Contacts of the helix formed by residues 584 - 598 (chain L) in PDB entry 6PSS
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 ARG 584 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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573L LEU* 3.5 37.5 - - + +
574L GLU* 3.3 42.2 + - - +
582L VAL* 2.9 13.9 + - - +
583L THR* 1.3 72.4 - - - +
585L GLU* 1.3 58.2 + - + +
586L ARG 3.8 0.4 - - - -
587L ILE* 4.0 6.7 - - - -
588L ARG* 3.3 26.1 + - - +
29O A 6.1 0.4 - - - -
55P T 3.2 45.5 + - - +
56P G 2.5 54.3 + - - -
57P T 4.4 12.3 + - + +
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Residues in contact with GLU 585 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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583L THR* 2.8 14.8 + - - +
584L ARG* 1.3 74.2 - - - +
586L ARG* 1.3 60.6 + - - +
587L ILE 3.2 0.9 - - - -
588L ARG* 3.0 31.1 + - - +
589L GLN* 2.9 56.8 + - - +
26O T 4.0 11.7 - - + -
27O T 3.3 31.0 - - + +
28O G 4.3 0.8 - - - +
57P T 3.3 25.5 - - - +
58P C 2.8 25.6 + - - +
59P A 4.0 3.1 + - - +
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Residues in contact with ARG 586 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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554L ARG* 5.3 2.7 - - - +
582L VAL* 3.6 21.4 - - + +
585L GLU* 1.3 74.9 - - - +
587L ILE* 1.3 57.6 + - + +
589L GLN* 3.3 27.3 + - - +
590L ILE* 2.7 65.9 + - + +
593L LYS* 4.8 13.5 - - - +
23O C 4.8 3.2 - - - +
24O C 2.8 69.8 + - - +
25O A 4.2 24.0 - - - +
26O T 3.6 15.2 - - + +
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Residues in contact with ILE 587 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554L ARG* 6.3 0.4 - - - +
558L VAL* 4.0 21.2 - - + +
573L LEU* 3.9 24.9 - - + +
576L VAL* 4.0 13.5 - - + +
577L GLY* 3.7 21.5 - - - -
580L PHE* 4.3 24.5 - - + -
582L VAL* 3.8 24.0 - - + -
584L ARG* 4.1 11.0 - - - -
585L GLU 3.2 1.0 - - - +
586L ARG* 1.3 79.8 - - + +
588L ARG* 1.3 56.2 + - - +
590L ILE* 3.4 14.1 - - + +
591L GLU* 3.0 27.7 + - - +
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Residues in contact with ARG 588 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573L LEU* 3.7 19.9 - - + +
584L ARG 3.3 18.9 + - - +
585L GLU* 3.0 28.0 + - - +
587L ILE* 1.3 78.7 - - - +
589L GLN* 1.3 74.0 + - - +
591L GLU* 3.5 11.7 + - - +
592L ALA* 3.0 32.6 + - + +
56P G 4.3 0.2 - - - -
57P T 3.4 73.2 + - - +
58P C 3.5 23.4 + - - -
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Residues in contact with GLN 589 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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585L GLU* 2.9 49.1 + - - +
586L ARG* 3.2 35.0 + - - +
588L ARG* 1.3 90.6 - - - +
590L ILE* 1.3 50.5 + - - +
592L ALA* 2.9 7.3 + - - +
593L LYS* 2.4 40.1 + - - +
25O A 4.2 6.8 - - - +
26O T 3.8 17.2 + - - +
59P A 5.0 2.4 - - - +
60P A 5.1 2.0 - - - +
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Residues in contact with ILE 590 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554L ARG* 4.4 28.9 - - + +
555L GLU* 4.5 25.9 - - + +
558L VAL* 4.1 18.5 - - + +
559L LEU* 4.7 0.9 - - - +
586L ARG* 2.7 53.6 + - + +
587L ILE* 3.4 20.4 - - + +
589L GLN* 1.3 70.0 - - - +
591L GLU* 1.3 65.2 + - - +
593L LYS* 3.8 14.6 - - + -
594L ALA* 3.2 23.0 + - - +
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Residues in contact with GLU 591 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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904I ALA* 5.7 2.6 - - - +
558L VAL* 4.9 7.4 - - + -
559L LEU* 3.8 24.6 - - + +
562L ARG* 4.1 33.2 + - + +
563L PHE* 4.2 18.9 - - + -
573L LEU* 4.8 1.9 - - + +
587L ILE 3.0 18.6 + - - +
588L ARG* 3.5 20.4 - - - +
590L ILE* 1.3 77.9 - - - +
592L ALA* 1.3 58.5 + - - +
594L ALA* 3.3 1.9 + - - +
595L LEU* 2.8 40.0 + - + +
57P T 4.6 5.5 + - - -
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Residues in contact with ALA 592 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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588L ARG* 3.0 22.5 + - + +
589L GLN* 2.9 8.3 + - - +
591L GLU* 1.3 76.2 - - - +
593L LYS* 1.3 62.1 + - - +
595L LEU* 3.8 12.2 - - + +
596L ARG* 3.1 28.1 + - - +
599L ARG* 5.3 0.7 + - - -
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Residues in contact with LYS 593 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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555L GLU* 6.1 3.8 - - + +
586L ARG* 4.8 17.6 - - - +
589L GLN 2.4 28.5 + - - +
590L ILE* 4.0 14.8 - - + +
591L GLU 3.2 0.2 - - - -
592L ALA* 1.3 69.6 - - - +
594L ALA* 1.3 61.6 + - + +
596L ARG* 3.4 33.0 + - - +
597L LYS* 2.8 47.8 + - - +
23O C 4.6 25.5 - - - +
24O C 4.8 3.3 + - - +
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Residues in contact with ALA 594 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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551L LEU* 3.8 25.4 - - + -
555L GLU* 4.0 13.2 - - + -
559L LEU* 4.1 14.8 - - + -
590L ILE 3.2 16.8 + - - +
591L GLU 3.9 2.0 - - - +
593L LYS* 1.3 78.6 - - + +
595L LEU* 1.3 59.4 - - - +
597L LYS* 3.2 10.4 + - - +
598L LEU* 3.0 34.3 + - - +
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Residues in contact with LEU 595 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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901I LEU* 4.6 9.2 - - + +
904I ALA* 3.3 48.5 - - + +
905I ILE* 3.7 16.0 - - + +
559L LEU* 4.8 4.9 - - + +
563L PHE* 5.5 3.6 - - + -
591L GLU* 2.8 26.9 + - + +
592L ALA* 4.0 11.0 - - + +
594L ALA* 1.3 78.3 - - - +
596L ARG* 1.3 60.1 + - - +
598L LEU* 3.3 14.0 + - - +
599L ARG* 3.1 40.5 + - - +
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Residues in contact with ARG 596 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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592L ALA 3.1 19.8 + - - +
593L LYS* 3.6 39.4 + - - +
595L LEU* 1.3 72.9 - - - +
597L LYS* 1.3 67.4 + - - +
599L ARG* 3.2 28.4 + - + +
600L HIS* 2.9 29.1 + - + +
258M ASP* 4.6 15.3 + - - -
261M GLU* 5.6 1.8 + - - -
264M VAL* 5.7 7.1 - - - +
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Residues in contact with LYS 597 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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550L GLY 5.4 0.2 - - - +
551L LEU* 3.7 23.1 - - + +
552L THR* 6.0 0.2 - - - +
555L GLU* 3.9 18.2 + - - -
593L LYS* 2.8 39.9 + - - +
594L ALA* 3.2 13.0 + - - +
596L ARG* 1.3 83.2 - - - +
598L LEU* 1.3 56.6 + - - +
599L ARG 3.2 0.2 - - - -
600L HIS* 3.1 25.1 + - - -
603L ARG* 3.3 31.7 - - - +
261M GLU* 3.2 21.0 - - + +
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Residues in contact with LEU 598 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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901I LEU* 4.4 6.5 - - + -
905I ILE* 3.7 33.8 - - + +
547L VAL* 3.7 38.6 - - + +
548L LEU* 4.9 6.3 - - + -
551L LEU* 4.6 11.0 - - + -
559L LEU* 4.4 20.4 - - + -
594L ALA 3.0 16.1 + - - +
595L LEU* 3.3 6.3 + - - +
596L ARG 3.2 0.4 - - - -
597L LYS* 1.3 76.0 - - - +
599L ARG* 1.3 54.5 + - - +
600L HIS 3.3 2.5 - - - -
603L ARG* 3.9 32.1 - - + +
604L SER* 2.4 30.2 + - - +
607L LEU* 5.6 0.7 - - + -
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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