Contacts of the helix formed by residues 619 - 622 (chain N) in PDB entry 2JA7
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 ILE 619 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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578N THR* 6.4 0.4 - - - -
617N ARG* 3.1 46.7 + - + +
618N ASP* 1.3 69.7 - - - +
620N ARG* 1.3 62.6 + - + +
621N GLU 2.7 1.9 + - - -
622N LYS* 2.6 35.6 + - - +
59U VAL* 4.0 11.3 - - + +
61U ASP* 3.6 26.9 - - + +
62U ILE* 4.1 10.1 - - + +
64U SER* 3.2 29.8 - - - +
65U ASP* 4.1 26.3 + - + +
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Residues in contact with ARG 620 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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780M VAL* 5.8 1.6 - - - +
781M ASP* 5.1 6.7 + - - -
789M LYS* 3.8 32.7 - - - +
790M ASP* 4.8 3.6 + - - -
618N ASP* 3.4 5.5 - - - +
619N ILE* 1.3 88.1 - - + +
621N GLU* 1.3 58.8 + - + +
622N LYS* 4.7 2.8 - - - +
56U ALA 5.1 0.5 - - - +
57U GLY* 3.8 30.4 + - - +
59U VAL* 5.1 3.4 - - - -
62U ILE* 4.7 9.5 - - + +
65U ASP* 4.7 5.2 - - - +
68U LEU* 3.8 35.1 - - + +
86U PHE* 3.1 40.1 - - - +
89U GLN* 2.5 41.1 + - - +
91U ARG* 6.0 0.2 - - - +
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Residues in contact with GLU 621 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384N ARG* 5.1 8.7 - - - +
387N LEU* 4.1 19.5 - - - +
393N LYS* 4.0 30.1 + - + +
579N ARG* 3.7 18.2 + - - -
618N ASP* 2.8 30.8 + - + +
619N ILE 2.7 1.0 + - - -
620N ARG* 1.3 75.3 - - + +
622N LYS* 1.3 73.8 + - - +
623N GLU* 4.0 22.4 - - + +
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Residues in contact with LYS 622 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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575N PRO 4.7 3.1 + - - +
576N ASP* 3.0 54.1 + - - +
577N ALA 4.0 10.1 - - - +
578N THR* 3.7 25.1 - - - +
579N ARG* 2.8 24.7 + - - +
618N ASP 2.8 3.6 + - - -
619N ILE* 2.6 26.9 + - - +
620N ARG 4.7 1.1 - - - +
621N GLU* 1.3 76.2 - - - +
623N GLU* 1.3 56.4 + - - +
57U GLY* 4.9 14.8 - - - -
58U VAL 5.4 0.2 - - - +
59U VAL* 3.2 32.8 - - + +
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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