Contacts of the helix formed by residues 326 - 343 (chain E) in PDB entry 4K81
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 GLU 326 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304E TYR* 3.5 15.1 - - + +
324E ALA* 3.3 7.2 - - - +
325E GLU* 1.3 87.8 - - + +
327E GLU* 1.3 67.8 + - - +
328E GLN* 3.2 23.5 + - - +
329E SER* 3.3 25.8 + - - +
330E ARG 3.4 8.0 + - - -
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Residues in contact with GLU 327 (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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304E TYR* 3.7 35.5 - - + -
326E GLU* 1.3 73.5 - - - +
328E GLN* 1.3 75.7 + - - +
330E ARG* 3.2 20.6 + - - +
331E THR* 3.0 27.8 + - - +
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Residues in contact with GLN 328 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326E GLU* 3.2 23.8 - - - +
327E GLU* 1.3 92.0 + - - +
329E SER* 1.3 62.7 + - - +
331E THR* 3.3 11.2 + - - -
332E CYS* 3.2 27.2 + - - -
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Residues in contact with SER 329 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208E MET* 4.1 5.7 - - - +
240E PHE 4.8 2.8 + - - -
241E LEU* 4.5 1.9 - - - +
324E ALA* 3.9 8.9 - - - +
325E GLU* 4.7 4.9 + - - +
326E GLU* 3.3 28.5 + - - +
327E GLU 3.3 0.6 - - - -
328E GLN* 1.3 81.2 - - - +
330E ARG* 1.3 60.1 + - - +
332E CYS* 3.4 8.9 + - - +
333E TRP* 3.0 45.1 + - - -
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Residues in contact with ARG 330 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290E VAL* 3.7 26.9 - - + +
291E SER* 4.0 9.5 + - - +
303E ASN 3.4 9.1 + - - -
304E TYR* 3.2 30.1 - - + +
305E GLY 2.8 51.3 + - - +
306E PHE* 3.7 14.1 - - + -
324E ALA* 3.6 20.3 - - + +
326E GLU 3.4 4.2 + - - +
327E GLU* 3.2 21.7 + - - +
329E SER* 1.3 75.6 - - - +
331E THR* 1.3 56.4 + - - +
333E TRP* 3.0 7.5 + - - +
334E VAL* 2.7 46.7 + - + +
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Residues in contact with THR 331 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192E ALA* 5.7 9.4 - - + +
195E GLU* 6.4 0.4 - - + -
203E PHE* 4.1 20.6 - - + -
327E GLU* 3.0 19.6 + - - +
328E GLN* 3.3 11.7 + - - -
330E ARG* 1.3 80.2 + - - +
332E CYS* 1.3 55.1 + - - +
334E VAL* 3.5 5.1 + - - +
335E THR* 2.6 40.1 + - - +
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Residues in contact with CYS 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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203E PHE* 3.8 33.2 - - - -
204E PHE* 3.2 30.9 - - + -
205E PRO* 3.9 18.8 - - - -
208E MET* 3.6 17.7 - - + -
328E GLN* 3.2 17.1 + - - -
329E SER* 3.7 3.8 - - - +
331E THR* 1.3 79.3 - - - +
333E TRP* 1.3 58.1 + - - +
336E ALA* 2.9 28.1 + - - +
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Residues in contact with TRP 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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208E MET* 3.4 16.5 - - + +
237E ILE* 3.6 35.7 - - + -
238E HIS* 3.9 4.3 - - - -
239E GLY* 3.7 27.8 - - - -
240E PHE 4.3 2.6 + - - -
241E LEU* 3.3 41.1 - - + +
256E PHE* 3.9 18.8 - - + -
258E LEU* 4.0 11.4 - - + -
263E LEU* 4.0 19.3 - - + -
306E PHE* 3.7 20.0 - + + -
329E SER* 3.0 32.7 + - - -
330E ARG 3.0 8.3 + - - +
332E CYS* 1.3 78.1 - - - +
334E VAL* 1.3 61.9 + - - +
336E ALA* 3.8 1.5 - - - +
337E ILE* 3.0 47.7 + - + +
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Residues in contact with VAL 334 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288E ILE* 4.7 15.7 - - + +
290E VAL* 3.9 31.2 - - + -
306E PHE* 4.1 17.3 - - + -
330E ARG* 2.7 32.9 + - + +
331E THR* 3.9 5.4 - - - +
333E TRP* 1.3 72.4 - - - +
335E THR* 1.3 57.1 + - - +
337E ILE* 3.9 5.1 - - - +
338E ARG* 2.9 53.8 + - + +
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Residues in contact with THR 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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193E LYS 5.8 1.3 - - - +
196E PHE* 3.8 20.2 - - + +
203E PHE* 3.5 33.1 - - + -
204E PHE* 4.6 0.4 - - + -
331E THR* 2.6 27.3 + - - +
332E CYS 3.8 0.9 - - - -
334E VAL* 1.3 73.6 - - - +
336E ALA* 1.3 56.7 + - - +
338E ARG* 3.0 22.3 + - - +
339E LEU* 2.8 50.7 + - + +
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Residues in contact with ALA 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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204E PHE* 3.9 20.3 - - + -
234E TYR* 2.5 28.2 + - - +
237E ILE* 4.1 17.0 - - + -
258E LEU* 3.7 19.7 - - + -
332E CYS 2.9 22.0 + - - +
333E TRP* 3.8 3.8 - - + +
335E THR* 1.3 73.2 - - - +
337E ILE* 1.3 56.9 + - - +
339E LEU* 3.3 3.0 + - - -
340E LEU* 2.9 14.7 + - - +
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Residues in contact with ILE 337 (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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258E LEU* 3.8 25.1 - - + -
263E LEU* 5.0 4.5 - - + -
283E PHE* 3.5 35.0 - - + -
288E ILE* 3.6 22.0 - - + -
306E PHE* 4.4 10.3 - - + -
308E PHE* 4.0 25.6 - - + -
333E TRP* 3.0 34.3 + - + +
334E VAL* 4.1 4.7 - - - +
336E ALA* 1.3 72.2 - - - +
338E ARG* 1.3 60.3 + - - +
340E LEU* 3.2 5.9 + - - +
341E LYS* 2.8 28.4 + - - +
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Residues in contact with ARG 338 (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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163E THR* 4.7 10.0 - - - +
165E GLU* 2.7 41.1 + - - +
193E LYS* 3.4 39.5 + - - +
194E TYR* 4.7 5.3 - - - -
288E ILE* 4.3 19.1 - - + +
334E VAL* 2.9 39.3 + - + +
335E THR* 3.0 21.0 + - - +
337E ILE* 1.3 73.4 - - - +
339E LEU* 1.3 54.0 + - - +
342E TYR* 2.8 48.1 + - + +
346E LEU* 3.9 21.3 - - + +
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Residues in contact with LEU 339 (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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196E PHE* 3.7 25.1 - - + -
197E PHE* 3.8 35.4 - - + -
204E PHE* 4.5 2.2 - - + -
228E PHE* 3.7 37.3 - - + +
229E LEU* 4.2 12.8 - - + -
234E TYR* 3.5 7.4 - - - +
335E THR* 2.8 34.5 + - + +
336E ALA* 3.4 8.5 - - - +
338E ARG* 1.3 71.7 - - - +
340E LEU* 1.3 57.0 + - - +
343E GLY* 2.8 29.7 + - - +
346E LEU* 4.0 12.5 - - + +
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Residues in contact with LEU 340 (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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234E TYR* 3.4 33.3 + - + -
258E LEU* 3.7 25.1 - - + -
259E ARG 3.6 18.4 - - - +
260E ARG* 3.6 50.2 + - - +
262E GLY* 4.6 4.3 - - - -
283E PHE* 3.9 21.8 - - + +
336E ALA 2.9 14.0 + - - +
337E ILE* 3.2 8.0 + - - +
339E LEU* 1.3 78.7 - - - +
341E LYS* 1.3 63.6 + - - +
343E GLY* 4.0 3.8 + - - -
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Residues in contact with LYS 341 (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 PHE* 4.0 26.2 - - + -
284E GLY* 3.9 27.4 + - - +
285E ASN 4.9 0.2 - - - -
286E SER 2.8 30.9 + - - +
287E ASP* 3.7 12.6 + - - +
288E ILE* 3.9 15.0 - - + -
311E ASN* 5.3 1.0 + - - +
337E ILE 2.8 19.6 + - - +
338E ARG 4.0 2.0 - - - +
340E LEU* 1.3 75.6 - - - +
342E TYR* 1.3 101.5 + - + +
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Residues in contact with TYR 342 (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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162E ARG* 3.2 25.6 + - - -
165E GLU* 3.4 37.2 - - + -
167E HIS* 4.0 25.1 - + + -
168E GLU* 3.4 10.5 + - + -
287E ASP* 4.2 1.7 + - - +
288E ILE* 4.8 4.4 + - + +
338E ARG* 2.8 43.0 + - + +
341E LYS* 1.3 114.9 - - + +
343E GLY* 1.3 61.2 + - - +
345E GLN* 3.6 16.3 + - - +
346E LEU* 3.6 19.7 - - + +
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Residues in contact with GLY 343 (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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228E PHE 5.1 0.2 - - - -
229E LEU* 3.7 20.2 - - - +
230E SER 5.4 3.4 - - - -
339E LEU* 2.8 27.8 + - - +
340E LEU 4.0 3.1 + - - -
341E LYS 3.7 1.4 - - - -
342E TYR* 1.3 71.8 - - - +
344E MET* 1.3 66.9 + - - -
345E GLN 2.9 1.9 + - - -
346E LEU* 3.1 18.7 + - - +
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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
------------------------------------------------------------
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