Contacts of the helix formed by residues 2347 - 2359 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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354E LYS* 3.5 18.8 - - - +
477E SER* 3.7 30.2 + - - +
478E GLN* 3.8 13.7 - - - +
481E GLU* 3.3 36.1 + - - +
2346F THR* 1.3 85.0 - - - +
2348F MET* 1.3 64.5 + - - +
2350F LEU* 3.2 23.4 + - - +
2351F GLU 3.2 15.4 + - - -
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Residues in contact with MET2348 (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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354E LYS* 4.4 2.2 - - - +
481E GLU* 3.2 7.4 + - - +
2347F ASN* 1.3 72.7 - - - +
2349F GLY* 1.3 64.7 + - - +
2351F GLU* 3.1 33.7 + - + +
2352F ALA* 3.1 26.1 + - + +
2355F ARG* 5.9 2.2 - - - +
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Residues in contact with GLY2349 (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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481E GLU* 3.1 22.6 + - - +
484E GLN* 3.3 42.4 + - - +
2347F ASN* 3.4 0.4 - - - -
2348F MET* 1.3 75.5 - - - +
2350F LEU* 1.3 61.7 + - - +
2352F ALA* 3.2 11.3 + - - +
2353F ILE* 3.4 8.5 + - - +
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Residues in contact with LEU2350 (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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328E ILE* 4.5 11.9 - - + -
353E LEU 4.8 1.8 - - - +
354E LYS* 3.7 24.2 - - + +
358E MET* 4.3 27.1 - - + +
477E SER* 3.3 31.6 + - - +
480E VAL* 4.9 7.5 - - + +
481E GLU* 5.1 0.6 - - - +
484E GLN* 4.2 0.2 - - - +
2346F THR 3.7 9.6 - - - +
2347F ASN* 3.2 23.2 + - - +
2349F GLY* 1.3 73.6 - - - +
2351F GLU* 1.3 61.9 + - - +
2353F ILE* 3.3 21.2 + - + +
2354F ILE* 3.1 42.0 + - + +
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Residues in contact with GLU2351 (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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350E ILE* 4.0 11.2 - - + +
354E LYS* 3.5 37.6 + - + +
2347F ASN 3.2 9.8 + - - +
2348F MET* 3.1 39.2 + - + +
2350F LEU* 1.3 76.7 - - - +
2352F ALA* 1.3 59.6 + - - +
2354F ILE* 3.2 4.4 + - - +
2355F ARG* 2.9 70.3 + - - +
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Residues in contact with ALA2352 (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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484E GLN* 4.3 9.2 - - - +
2348F MET* 3.1 14.1 + - + +
2349F GLY* 3.2 10.3 + - - +
2351F GLU* 1.3 75.7 - - - +
2353F ILE* 1.3 65.0 + - - +
2355F ARG* 3.5 7.4 + - - +
2356F LYS* 3.2 24.4 + - - +
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Residues in contact with ILE2353 (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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325E THR* 3.7 43.5 - - + +
328E ILE* 4.4 17.0 - - + -
329E GLN* 4.3 17.8 + - + +
480E VAL* 3.8 22.7 - - + -
484E GLN* 4.2 11.0 - - - +
2349F GLY 3.4 14.6 + - - +
2350F LEU* 3.3 17.6 + - + +
2352F ALA* 1.3 78.2 - - - +
2354F ILE* 1.3 57.6 + - + +
2356F LYS* 3.5 5.2 + - - +
2357F ALA* 3.0 26.6 + - + +
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Residues in contact with ILE2354 (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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328E ILE* 4.2 18.2 - - + -
332E VAL* 4.5 5.3 - - + +
350E ILE* 4.7 11.7 - - + -
353E LEU* 3.7 60.8 - - + +
354E LYS* 3.8 13.0 - - + +
357E ALA* 4.7 3.6 - - + -
2350F LEU* 3.1 33.4 + - + +
2351F GLU* 3.2 5.1 + - - +
2353F ILE* 1.3 75.4 - - - +
2355F ARG* 1.3 65.6 + - - +
2357F ALA* 3.2 7.3 + - - +
2358F LEU* 2.9 30.4 + - + +
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Residues in contact with ARG2355 (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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346E GLN* 4.2 17.7 + - - +
350E ILE* 3.7 33.2 - - + +
2348F MET* 5.9 1.9 - - - +
2351F GLU* 2.9 56.3 + - + +
2352F ALA* 3.8 7.2 - - - +
2354F ILE* 1.3 75.1 - - - +
2356F LYS* 1.3 63.9 + - - +
2358F LEU* 3.3 19.1 + - - +
2359F MET* 3.6 8.7 + - - +
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Residues in contact with LYS2356 (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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2352F ALA 3.2 15.1 + - - +
2353F ILE* 3.8 4.9 - - - +
2355F ARG* 1.3 80.0 - - - +
2357F ALA* 1.3 65.0 + - - +
2359F MET* 3.6 20.6 + - + +
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Residues in contact with ALA2357 (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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329E GLN* 4.3 22.9 - - + +
332E VAL* 4.1 26.2 - - + -
333E GLU* 4.2 6.1 - - - +
336E LYS* 3.2 16.3 + - - -
2353F ILE* 3.0 18.6 + - + +
2354F ILE 3.2 4.2 + - - +
2356F LYS* 1.3 77.6 - - - +
2358F LEU* 1.3 62.4 + - - +
2359F MET 3.4 3.5 + - - +
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Residues in contact with LEU2358 (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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332E VAL* 3.9 10.1 - - + -
336E LYS* 3.0 31.3 + - + +
341E PHE* 4.3 8.7 - - + -
342E MET* 6.0 1.1 - - - -
346E GLN* 5.0 6.1 - - + +
349E GLN* 3.5 32.3 - - + +
350E ILE* 3.4 35.0 - - + -
353E LEU* 3.8 26.0 - - + -
2354F ILE* 2.9 16.1 + - + +
2355F ARG* 3.3 10.9 + - - +
2357F ALA* 1.3 76.3 - - - +
2359F MET* 1.3 57.2 + - - +
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Residues in contact with MET2359 (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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286A GLN* 4.1 22.2 - - + +
287A LEU* 5.0 10.1 - - + -
330A TYR* 5.9 2.2 - - - -
336E LYS* 3.3 14.4 + - - -
2355F ARG 3.6 6.7 + - - +
2356F LYS* 3.6 16.1 + - + +
2357F ALA 3.4 5.5 - - - +
2358F LEU* 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