Contacts of the helix formed by residues 585 - 589 (chain B) in PDB entry 2J0M
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 PRO 585 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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545B ARG 5.0 2.9 - - - +
546B ASP* 3.7 24.2 - - - +
550B ARG* 3.3 25.8 - - - +
584B LEU* 1.3 84.9 - - + +
586B ILE* 1.3 63.9 + - - +
587B LYS 3.3 3.1 - - - -
588B TRP* 3.1 30.8 + - + +
589B MET* 3.1 32.1 + - + +
607B MET* 4.4 4.3 - - + -
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Residues in contact with ILE 586 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A GLU* 4.2 17.5 - - - +
584B LEU* 3.0 27.0 + - + +
585B PRO* 1.3 70.0 - - - +
587B LYS* 1.3 61.1 + - - +
588B TRP 3.0 5.9 + - - -
589B MET* 3.1 31.4 + - + +
594B ILE* 3.6 33.3 - - + +
628B ASN* 3.6 54.0 - - + +
631B VAL* 4.5 7.9 - - + +
632B ILE* 3.9 13.5 - - + -
635B ILE* 6.1 0.7 - - - +
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Residues in contact with LYS 587 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
585B PRO 3.3 1.6 + - - -
586B ILE* 1.3 75.1 - - + +
588B TRP* 1.3 81.1 + - + +
589B MET 5.2 0.2 - - - -
606B TRP* 5.5 0.5 + - - -
610B VAL* 4.1 7.1 - - - +
621B LYS* 6.1 0.9 - - + -
622B PRO* 3.3 39.0 - - + +
623B PHE* 3.6 25.2 + - + -
624B GLN* 5.4 2.0 - - - +
625B GLY 5.4 1.0 - - - +
626B VAL 3.0 28.9 + - - +
627B LYS* 5.2 0.2 - - - +
628B ASN* 3.4 23.5 + - - +
631B VAL* 3.9 27.6 - - + -
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Residues in contact with TRP 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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508B ARG* 6.0 1.3 - - - -
547B ILE 4.1 5.2 - - - +
548B ALA* 3.6 21.1 - - + +
550B ARG* 3.8 21.3 - - - -
585B PRO* 3.1 24.1 + - + +
586B ILE 3.0 1.0 - - - -
587B LYS* 1.3 105.2 - - + +
589B MET* 1.3 61.6 + - - +
606B TRP* 3.2 21.5 - - - -
607B MET* 3.3 31.8 - - + +
610B VAL* 3.5 25.8 - - + +
614B GLU* 2.7 37.9 + - - -
621B LYS* 4.4 25.1 - - + -
622B PRO* 3.4 20.9 - - + -
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Residues in contact with MET 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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545B ARG 5.6 0.4 - - - +
584B LEU* 4.7 13.5 - - + -
585B PRO* 3.1 43.5 - - + +
586B ILE* 3.1 26.8 + - + +
587B LYS 5.2 0.3 - - - -
588B TRP* 1.3 79.5 - - - +
590B ALA* 1.3 69.1 + - - +
591B PRO* 3.7 0.7 - - - +
593B SER* 3.6 37.5 - - - +
594B ILE* 4.0 16.5 - - + +
599B PHE* 4.2 17.0 - - + -
606B TRP* 3.3 12.0 + - - -
607B MET* 4.1 19.7 - - + -
635B ILE* 4.8 5.5 - - - +
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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
------------------------------------------------------------
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