Contacts of the helix formed by residues 579 - 593 (chain B) in PDB entry 5IYB
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 579 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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548B TRP* 6.4 0.4 - - + -
577B HIS* 2.8 27.1 + - + -
578B LYS* 1.3 80.4 - - - +
580B PRO* 1.3 66.0 - - - +
581B GLU* 3.4 5.7 + - - +
582B GLN* 3.4 34.8 + - + +
583B LEU* 3.4 10.7 + - - +
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Residues in contact with PRO 580 (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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565B THR* 3.2 30.5 - - - +
577B HIS* 4.0 5.1 - - + +
578B LYS 3.9 4.9 - - - +
579B ASP* 1.3 89.5 - - - +
581B GLU* 1.3 56.7 + - + +
583B LEU* 4.0 2.8 - - + +
584B MET* 2.8 39.0 + - - +
605B ARG* 3.4 34.1 - - - +
612B ILE* 3.8 19.4 - - + +
71I ASP* 5.4 7.2 - - - +
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Residues in contact with GLU 581 (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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579B ASP* 3.4 5.3 - - - +
580B PRO* 1.3 81.6 - - + +
582B GLN* 1.3 62.9 + - + +
584B MET* 3.9 3.9 - - - +
585B ASN* 2.9 30.7 + - + +
605B ARG* 4.2 10.0 - - - +
74I GLN* 3.6 45.2 + - + +
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Residues in contact with GLN 582 (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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548B TRP* 4.8 11.4 - - + -
579B ASP* 3.4 30.8 + - - +
580B PRO 3.5 0.4 - - - -
581B GLU* 1.3 81.1 + - + +
583B LEU* 1.3 53.9 + - - +
585B ASN* 3.2 14.8 + - - +
586B THR* 2.7 42.1 + - - +
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Residues in contact with LEU 583 (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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544B PHE* 4.6 5.4 - - + -
545B LEU* 3.9 29.6 - - + -
548B TRP* 3.8 32.0 - - + -
549B SER* 4.8 0.7 - - - +
550B MET* 5.7 2.2 - - + -
567B ILE* 4.6 14.8 - - + -
577B HIS* 3.8 37.7 - - + +
579B ASP 3.4 15.3 + - - +
580B PRO* 4.0 2.9 - - + +
582B GLN* 1.3 77.5 - - - +
584B MET* 1.3 57.9 + - - +
586B THR* 3.2 6.2 + - - -
587B LEU* 2.9 43.4 + - + +
612B ILE* 5.4 5.2 - - + -
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Residues in contact with MET 584 (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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580B PRO 2.8 24.8 + - - +
581B GLU* 3.9 5.2 - - - +
583B LEU* 1.3 74.6 - - - +
585B ASN* 1.3 61.6 + - - +
587B LEU* 3.5 11.0 + - - +
588B ARG* 3.1 61.6 + - + +
603B MET* 3.2 45.3 - - + +
604B ILE 3.7 3.6 - - - +
605B ARG* 3.8 34.5 - - + +
612B ILE* 4.1 23.0 - - + +
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Residues in contact with ASN 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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581B GLU* 2.9 21.0 + - + +
582B GLN* 3.4 16.0 + - - +
584B MET* 1.3 77.5 - - - +
586B THR* 1.3 60.5 + - - +
588B ARG* 3.5 11.8 + - - +
589B LYS* 2.9 34.2 + - - +
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Residues in contact with THR 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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544B PHE* 4.1 13.2 - - + -
548B TRP* 3.6 41.4 - - + +
582B GLN* 2.7 28.4 + - - +
583B LEU* 3.2 6.9 + - - -
585B ASN* 1.3 76.5 + - - +
587B LEU* 1.3 58.8 + - - +
589B LYS* 3.1 12.3 + - + +
590B LEU* 2.8 33.1 + - + +
125T MET* 6.4 0.9 - - + -
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Residues in contact with LEU 587 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541B ILE* 5.2 3.6 - - + -
544B PHE* 3.8 27.6 - - + -
545B LEU* 4.2 16.8 - - + -
583B LEU* 2.9 30.5 + - + +
584B MET* 3.9 14.4 - - - +
586B THR* 1.3 69.3 - - - +
588B ARG* 1.3 62.0 + - - +
590B LEU* 3.2 4.9 + - - +
591B ARG* 3.0 30.7 + - - +
596B ILE* 3.7 26.3 - - + +
603B MET* 3.7 21.3 - - + +
612B ILE* 5.5 3.4 - - + -
614B ILE* 4.0 26.9 - - + -
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Residues in contact with ARG 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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584B MET* 3.1 50.9 + - + +
585B ASN* 3.6 10.4 - - - +
587B LEU* 1.3 75.8 - - - +
589B LYS* 1.3 61.6 + - - +
591B ARG* 3.6 2.6 + - - +
592B ARG* 3.2 52.7 + - - +
603B MET* 4.1 18.2 + - + -
605B ARG* 5.9 2.2 - - - +
663B GLU* 5.2 8.3 + - - +
669B GLU* 5.2 9.7 + - - +
672B THR* 5.0 10.5 + - - -
673B VAL* 6.1 2.4 - - - +
695B HIS* 6.4 0.6 - - - -
76I PRO* 6.2 2.0 - - - +
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Residues in contact with LYS 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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585B ASN* 2.9 23.0 + - - +
586B THR* 3.1 15.7 + - + +
588B ARG* 1.3 78.0 - - - +
590B LEU* 1.3 58.5 + - + +
592B ARG* 3.9 6.2 - - - +
593B GLN* 3.0 50.2 + - + +
122T GLU* 3.1 29.4 + - - +
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Residues in contact with LEU 590 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544B PHE* 3.3 50.5 - - + -
586B THR* 2.8 19.6 + - + +
587B LEU* 3.2 6.9 + - + +
589B LYS* 1.3 75.0 - - + +
591B ARG* 1.3 60.8 + - - +
593B GLN* 3.0 13.2 + - - +
594B MET 2.9 24.1 + - - -
595B ASP* 3.0 41.5 + - + +
596B ILE* 4.1 20.4 - - + -
122T GLU* 6.1 2.7 - - + -
125T MET* 5.0 14.1 - - + -
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Residues in contact with ARG 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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587B LEU 3.0 17.2 + - - +
588B ARG 4.0 2.9 - - - +
590B LEU* 1.3 75.8 - - - +
592B ARG* 1.3 63.4 + - - +
594B MET* 3.3 21.1 + - - +
596B ILE* 3.7 22.4 - - + +
598B VAL* 3.4 34.9 + - - +
601B VAL 2.3 34.4 + - - +
602B SER* 3.6 11.1 + - - +
603B MET* 3.8 31.7 - - + +
663B GLU* 2.1 52.8 + - - +
664B TYR 3.3 17.6 + - - -
669B GLU* 3.6 16.2 + - - -
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Residues in contact with ARG 592 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588B ARG* 3.2 38.2 + - - +
589B LYS* 4.0 6.5 - - - +
591B ARG* 1.3 76.6 - - - +
593B GLN* 1.3 60.7 + - + +
594B MET* 3.3 12.0 + - - +
598B VAL* 6.2 0.4 - - - -
627B ILE* 3.4 47.1 - - + +
629B GLU* 5.2 6.5 + - - +
634B LEU* 5.9 1.6 - - - +
657B VAL 5.5 0.2 - - - -
658B ALA 3.9 15.1 - - - +
660B GLY* 4.1 20.6 + - - +
662B VAL 5.8 0.9 - - - +
663B GLU* 3.0 34.9 + - + +
694B THR 5.4 0.4 + - - -
695B HIS* 4.5 10.5 - - - -
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Residues in contact with GLN 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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589B LYS* 3.0 51.3 + - + +
590B LEU* 3.0 19.4 + - - +
592B ARG* 1.3 77.0 - - + +
594B MET* 1.3 69.2 + - - +
595B ASP* 3.3 15.1 + - - +
658B ALA 5.5 1.3 - - - -
122T GLU* 3.2 32.6 + - - +
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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