Contacts of the helix formed by residues 395 - 404 (chain i) in PDB entry 5JPQ
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 395 (chain i).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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394i ILE* 1.3 73.5 - - - +
396i LEU* 1.3 55.2 + - - +
397i PRO* 4.4 6.1 - - + -
398i LEU* 3.8 14.3 - - + +
399i VAL* 2.8 36.6 + - - +
753i ASP 4.8 4.3 - - - +
754i LEU 3.1 13.9 - - - +
755i THR* 3.1 26.7 - - - +
756i GLY* 4.2 7.4 - - - -
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Residues in contact with LEU 396 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394i ILE 3.5 3.2 + - - -
395i PRO* 1.3 71.0 - - - +
397i PRO* 1.3 64.7 - - - +
399i VAL* 4.5 4.5 - - - -
400i LYS* 3.0 27.2 + - - +
755i THR* 4.6 3.0 + - - +
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Residues in contact with PRO 397 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395i PRO* 3.2 3.9 - - + -
396i LEU* 1.3 82.7 - - - +
398i LEU* 1.3 61.8 + - - +
400i LYS* 4.0 3.6 - - + +
401i LYS* 3.4 19.2 + - - +
755i THR 5.6 0.2 - - - -
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Residues in contact with LEU 398 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374i PRO* 5.4 13.2 - - + +
375i GLN* 6.3 1.6 - - - -
394i ILE* 5.9 2.5 - - + -
395i PRO* 3.4 17.8 + - + +
396i LEU 3.3 0.2 - - - -
397i PRO* 1.3 76.0 - - - +
399i VAL* 1.3 67.4 + - - +
401i LYS* 3.5 6.1 + - - +
402i LEU* 3.4 19.9 + - - +
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Residues in contact with VAL 399 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391i ALA* 5.2 9.4 - - + +
394i ILE* 4.5 16.6 - - + +
395i PRO 2.8 20.3 + - - +
396i LEU* 3.9 4.7 - - - +
398i LEU* 1.3 77.4 - - - +
400i LYS* 1.4 61.6 - - - +
402i LEU* 3.2 8.1 + - - +
403i MET* 3.1 21.5 + - - +
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Residues in contact with LYS 400 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396i LEU 3.0 17.8 + - - +
397i PRO* 4.0 3.6 - - + +
399i VAL* 1.4 72.7 - - - +
401i LYS* 1.3 69.5 + - - +
403i MET* 3.2 16.1 + - - +
404i GLY* 3.4 7.6 + - - -
431i GLN* 6.4 2.2 - - + -
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Residues in contact with LYS 401 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397i PRO 3.4 10.8 + - - +
398i LEU* 3.9 7.9 - - - +
399i VAL 3.3 0.8 - - - -
400i LYS* 1.3 81.2 - - - +
402i LEU* 1.3 63.2 + - - +
404i GLY* 3.1 13.0 + - - -
405i PRO* 3.9 4.7 - - - +
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Residues in contact with LEU 402 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374i PRO* 6.6 0.4 - - + -
377i ALA* 6.4 1.8 - - + -
398i LEU 3.4 10.3 + - - +
399i VAL* 3.2 10.0 + - - +
400i LYS 3.2 0.4 - - - -
401i LYS* 1.3 76.7 - - - +
403i MET* 1.3 66.1 + - - +
404i GLY 3.1 0.9 + - - -
405i PRO* 3.3 16.0 - - - +
406i TYR* 4.2 5.7 + - - +
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Residues in contact with MET 403 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280i THR* 5.7 9.6 - - - -
399i VAL 3.1 12.5 + - - +
400i LYS* 3.2 11.2 + - - +
402i LEU* 1.3 76.5 - - - +
404i GLY* 1.3 61.2 + - - +
406i TYR* 3.5 18.9 + - - +
408i VAL* 5.7 11.8 - - + +
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Residues in contact with GLY 404 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400i LYS 3.4 4.8 + - - -
401i LYS 3.1 9.6 + - - -
402i LEU 3.1 1.6 - - - -
403i MET* 1.3 79.6 - - - +
405i PRO* 1.3 62.0 - - - +
406i TYR 3.2 4.5 + - - +
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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