Contacts of the helix formed by residues 627 - 637 (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 LYS 627 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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587B LYS* 5.2 0.4 - - - +
625B GLY 4.2 1.5 - - - +
626B VAL* 1.3 75.5 - - - +
628B ASN* 1.3 67.3 + - - +
629B ASN* 4.4 7.9 - - + +
630B ASP* 3.1 32.0 + - - +
631B VAL* 3.1 11.3 + - - +
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Residues in contact with ASN 628 (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 LEU 4.3 9.1 + - - -
586B ILE* 3.6 36.8 - - + +
587B LYS* 3.4 27.1 + - - +
626B VAL 3.6 0.4 + - - -
627B LYS* 1.3 71.9 - - - +
629B ASN* 1.3 66.9 + - - +
631B VAL* 3.3 20.3 + - - +
632B ILE* 3.3 13.3 - - - +
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Residues in contact with ASN 629 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A GLU* 5.5 2.3 - - - +
627B LYS* 3.2 5.5 - - + +
628B ASN* 1.3 80.4 - - - +
630B ASP* 1.3 62.0 + - - +
632B ILE* 3.1 36.5 - - + +
633B GLY* 3.9 1.7 + - - -
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Residues in contact with ASP 630 (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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626B VAL* 4.2 12.0 - - + +
627B LYS* 3.1 27.8 + - - +
629B ASN* 1.3 77.0 - - - +
631B VAL* 1.3 56.6 + - - +
632B ILE 3.0 1.6 - - - -
633B GLY* 2.6 25.7 + - - -
634B ARG* 2.9 19.0 + - + +
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Residues in contact with VAL 631 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586B ILE* 4.5 8.3 - - + +
587B LYS* 3.9 22.7 - - + -
594B ILE* 5.9 1.3 - - + -
623B PHE* 3.7 46.7 - - + -
626B VAL* 3.5 24.8 - - + +
627B LYS 3.1 12.5 + - - +
628B ASN* 3.3 11.0 - - - +
630B ASP* 1.3 77.1 - - - +
632B ILE* 1.3 63.0 + - + +
634B ARG* 3.7 8.0 - - - +
635B ILE* 3.2 29.9 + - + +
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Residues in contact with ILE 632 (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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182A GLU* 3.8 26.5 - - - +
184A ARG* 6.1 3.6 - - + +
586B ILE* 3.9 20.4 - - + -
594B ILE* 3.9 34.3 - - + -
628B ASN 3.3 16.4 - - - +
629B ASN* 3.1 30.7 - - + +
630B ASP 2.9 1.2 + - - -
631B VAL* 1.3 77.0 - - - +
633B GLY* 1.3 59.0 + - - +
635B ILE* 3.8 5.0 + - - +
636B GLU* 3.2 29.1 + - - +
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Residues in contact with GLY 633 (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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629B ASN 3.9 1.3 + - - -
630B ASP* 2.6 15.5 + - - -
632B ILE* 1.3 79.0 - - - +
634B ARG* 1.3 63.9 + - - -
635B ILE 3.3 0.2 - - - -
636B GLU* 3.1 10.7 + - - +
637B ASN* 3.0 29.3 + - - -
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Residues in contact with ARG 634 (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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623B PHE* 4.0 24.1 - - + -
626B VAL* 3.7 42.8 - - - +
630B ASP* 2.9 18.1 + - + +
631B VAL* 3.7 8.5 - - - +
633B GLY* 1.3 74.6 - - - +
635B ILE* 1.3 59.3 + - + +
637B ASN* 2.9 22.5 + - - +
639B GLU* 3.3 46.6 + - + +
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Residues in contact with ILE 635 (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 ILE 6.1 0.9 - - - +
587B LYS 5.6 2.9 - - - +
589B MET 4.8 6.7 - - - +
591B PRO* 3.8 28.3 - - + -
594B ILE* 6.1 4.9 - - + -
606B TRP* 3.5 27.6 - - + +
623B PHE* 4.3 27.8 - - + -
631B VAL* 3.2 21.2 + - + +
632B ILE* 4.1 5.2 - - - +
634B ARG* 1.3 78.6 - - + +
636B GLU* 1.3 63.9 + - - +
637B ASN 3.0 1.2 + - - -
638B GLY* 3.2 5.7 + - - -
639B GLU 3.7 10.3 - - - +
640B ARG* 3.0 36.6 + - - +
661B TYR* 4.5 4.1 - - + -
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Residues in contact with GLU 636 (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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184A ARG* 5.3 10.6 + - + +
186A ASN* 5.3 3.1 - - - +
187A ALA* 4.4 17.8 - - - +
190A LYS* 3.0 49.7 + - - +
591B PRO* 5.2 1.0 - - - +
595B ASN* 4.4 12.3 + - - +
632B ILE 3.2 16.8 + - - +
633B GLY* 3.1 16.4 + - - +
635B ILE* 1.3 78.7 - - - +
637B ASN* 1.3 63.1 + - - +
638B GLY 3.4 2.4 + - - -
661B TYR* 3.2 24.0 + - - -
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Residues in contact with ASN 637 (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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633B GLY* 3.0 14.9 + - - +
634B ARG* 2.9 13.8 + - - +
636B GLU* 1.3 90.3 + - - +
638B GLY* 1.3 59.0 + - - +
639B GLU* 3.3 16.7 + - - +
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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