.3 - - - -
453D PHE 5.1 0.2 - - - -
456D GLY* 3.5 30.3 - - - -
534D LEU* 3.6 6.0 - - - +
535D VAL* 4.9 7.9 - - - -
538D VAL* 3.5 30.4 - - + +
595D PHE 2.8 19.4 + - - +
596D LEU* 3.6 8.3 - - - +
598D TRP* 1.3 76.9 - - - +
600D PHE* 1.3 58.8 + - - +
603D LEU* 2.8 54.5 + - - +
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Residues in contact with PHE 600 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449D ALA* 4.0 11.0 - - + -
452D LEU* 4.2 10.0 - - - +
453D PHE* 3.5 37.0 - + + -
575D GLY* 4.0 25.4 - - - -
576D PHE* 3.9 24.9 - + + -
596D LEU 3.4 10.7 + - - +
597D ARG* 2.8 17.6 + - + +
599D CYS* 1.3 72.7 - - - +
601D GLU* 1.3 63.0 + - + +
603D LEU* 4.0 1.3 - - - +
604D MET* 2.8 64.5 + - + +
633D MET* 5.7 4.5 - - - -
635D LEU* 3.3 26.9 - - + -
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Residues in contact with GLU 601 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597D ARG* 2.8 49.7 + - + +
598D TRP* 3.4 18.9 - - + -
600D PHE* 1.3 71.3 - - + +
602D GLY* 1.3 56.7 + - - +
604D MET* 3.2 0.7 + - - +
605D LYS* 2.7 36.6 + - + +
634D GLU 5.3 0.2 - - - +
635D LEU* 2.7 59.3 - - + +
637D SER* 4.3 1.1 + - - -
638D TYR* 3.5 28.3 + - - +
643D ILE* 4.5 6.9 - - + +
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Residues in contact with GLY 602 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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534D LEU* 3.5 11.4 - - - -
598D TRP 2.8 19.4 + - - -
601D GLU* 1.3 75.5 - - - +
603D LEU* 1.3 65.1 + - - +
605D LYS* 2.8 14.7 + - - +
606D ILE* 2.8 22.1 + - - +
643D ILE* 3.5 21.9 - - - +
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Residues in contact with LEU 603 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452D LEU* 3.5 39.5 - - + +
455D ILE* 3.6 19.1 - - + -
531D HIS* 3.1 61.7 - - + +
534D LEU* 3.5 8.2 - - + +
535D VAL* 4.3 6.5 - - + -
599D CYS* 2.8 34.8 + - - +
600D PHE 4.0 1.8 - - - +
602D GLY* 1.3 70.0 - - - +
604D MET* 1.3 65.6 + - - +
606D ILE* 3.4 4.6 - - + +
607D GLN* 2.8 27.0 + - - +
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Residues in contact with MET 604 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448D THR 5.6 0.2 - - - -
449D ALA* 3.5 23.6 - - + +
452D LEU* 3.7 15.0 - - + +
600D PHE* 2.8 72.4 + - + +
601D GLU* 3.5 6.7 - - - +
603D LEU* 1.3 74.1 - - - +
605D LYS* 1.3 58.1 + - - +
608D PHE* 2.8 63.1 + - + +
609D SER 3.4 2.8 + - - -
630D LEU* 3.7 21.3 - - + +
633D MET* 4.9 9.2 - - + -
635D LEU* 4.3 6.7 - - + -
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Residues in contact with LYS 605 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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601D GLU* 2.7 22.0 + - + +
602D GLY* 2.8 5.6 + - - +
604D MET* 1.3 72.7 - - - +
606D ILE* 1.3 63.4 + - + +
610D ARG* 2.8 45.6 + - - +
627D ASP* 5.9 0.9 - - - -
630D LEU* 3.3 38.5 - - + +
635D LEU 4.2 5.8 - - - +
636D ASP* 4.3 11.0 + - - +
638D TYR 3.8 13.9 + - - +
639D PRO* 3.7 8.8 - - - +
640D LEU* 3.3 52.7 - - + +
643D ILE* 4.7 5.8 - - + -
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Residues in contact with ILE 606 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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522D ARG* 4.7 4.2 - - - -
527D PRO* 3.9 23.6 - - + +
530D LEU* 3.4 52.5 - - + -
531D HIS* 4.2 10.1 - - + +
534D LEU* 5.2 1.3 - - + -
602D GLY* 2.8 28.1 + - - +
603D LEU* 3.4 8.7 - - + +
605D LYS* 1.3 82.3 - - + +
607D GLN* 1.3 68.7 + - + +
610D ARG* 3.5 28.8 + - - +
640D LEU* 4.1 22.4 - - - +
644D TYR* 4.1 9.0 - - + +
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Residues in contact with GLN 607 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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448D THR* 5.8 3.4 - - + -
452D LEU* 3.8 16.2 - - + -
516D TYR* 3.2 18.5 + - - -
521D LEU* 3.0 39.4 - - + +
522D ARG* 2.5 75.3 - - - +
527D PRO* 4.6 2.9 - - - +
531D HIS* 3.8 8.3 - - - +
603D LEU* 2.8 17.4 + - + +
606D ILE* 1.3 84.3 - - + +
608D PHE* 1.3 65.8 + - + +
609D SER 3.5 1.3 + - - -
612D THR* 3.9 4.2 + - - -
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Residues in contact with PHE 608 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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445D PHE* 3.4 31.6 - + + -
448D THR* 5.3 12.1 - - + -
449D ALA* 5.8 1.8 - - + -
452D LEU* 4.7 2.5 - - + -
604D MET* 2.8 45.9 + - + +
607D GLN* 1.3 83.3 - - + +
609D SER* 1.3 60.6 + - - +
612D THR* 4.4 5.5 + - - +
614D LYS* 3.5 44.6 - - + +
626D GLY 5.3 0.5 - - - +
629D ILE* 3.3 47.2 - - + +
630D LEU* 5.6 1.8 - - + -
633D MET* 4.3 8.3 - - + -
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Residues in contact with SER 609 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
604D MET 3.4 3.0 + - - -
605D LYS 3.6 1.1 - - - -
607D GLN 4.7 0.2 - - - -
608D PHE* 1.3 82.7 - - - +
610D ARG* 1.3 73.6 + - - +
612D THR* 2.3 31.9 + - - -
627D ASP* 2.6 47.5 + - - +
629D ILE* 4.5 2.5 - - - -
630D LEU* 3.4 33.1 - - - +
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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
------------------------------------------------------------
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