Contacts of the helix formed by residues 2347 - 2360 (chain H) in PDB entry 5X8X
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 ASN2347 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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455C CYS* 5.7 3.1 - - - -
354G LYS* 3.7 17.2 - - - +
474G SER 4.8 0.4 + - - -
477G SER* 3.5 35.0 - - - +
478G GLN* 3.6 15.2 - - - +
481G GLU* 3.6 28.3 + - - +
2346H THR* 1.3 82.9 + - - +
2348H MET* 1.3 62.7 + - - +
2349H GLY 3.6 2.9 + - - -
2350H LEU* 3.2 23.9 + - - +
2351H GLU* 3.2 15.8 + - - +
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Residues in contact with MET2348 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460C GLN* 4.0 21.9 + - + +
461C SER* 4.5 17.7 - - - +
354G LYS* 4.9 0.4 - - - +
481G GLU* 3.3 7.7 + - - +
2347H ASN* 1.3 72.8 - - - +
2349H GLY* 1.3 65.5 + - - +
2351H GLU* 3.1 29.1 + - + +
2352H ALA* 3.1 28.4 + - + +
2355H ARG* 6.0 2.2 - - - +
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Residues in contact with GLY2349 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480G VAL* 5.4 0.4 - - - -
481G GLU* 3.0 24.8 + - - -
484G GLN* 3.2 36.8 + - - +
2347H ASN 3.4 0.4 - - - -
2348H MET* 1.3 74.8 - - - +
2350H LEU* 1.3 61.5 + - - +
2352H ALA* 3.2 11.5 + - - +
2353H ILE* 3.4 11.0 + - - +
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Residues in contact with LEU2350 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328G ILE* 4.3 16.8 - - + -
353G LEU 4.5 2.2 - - - +
354G LYS* 3.4 27.6 - - + +
357G ALA* 5.2 0.2 - - + -
358G MET* 4.3 26.0 - - + +
477G SER* 3.6 26.4 + - - +
480G VAL* 5.0 6.3 - - + +
481G GLU* 5.1 0.4 - - - +
2346H THR 3.5 11.7 - - - +
2347H ASN* 3.2 23.0 + - - +
2348H MET 3.3 0.2 - - - -
2349H GLY* 1.3 74.0 - - - +
2351H GLU* 1.3 62.8 + - - +
2353H ILE* 3.3 16.2 + - + +
2354H ILE* 3.1 42.9 + - + +
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Residues in contact with GLU2351 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350G ILE* 4.3 9.1 - - + +
354G LYS* 3.8 35.4 + - + +
2347H ASN 3.2 9.4 + - - +
2348H MET* 3.1 31.9 + - + +
2350H LEU* 1.3 76.1 - - - +
2352H ALA* 1.3 61.3 + - - +
2354H ILE* 3.2 4.3 + - - +
2355H ARG* 2.9 70.7 + - - +
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Residues in contact with ALA2352 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484G GLN* 4.3 9.4 - - - +
2348H MET* 3.1 19.2 + - + +
2349H GLY* 3.2 10.0 + - - +
2351H GLU* 1.3 76.0 - - - +
2353H ILE* 1.3 64.9 + - - +
2355H ARG* 3.5 7.7 + - - +
2356H LYS* 3.2 23.7 + - - +
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Residues in contact with ILE2353 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325G THR* 3.6 37.7 - - + +
328G ILE* 4.1 24.5 - - + -
329G GLN* 4.4 14.2 + - + +
480G VAL* 3.5 31.9 - - + -
484G GLN* 3.7 19.1 - - - +
2349H GLY 3.4 9.4 + - - +
2350H LEU* 3.3 14.0 + - + +
2352H ALA* 1.3 77.8 - - - +
2354H ILE* 1.3 56.4 + - - +
2356H LYS* 3.5 5.5 + - - +
2357H ALA* 3.0 26.7 + - + +
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Residues in contact with ILE2354 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328G ILE* 4.4 17.3 - - + -
332G VAL* 4.5 5.3 - - + +
350G ILE* 4.5 12.3 - - + -
353G LEU* 3.6 41.1 - - + +
354G LYS* 3.5 42.0 - - + +
357G ALA* 4.9 2.0 - - + -
2350H LEU* 3.1 30.7 + - + +
2351H GLU* 3.7 4.5 - - - +
2352H ALA 3.2 0.4 - - - -
2353H ILE* 1.3 74.8 - - - +
2355H ARG* 1.3 67.3 + - - +
2357H ALA* 3.2 7.5 + - - +
2358H LEU* 2.9 29.5 + - + +
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Residues in contact with ARG2355 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346G GLN* 3.4 28.8 + - - +
350G ILE* 3.5 28.0 - - + +
2348H MET* 6.0 2.4 - - - +
2351H GLU* 2.9 51.8 + - + +
2352H ALA* 3.8 7.0 - - - +
2354H ILE* 1.3 78.9 - - - +
2356H LYS* 1.3 62.6 + - - +
2358H LEU* 3.3 9.0 + - - +
2359H MET* 3.3 27.5 + - - +
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Residues in contact with LYS2356 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329G GLN* 6.4 0.2 - - - +
2352H ALA 3.2 14.6 + - - +
2353H ILE* 3.8 5.8 - - - +
2355H ARG* 1.3 79.0 - - - +
2357H ALA* 1.3 57.9 + - - +
2359H MET* 3.3 31.6 + - + +
2360H GLY* 2.9 40.5 + - - +
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Residues in contact with ALA2357 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329G GLN* 4.0 25.4 - - + +
332G VAL* 4.0 26.5 - - + -
333G GLU* 4.0 6.8 - - - +
336G LYS* 3.2 15.2 + - - -
2353H ILE* 3.0 19.2 + - + +
2354H ILE 3.2 4.7 + - - +
2356H LYS* 1.3 76.2 - - - +
2358H LEU* 1.3 63.5 + - - +
2360H GLY* 3.2 11.2 + - - +
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Residues in contact with LEU2358 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332G VAL* 3.9 19.7 - - + +
336G LYS* 3.0 36.7 + - + +
341G PHE* 4.6 5.8 - - + -
342G MET* 5.2 5.3 - - + +
346G GLN* 5.4 3.6 - - + +
349G GLN* 3.8 27.6 - - + +
350G ILE* 3.7 31.2 - - + -
353G LEU* 4.2 17.9 - - + -
2354H ILE* 2.9 16.1 + - + +
2355H ARG* 3.3 10.5 + - - +
2357H ALA* 1.3 76.8 - - - +
2359H MET* 1.3 57.7 + - + +
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Residues in contact with MET2359 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336G LYS* 4.6 1.1 + - - -
2355H ARG* 3.3 14.7 + - - +
2356H LYS* 3.3 31.2 + - + +
2358H LEU* 1.3 79.9 - - + +
2360H GLY* 1.3 63.4 + - - +
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Residues in contact with GLY2360 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333G GLU* 5.7 1.1 - - - -
336G LYS* 4.6 5.2 - - - -
2356H LYS* 2.9 31.6 + - - +
2357H ALA* 3.2 14.7 + - - -
2359H MET* 1.3 81.5 - - - +
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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