Contacts of the helix formed by residues 631 - 638 (chain F) in PDB entry 5JLH
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 631 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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367F ARG* 5.2 10.2 + - - -
402F ARG 4.9 2.1 - - - +
403F LEU 4.0 17.7 - - - +
404F LEU* 4.1 13.3 - - + +
405F GLY* 4.4 0.4 - - - +
629F SER* 3.5 1.3 - - - +
630F THR* 1.3 97.2 - - - +
632F ARG* 1.3 64.5 + - - +
633F LEU* 4.3 7.9 - - + +
634F THR* 3.9 13.6 - - + +
635F ALA* 3.4 22.0 + - - +
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Residues in contact with ARG 632 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360F GLU* 3.2 43.5 + - - +
361F GLU* 5.5 5.1 - - - +
364F SER* 4.6 9.7 + - - -
630F THR 4.5 2.7 - - - +
631F ASP* 1.3 73.1 - - - +
633F LEU* 1.3 69.2 + - - +
635F ALA* 4.0 2.4 - - - +
636F GLU* 2.9 29.5 + - + +
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Residues in contact with LEU 633 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361F GLU* 5.4 2.7 - - + +
364F SER* 3.4 53.6 - - - +
365F MET* 3.6 11.9 - - + +
368F MET* 4.4 16.2 - - + -
451F LEU* 5.8 0.4 - - + -
454F TRP* 3.7 42.8 - - + +
631F ASP* 3.3 4.9 - - + +
632F ARG* 1.3 83.6 - - - +
634F THR* 1.3 59.1 + - - +
636F GLU* 3.2 6.6 + - - +
637F ILE* 2.9 37.9 + - + +
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Residues in contact with THR 634 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368F MET* 5.1 10.6 - - - +
404F LEU* 3.8 33.0 - - + +
626F LEU* 4.6 3.6 - - - +
629F SER* 3.3 27.9 + - - +
631F ASP* 3.9 15.2 - - + +
633F LEU* 1.3 79.6 - - - +
635F ALA* 1.3 73.2 + - - +
637F ILE* 3.0 20.0 + - - +
638F TRP* 3.1 39.2 + - - -
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Residues in contact with ALA 635 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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626F LEU 3.6 14.8 - - - +
627F HIS* 4.3 14.1 + - - +
629F SER* 3.5 24.5 - - - +
631F ASP 3.4 17.2 + - - +
632F ARG* 3.6 2.2 + - - +
633F LEU 3.2 0.6 - - - -
634F THR* 1.3 82.6 - - - +
636F GLU* 1.3 63.0 + - - +
638F TRP* 3.3 16.9 + - - +
639F LYS* 4.0 4.3 + - - +
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Residues in contact with GLU 636 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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454F TRP* 2.8 44.8 + - - -
632F ARG* 2.9 20.7 + - + +
633F LEU* 3.4 8.4 - - - +
635F ALA* 1.3 77.8 - - - +
637F ILE* 1.3 73.5 + - - +
639F LYS* 3.3 31.3 - - + +
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Residues in contact with ILE 637 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368F MET* 3.3 37.2 - - + -
450F ARG* 3.2 46.1 + - + +
451F LEU* 4.2 10.1 - - + +
454F TRP* 4.0 19.1 - - + -
633F LEU* 2.9 32.2 + - + +
634F THR* 3.0 10.1 + - - +
636F GLU* 1.3 89.3 - - - +
638F TRP* 1.3 63.6 + - + +
639F LYS* 2.9 6.8 + - - +
640F ASP 5.0 0.2 + - - -
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Residues in contact with TRP 638 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368F MET* 5.4 1.8 - - - +
443F LEU* 4.3 10.8 - - + -
446F ALA* 4.0 23.8 - - + -
447F THR* 3.4 32.4 + - - +
450F ARG* 3.1 49.4 - - + +
618F LEU* 4.6 12.6 - - + -
623F ALA* 4.7 15.7 - - + +
626F LEU* 3.2 49.1 - - + +
627F HIS* 3.2 25.9 + - + +
634F THR* 3.1 39.5 + - - +
635F ALA 3.3 7.4 + - - +
636F GLU 3.3 1.0 - - - -
637F ILE* 1.3 79.4 - - + +
639F LYS* 1.3 55.5 + - - +
640F ASP* 3.1 15.5 + - + +
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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
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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