Contacts of the helix formed by residues 331 - 336 (chain E) in PDB entry 4KRM
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 ASN 331 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316E ILE* 4.1 3.6 - - - +
321E PHE* 3.7 18.1 - - + -
324E SER* 3.9 9.5 + - - -
326E SER 3.1 12.5 + - - -
327E ILE* 3.5 7.3 - - - +
328E ASN* 2.2 59.1 + - - +
330E THR* 1.3 70.6 - - - +
332E ILE* 1.3 71.1 + - - +
333E LYS 3.2 3.1 - - - -
334E HIS* 3.1 22.9 + - - +
335E PHE* 3.5 18.1 - - - -
1P NAG 2.9 22.0 + - - +
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Residues in contact with ILE 332 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327E ILE* 3.7 23.6 - - + -
328E ASN 3.1 16.3 + - - +
329E ALA 3.8 7.9 - - - +
331E ASN* 1.3 84.0 + - - +
333E LYS* 1.3 64.3 + - + +
334E HIS 3.2 0.2 - - - -
335E PHE* 3.3 23.1 + - + +
363E LEU* 4.0 12.8 - - + -
367E GLU* 3.1 65.1 - - + +
368E LEU* 4.0 13.2 - - + +
370E ILE* 3.6 15.5 - - + +
371E LEU* 5.2 5.4 - - + -
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Residues in contact with LYS 333 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330E THR 4.2 7.1 + - - +
331E ASN 3.2 0.6 - - - -
332E ILE* 1.3 83.9 - - + +
334E HIS* 1.3 67.2 + - + +
335E PHE 3.1 0.4 - - - -
336E LYS* 3.1 29.5 + - - +
367E GLU* 5.7 5.6 - - - +
370E ILE* 5.3 4.9 - - - -
605E NAG 5.8 0.2 - - - +
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Residues in contact with HIS 334 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311E LYS* 4.7 6.0 + - - -
313E CYS* 4.4 4.2 - - - +
320E GLU* 2.6 35.3 + - + +
321E PHE* 3.7 20.1 - + + -
330E THR* 4.7 9.2 + - + -
331E ASN* 3.1 15.3 + - - +
333E LYS* 1.3 87.1 - - + +
335E PHE* 1.3 60.6 + - - +
336E LYS 3.3 3.7 + - - +
338E CYS* 3.7 10.2 - - - -
2P NAG 6.0 6.1 - - + -
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Residues in contact with PHE 335 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313E CYS* 4.7 0.9 - - + -
314E ASN 3.3 20.4 - - - -
315E GLY* 4.7 0.2 - - - -
316E ILE* 4.0 18.4 - - + -
321E PHE* 3.4 26.9 - + - -
327E ILE* 4.2 9.9 - - + -
331E ASN* 3.5 29.4 - - - -
332E ILE* 3.3 16.4 + - + +
333E LYS 3.1 1.8 - - - -
334E HIS* 1.3 78.8 - - - +
336E LYS* 1.3 66.6 + - - +
337E ASN 3.3 0.7 + - - -
338E CYS* 3.1 27.8 + - + +
341E ILE* 3.8 28.0 - - + -
345E LEU* 3.9 15.7 - - + -
370E ILE* 3.6 18.8 - - + +
371E LEU* 4.2 14.0 - - + +
374E VAL* 5.5 1.4 - - + +
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Residues in contact with LYS 336 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311E LYS* 3.4 18.4 + - - -
333E LYS* 3.1 17.7 + - - +
334E HIS 3.3 1.6 - - - -
335E PHE* 1.3 77.9 - - - +
337E ASN* 1.3 84.2 + - - +
338E CYS 2.9 6.2 + - - -
370E ILE* 3.7 33.4 - - + +
605E NAG 4.0 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