Contacts of the helix formed by residues 395 - 406 (chain i) in PDB entry 5GAG
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 395 (chain i).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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487A C 3.6 13.5 - - - +
488A G 3.0 41.0 + - - +
489A G 4.7 5.7 + - - -
392i GLU 4.1 15.5 + - - +
393i ILE* 3.5 14.1 + - - +
394i ILE* 1.3 80.3 - - - +
396i GLY* 1.3 67.4 + - - +
397i SER 3.3 2.7 - - - +
398i ARG* 3.1 11.1 + - + +
399i LYS* 2.9 31.8 + - - +
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Residues in contact with GLY 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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486A C 3.8 33.3 + - - +
487A C 3.1 16.7 + - - -
395i LYS* 1.3 76.2 - - - +
397i SER* 1.3 54.8 + - - +
399i LYS* 3.4 2.9 + - - +
400i ARG* 2.9 36.3 + - - +
410i VAL* 5.1 0.5 - - - +
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Residues in contact with SER 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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391 A 3.5 17.8 - - - +
401 C 2.7 37.3 + - - +
395i LYS* 3.3 2.2 - - - +
396i GLY* 1.3 71.6 - - - +
398i ARG* 1.3 62.3 + - - +
400i ARG* 3.3 24.5 + - - +
401i ARG* 3.0 27.9 + - - +
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Residues in contact with ARG 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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391 A 3.4 55.4 + - + +
387i GLU* 3.3 32.6 + - - +
393i ILE* 3.0 57.6 + - - +
394i ILE* 3.7 11.7 - - + +
395i LYS* 3.1 23.1 + - + +
397i SER* 1.3 78.4 - - - +
399i LYS* 1.3 56.5 + - - +
401i ARG* 3.4 2.8 + - - +
402i ILE* 2.9 35.4 + - - +
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Residues in contact with LYS 399 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486A C 3.9 14.6 + - - +
487A C 5.5 4.0 + - - -
394i ILE* 3.7 29.4 + - + -
395i LYS* 2.9 20.3 + - - +
396i GLY 3.9 3.1 - - - +
398i ARG* 1.3 74.1 - - - +
400i ARG* 1.3 65.1 + - - +
402i ILE* 4.1 6.0 - - - +
403i ALA* 2.9 26.3 + - - +
410i VAL* 3.6 20.0 - - + +
413i VAL* 4.1 8.9 - - + +
414i ASN* 3.2 28.0 + - - +
417i LEU* 3.5 30.6 - - + +
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Residues in contact with ARG 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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401 C 5.0 3.4 + - - -
59T GLU* 5.3 8.9 + - - +
60T HIS* 4.1 32.7 + - - +
396i GLY 2.9 17.9 + - - +
397i SER* 3.3 31.3 + - - +
399i LYS* 1.3 77.3 - - - +
401i ARG* 1.3 55.9 - - - +
403i ALA* 3.4 6.2 + - - +
404i ALA* 3.0 28.1 + - - +
410i VAL* 4.2 14.0 - - + +
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Residues in contact with ARG 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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391 A 2.7 39.1 + - + -
401 C 3.2 47.8 - - - +
621 C 3.4 35.3 + - - +
382i SER 3.4 19.4 + - - -
383i MET* 3.8 8.1 - - - +
384i THR* 3.9 3.0 - - - +
387i GLU* 3.1 31.3 + - - -
397i SER 3.0 17.4 + - - +
398i ARG 3.8 3.1 - - - +
399i LYS 3.2 0.2 - - - -
400i ARG* 1.3 75.8 - - - +
402i ILE* 1.3 74.4 + - - +
403i ALA 3.2 0.4 - - - -
404i ALA* 3.8 7.2 - - + +
405i GLY* 2.9 26.2 + - - -
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Residues in contact with ILE 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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379i ILE* 3.8 25.8 - - + +
382i SER* 4.3 11.5 + - - -
383i MET* 3.6 35.0 - - + -
387i GLU* 4.2 5.4 - - - +
394i ILE* 4.1 19.5 - - + -
398i ARG 2.9 25.7 + - - +
399i LYS 4.1 0.4 - - - +
401i ARG* 1.3 91.5 - - - +
403i ALA* 1.3 62.4 + - - +
406i CYS* 3.2 24.9 + - - +
413i VAL* 3.7 30.7 - - + -
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Residues in contact with ALA 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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399i LYS 2.9 19.5 + - - +
400i ARG 3.5 4.9 - - - +
402i ILE* 1.3 78.5 - - - +
404i ALA* 1.3 56.9 + - - +
406i CYS* 4.5 0.4 - - - -
407i GLY* 3.3 4.5 + - - -
408i MET 2.8 48.8 + - - +
409i GLN 3.9 2.0 - - - +
410i VAL* 3.7 28.9 - - + +
413i VAL* 4.1 6.7 - - + +
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Residues in contact with ALA 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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601 A 4.7 8.7 - - - +
611 G 4.3 6.3 + - - +
621 C 6.0 1.1 - - - -
400i ARG 3.0 16.0 + - - +
401i ARG* 3.3 10.7 + - + +
402i ILE 3.3 0.2 - - - -
403i ALA* 1.3 78.5 - - - +
405i GLY* 1.3 61.7 + - - +
407i GLY* 3.7 8.5 + - - -
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Residues in contact with GLY 405 (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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481 G 3.3 14.0 + - - +
491 G 2.8 23.4 + - - -
601 A 4.6 0.2 - - - -
611 G 3.7 8.8 + - - -
621 C 3.0 33.0 + - - -
382i SER* 3.7 6.1 - - - -
401i ARG 2.9 11.8 + - - -
402i ILE 3.9 0.2 + - - -
403i ALA 3.6 0.2 - - - -
404i ALA* 1.3 78.0 - - - +
406i CYS* 1.3 51.4 + - - +
407i GLY 3.3 1.1 - - - -
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Residues in contact with CYS 406 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481 G 3.6 13.0 - - - +
491 G 3.6 13.0 + - - +
501 U 3.3 17.8 - - - +
378i ALA* 4.1 12.6 - - + +
379i ILE* 3.6 23.1 - - - -
382i SER* 3.3 18.6 + - - +
402i ILE 3.2 20.9 + - - +
403i ALA* 4.5 0.7 - - - -
405i GLY* 1.3 75.3 - - - +
407i GLY* 1.3 64.0 + - - +
408i MET* 3.4 32.6 - - - +
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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