Contacts of the helix formed by residues 584 - 595 (chain B) in PDB entry 5FS9
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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493B GLU* 5.1 1.2 + - - -
578B LEU* 4.4 6.0 - - + +
581B ILE* 3.7 16.4 + - + +
582B PHE 3.2 12.6 + - - +
583B ASN* 1.3 83.5 + - - +
585B MET* 1.3 68.1 + - - +
586B PRO* 3.2 4.3 - - - -
587B ILE* 3.0 35.4 + - + +
588B ALA 3.2 7.8 + - - -
606B LYS 4.9 0.6 + - - -
607B LEU 2.9 27.1 + - - -
608B PHE* 3.8 28.2 + - + +
609B ASN* 3.6 31.7 - - - +
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Residues in contact with MET 585 (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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481B MET* 3.9 20.4 - - + -
493B GLU* 3.4 45.0 + - + +
494B ALA* 4.0 12.6 - - - +
495B ILE* 3.6 32.8 - - + -
576B ILE 5.7 0.2 - - - +
578B LEU* 4.5 8.1 - - + -
583B ASN* 3.7 0.6 - - - +
584B ARG* 1.3 77.5 - - - +
586B PRO* 1.3 63.8 - - + +
588B ALA* 3.0 7.1 + - + +
589B ARG* 2.8 37.8 + - - +
1001B GOL 3.7 31.6 - - - +
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Residues in contact with PRO 586 (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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583B ASN* 4.7 4.9 - - - +
584B ARG* 3.4 7.9 - - - +
585B MET* 1.3 94.5 - - + +
587B ILE* 1.3 56.6 + - + +
589B ARG* 3.4 12.8 + - + +
590B LYS* 3.0 28.4 + - - +
1001B GOL 3.6 19.7 - - - +
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Residues in contact with ILE 587 (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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583B ASN 5.1 1.1 - - - +
584B ARG* 3.0 37.8 + - + +
586B PRO* 1.3 75.6 - - + +
588B ALA* 1.3 67.6 + - - +
590B LYS* 3.3 11.0 + - + +
591B ILE* 3.0 28.7 + - + +
607B LEU* 3.5 44.9 - - + +
608B PHE* 3.8 16.6 - - + -
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Residues in contact with ALA 588 (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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495B ILE* 3.9 19.7 - - + -
576B ILE* 3.7 30.4 - - + +
578B LEU* 4.8 2.5 - - + -
584B ARG 3.2 3.6 + - - +
585B MET* 3.0 15.3 + - - +
587B ILE* 1.3 80.5 - - - +
589B ARG* 1.3 61.7 + - - +
591B ILE* 3.4 2.3 + - - +
592B ILE* 3.2 27.0 + - - +
608B PHE* 3.8 14.7 - - + -
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Residues in contact with ARG 589 (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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456B ASP* 4.6 0.6 + - - -
478B HIS* 3.5 35.5 + - - +
479B GLN* 2.8 44.4 + - + +
481B MET* 4.3 5.9 - - - +
495B ILE* 3.9 18.8 - - + +
585B MET* 2.8 31.4 + - - +
586B PRO* 3.8 13.6 - - + +
588B ALA* 1.3 73.4 - - - +
590B LYS* 1.3 58.0 + - - +
592B ILE* 3.4 4.4 + - - +
593B LYS* 2.9 31.9 + - + +
1001B GOL 2.6 48.3 + - - -
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Residues in contact with LYS 590 (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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586B PRO 3.0 17.6 + - - +
587B ILE* 3.6 10.1 - - + +
589B ARG* 1.3 74.0 - - - +
591B ILE* 1.3 64.0 + - + +
593B LYS* 3.1 8.9 + - + +
594B ASP* 2.8 57.6 + - - +
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Residues in contact with ILE 591 (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 PHE* 4.7 0.7 - - + -
573B VAL* 4.1 26.3 - - + +
576B ILE* 4.2 7.6 - - + -
587B ILE* 3.0 27.6 + - + +
588B ALA 3.7 3.8 - - - +
590B LYS* 1.3 80.8 - - + +
592B ILE* 1.3 63.2 + - - +
594B ASP* 3.3 7.1 + - - +
595B GLY* 3.3 16.8 + - - -
596B GLU 4.5 1.7 + - - -
598B HIS* 3.9 26.9 + - + +
604B VAL* 3.6 28.3 - - + -
607B LEU* 4.2 10.5 - - + -
608B PHE* 3.7 25.6 - - + -
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Residues in contact with ILE 592 (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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446B LYS* 4.7 2.6 + - - -
447B LEU* 4.4 23.2 - - + +
479B GLN* 4.9 12.3 - - + -
495B ILE* 3.8 45.8 - - + +
496B GLY* 4.3 1.1 - - - -
572B VAL* 5.6 0.2 - - - +
573B VAL* 3.9 32.9 - - + +
574B VAL 4.0 11.4 - - - +
575B GLY* 3.9 13.5 - - - -
576B ILE* 4.2 4.9 - - + +
588B ALA 3.2 13.6 + - - +
589B ARG* 3.8 4.3 - - - +
591B ILE* 1.3 72.3 - - - +
593B LYS* 1.3 67.2 + - - +
595B GLY* 3.3 11.6 + - - -
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Residues in contact with LYS 593 (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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446B LYS* 3.2 32.8 + - - +
477B TRP* 3.5 38.8 - - + +
589B ARG* 2.9 20.9 + - + +
590B LYS* 3.1 9.8 + - + +
592B ILE* 1.3 77.4 - - - +
594B ASP* 1.3 68.2 + - - +
595B GLY* 3.2 1.2 + - - -
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Residues in contact with ASP 594 (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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590B LYS* 2.8 53.9 + - - +
591B ILE* 3.8 8.5 - - - +
592B ILE 3.2 0.2 - - - -
593B LYS* 1.3 81.8 - - - +
595B GLY* 1.3 64.8 + - - +
596B GLU* 3.0 22.7 + - + +
598B HIS* 6.0 0.9 - - + +
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Residues in contact with GLY 595 (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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572B VAL* 3.5 33.8 - - - +
573B VAL 5.1 0.2 - - - -
591B ILE 3.3 5.8 + - - -
592B ILE 3.3 10.5 + - - -
593B LYS 3.2 4.4 - - - -
594B ASP* 1.3 78.2 - - - +
596B GLU* 1.3 63.0 + - - +
597B GLN* 3.9 0.5 + - - +
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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