Contacts of the helix formed by residues 275 - 289 (chain E) in PDB entry 3K75
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 SER 275 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183E ARG* 3.8 18.6 - - - +
274E GLY* 1.3 73.7 - - - -
276E ASP* 1.3 71.4 + - - +
277E ILE* 2.7 3.9 + - - -
278E PHE* 2.7 31.3 + - - +
279E ASN* 3.1 9.7 + - - +
333E ARG 2.7 27.2 + - - -
334E SER* 3.4 13.0 + - - -
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Residues in contact with ASP 276 (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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275E SER* 1.3 74.3 - - - +
277E ILE* 1.3 63.9 + - + +
279E ASN* 3.7 10.0 + - - +
280E LYS* 3.4 20.8 + - - +
283E ARG* 5.2 1.7 + - - -
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Residues in contact with ILE 277 (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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275E SER* 2.7 7.3 + - - +
276E ASP* 1.3 75.9 - - + +
278E PHE* 1.3 64.8 + - - +
280E LYS* 3.1 14.0 + - + +
281E ASN* 2.9 37.7 + - - +
334E SER 4.8 10.3 - - - +
335E GLU* 4.8 7.9 - - + -
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Residues in contact with PHE 278 (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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270E LEU* 4.1 11.4 - - + -
274E GLY* 4.2 4.0 - - - -
275E SER* 2.7 29.3 + - - +
277E ILE* 1.3 73.9 - - - +
279E ASN* 1.3 68.4 + - - +
281E ASN* 2.9 6.3 + - + +
282E MET* 2.8 49.9 + - - +
320E PHE* 3.8 23.3 - + - -
325E TRP* 3.6 25.6 - + - -
328E ARG* 4.3 11.9 - - + -
332E ASP 5.1 0.4 - - - -
333E ARG* 3.8 42.0 - - + +
335E GLU 3.5 28.8 - - - -
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Residues in contact with ASN 279 (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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270E LEU* 3.5 12.7 - - - +
271E TYR* 2.9 41.3 + - - +
274E GLY* 3.5 24.5 - - - -
275E SER 3.1 13.3 + - - +
276E ASP* 3.9 10.6 + - - +
278E PHE* 1.3 85.3 - - - +
280E LYS* 1.3 63.1 + - - +
282E MET* 3.3 5.5 + - - +
283E ARG* 3.0 50.8 + - + +
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Residues in contact with LYS 280 (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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276E ASP 3.4 11.6 + - - +
277E ILE* 3.1 17.1 + - + +
279E ASN* 1.3 80.3 - - - +
281E ASN* 1.3 59.9 + - - +
283E ARG* 4.1 14.3 - - - +
284E ALA* 3.0 29.5 + - - +
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Residues in contact with ASN 281 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277E ILE* 2.9 27.4 + - - +
278E PHE* 2.9 9.0 + - - +
280E LYS* 1.3 76.6 - - - +
282E MET* 1.3 59.9 + - - +
284E ALA* 3.6 6.7 - - - +
285E HIS* 3.1 26.9 + - - +
325E TRP* 4.5 15.2 - - + -
335E GLU* 3.8 26.4 + - - +
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Residues in contact with MET 282 (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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270E LEU* 3.4 33.4 - - + -
278E PHE* 2.8 37.2 + - + +
279E ASN* 3.7 7.6 - - - +
280E LYS 3.3 0.2 - - - -
281E ASN* 1.3 74.1 - - - +
283E ARG* 1.3 56.0 + - + +
285E HIS* 3.1 4.9 + - - +
286E ALA* 2.6 36.0 + - - +
293E ILE* 3.7 23.6 - - + -
319E ILE* 3.9 10.1 - - + +
320E PHE* 3.8 30.7 - - + -
323E ILE* 4.2 11.7 - - + +
325E TRP* 4.0 21.9 - - + -
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Residues in contact with ARG 283 (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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271E TYR* 3.6 35.8 - - - -
276E ASP 5.2 1.6 + - - -
279E ASN* 3.0 37.2 + - - +
280E LYS* 4.1 14.7 - - - +
282E MET* 1.3 76.2 - - + +
284E ALA* 1.3 57.8 + - - +
286E ALA* 3.4 8.7 - - - +
287E LEU* 2.8 41.6 + - + +
293E ILE* 2.9 45.7 + - + +
294E ASN* 5.0 4.6 - - - +
295E GLU 5.4 0.4 - - - +
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Residues in contact with ALA 284 (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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280E LYS 3.0 20.1 + - - +
281E ASN* 3.6 8.5 - - - +
283E ARG* 1.3 77.7 - - - +
285E HIS* 1.3 64.1 + - - +
287E LEU* 3.0 11.0 + - - +
288E GLU* 2.9 22.2 + - - +
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Residues in contact with HIS 285 (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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281E ASN 3.1 10.8 + - - +
282E MET* 3.1 8.2 + - - +
284E ALA* 1.3 77.1 - - - +
286E ALA* 1.3 55.3 + - - +
288E GLU* 2.7 51.9 + - - +
289E LYS* 3.0 24.7 + - + +
323E ILE* 3.5 31.9 + - + -
324E GLN 4.2 2.1 + - - -
325E TRP* 3.2 50.2 + + + -
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Residues in contact with ALA 286 (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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282E MET 2.6 21.8 + - - +
283E ARG* 3.4 7.4 - - - +
285E HIS* 1.3 72.8 - - - +
287E LEU* 1.3 61.0 + - - +
289E LYS* 3.0 10.8 + - - +
290E GLY 3.1 0.3 + - - -
291E PHE* 2.9 33.4 + - + +
293E ILE* 3.7 30.3 - - + +
323E ILE* 3.9 21.3 - - + -
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Residues in contact with LEU 287 (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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283E ARG* 2.8 27.5 + - + +
284E ALA* 3.4 10.5 - - - +
286E ALA* 1.3 72.7 - - - +
288E GLU* 1.3 58.2 + - - +
289E LYS 3.0 0.2 - - - -
290E GLY* 3.1 17.0 + - - -
291E PHE 3.1 15.6 + - - +
292E THR* 4.8 9.9 - - - +
293E ILE 6.1 0.2 - - - +
301E LEU* 3.6 29.9 - - + +
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Residues in contact with GLU 288 (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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284E ALA 2.9 10.6 + - - +
285E HIS* 2.7 39.9 + - - +
287E LEU* 1.3 71.8 - - - +
289E LYS* 1.3 62.9 + - + +
290E GLY 3.5 0.2 - - - -
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Residues in contact with LYS 289 (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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41C LYS* 4.2 25.7 + - - +
135C PRO* 6.3 0.4 - - + -
285E HIS* 3.0 29.9 + - + +
286E ALA* 3.0 11.6 + - - +
288E GLU* 1.3 83.7 - - + +
290E GLY* 1.3 61.0 + - - +
291E PHE* 3.5 20.9 - - + -
323E ILE* 3.7 25.1 - - - +
324E GLN* 2.8 37.5 + - - +
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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