Contacts of the helix formed by residues 584 - 594 (chain B) in PDB entry 3JUE
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 584 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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578B ALA* 2.9 12.7 + - - +
582B PRO 3.5 4.0 + - - -
583B PRO* 1.3 71.0 - - - +
585B LEU* 1.3 62.8 + - - +
586B PRO* 3.7 9.3 - - - +
587B THR* 2.8 33.6 + - - -
588B MET* 3.1 23.8 + - - +
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Residues in contact with LEU 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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472B LEU* 4.0 9.6 - - + -
475B GLU* 3.6 29.6 - - + +
476B LEU* 3.8 14.2 - - + +
583B PRO* 3.8 6.0 + - + +
584B SER* 1.3 73.1 - - - +
586B PRO* 1.4 65.1 - - + +
588B MET* 3.3 15.8 + - - +
589B ALA* 2.9 30.3 + - - +
621B LEU* 3.9 24.9 - - + -
622B ALA* 4.1 9.9 - - + -
625B PHE* 3.5 44.4 - - + -
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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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475B GLU* 4.3 13.5 - - + +
476B LEU* 4.3 2.0 - - + -
480B ILE* 3.9 40.6 - - + -
484B ILE* 3.8 4.7 - - + +
584B SER* 3.5 10.8 - - - +
585B LEU* 1.4 94.7 - - + +
587B THR* 1.3 55.2 + - - +
589B ALA* 3.4 3.5 + - + +
590B ASP* 3.0 27.4 + - - +
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Residues in contact with THR 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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574B LEU* 3.9 31.4 - - + -
578B ALA* 3.8 18.2 - - + -
584B SER* 2.8 27.2 + - - -
586B PRO* 1.3 73.8 - - - +
588B MET* 1.3 55.5 + - - +
590B ASP* 3.1 8.7 + - + +
591B ALA* 2.8 33.3 + - - +
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Residues in contact with MET 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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575B LEU* 3.8 16.3 - - + +
578B ALA* 3.6 31.1 - - + +
579B SER* 3.7 13.0 - - - +
583B PRO* 4.6 0.9 - - - -
584B SER 3.1 15.7 + - - +
585B LEU* 3.6 22.2 - - - +
587B THR* 1.3 76.5 - - - +
589B ALA* 1.3 56.1 + - - +
591B ALA* 3.3 3.3 + - - +
592B LEU* 3.0 34.5 + - - +
622B ALA* 3.8 19.7 - - + +
625B PHE* 3.7 22.2 - - + -
626B LEU* 3.5 37.7 - - + -
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Residues in contact with ALA 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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476B LEU* 4.6 1.8 - - + -
481B ILE* 3.8 28.7 - - + -
484B ILE* 3.8 7.0 - - + -
485B TYR* 4.9 3.1 + - + -
585B LEU 2.9 17.4 + - - +
586B PRO* 3.6 7.0 - - + +
588B MET* 1.3 75.0 - - - +
590B ASP* 1.3 58.1 + - - +
592B LEU* 3.4 4.4 + - - +
593B ALA* 2.9 30.7 + - - +
625B PHE* 3.7 21.2 - - + -
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Residues in contact with ASP 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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484B ILE* 3.6 27.3 - - + +
521B THR* 5.0 0.7 + - - -
524B PRO* 3.1 30.2 - - + +
574B LEU* 5.6 0.2 - - + -
586B PRO 3.0 14.6 + - - +
587B THR* 3.3 14.2 - - + +
589B ALA* 1.3 76.1 - - - +
591B ALA* 1.3 60.4 + - - +
593B ALA* 3.3 1.6 + - - +
594B HIS* 2.8 58.6 + - - -
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Residues in contact with ALA 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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524B PRO* 4.3 11.1 - - - +
571B PRO* 3.5 24.4 - - - +
574B LEU* 4.3 9.4 - - + -
575B LEU* 3.7 22.7 - - + +
587B THR 2.8 18.5 + - - +
588B MET 3.7 4.0 - - - +
590B ASP* 1.3 74.0 - - - +
592B LEU* 1.3 59.1 + - - +
594B HIS* 3.2 11.2 + - - +
595B GLY 3.3 0.5 + - - -
596B ALA* 2.9 24.2 + - - +
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Residues in contact with LEU 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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485B TYR* 4.9 1.6 - - - +
517B LYS* 5.0 4.3 + - - -
575B LEU* 4.1 19.1 - - + -
588B MET 3.0 21.5 + - - +
589B ALA* 3.7 4.3 - - - +
591B ALA* 1.3 72.2 - - - +
593B ALA* 1.3 65.5 + - - +
595B GLY* 3.1 13.7 + - - -
596B ALA* 3.8 21.6 + - - +
598B VAL* 4.0 27.1 - - + -
625B PHE* 3.5 30.5 - - + -
626B LEU* 4.9 4.5 - - + -
629B ASN* 4.0 25.4 - - + +
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Residues in contact with ALA 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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484B ILE* 3.6 19.1 - - + -
485B TYR* 3.4 37.9 + - + +
517B LYS* 3.2 19.6 - - - +
520B LEU* 3.1 22.3 - - + +
589B ALA 2.9 16.1 + - - +
590B ASP 3.3 6.3 + - - +
592B LEU* 1.3 77.3 - - - +
594B HIS* 1.3 56.8 + - + +
595B GLY 3.2 3.7 + - - -
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Residues in contact with HIS 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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484B ILE* 4.7 2.6 + - - +
520B LEU* 4.0 19.3 - - + +
521B THR* 2.7 46.3 + - - -
522B LYS 3.7 11.1 + - - -
523B LEU 3.6 7.0 - - - -
524B PRO* 3.5 25.0 - - + +
571B PRO* 3.6 16.5 - - + +
590B ASP* 2.8 46.7 + - - +
591B ALA 3.2 6.2 + - - +
593B ALA* 1.3 81.0 - - + +
595B GLY* 1.3 58.2 + - - +
596B ALA 3.5 0.2 - - - -
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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