Contacts of the helix formed by residues 272 - 287 (chain E) in PDB entry 1KYZ
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 272 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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271E TRP* 1.3 77.8 - - - +
273E ASP* 1.3 65.3 + - - +
274E GLU* 3.5 14.1 - - - +
275E HIS* 3.2 28.8 + - - +
276E CYS* 2.9 21.1 + - - -
326E GLY* 3.3 26.8 + - - -
328E LYS* 5.6 1.3 - - - +
330E ARG* 3.3 1.8 - - - +
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Residues in contact with ASP 273 (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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272E SER* 1.3 73.8 - - - +
274E GLU* 1.3 65.0 + - - +
276E CYS* 3.2 4.4 + - - +
277E LEU* 2.9 32.4 + - + +
328E LYS* 3.1 25.0 + - - +
330E ARG* 2.9 32.6 + - - +
334E GLU* 5.6 1.7 - - - +
338E LEU* 4.2 12.9 - - + +
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Residues in contact with GLU 274 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272E SER* 3.5 12.5 + - - +
273E ASP* 1.3 78.8 - - - +
275E HIS* 1.3 83.7 + - + +
277E LEU* 3.5 11.0 + - - +
278E LYS* 3.2 20.8 + - - +
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Residues in contact with HIS 275 (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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253E PHE* 3.6 15.3 - + + -
271E TRP* 3.4 38.4 - + + -
272E SER* 3.2 23.1 + - - +
274E GLU* 1.3 98.3 + - - +
276E CYS* 1.3 64.1 + - - +
278E LYS* 3.1 18.7 + - - +
279E PHE* 3.3 18.5 + - - -
326E GLY* 6.3 0.4 - - - -
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Residues in contact with CYS 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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268E CYS* 3.4 44.4 - - - -
271E TRP* 3.7 3.8 - - - -
272E SER 2.9 18.9 + - - +
273E ASP* 3.2 5.1 + - - +
275E HIS* 1.3 75.0 - - - +
277E LEU* 1.3 66.3 + - - +
279E PHE* 3.4 18.2 + - + -
280E LEU* 2.9 31.1 + - + +
330E ARG* 3.5 12.3 - - - -
338E LEU* 4.1 18.6 - - + -
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Residues in contact with LEU 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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273E ASP* 2.9 22.4 + - + +
274E GLU* 3.8 10.5 - - - +
275E HIS 3.3 0.2 - - - -
276E CYS* 1.3 76.2 - - - +
278E LYS* 1.3 57.4 + - - +
280E LEU* 3.7 3.1 - - - +
281E LYS* 2.9 48.1 + - - +
337E ASP 5.0 0.2 - - - +
338E LEU* 3.7 23.6 - - + +
341E GLY* 3.4 39.3 - - - +
342E ALA* 3.6 7.0 - - + +
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Residues in contact with LYS 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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253E PHE* 3.5 48.9 - - + +
274E GLU 3.2 10.0 + - - +
275E HIS* 3.1 17.1 + - - +
277E LEU* 1.3 80.9 - - - +
279E PHE* 1.3 63.1 + - - +
281E LYS* 3.4 14.2 + - - +
282E ASN* 3.4 15.8 + - - +
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Residues in contact with PHE 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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207E VAL* 6.0 0.2 - - + -
252E MET* 3.4 58.6 - - + +
253E PHE* 3.8 13.9 - + + -
256E ILE* 4.3 0.7 - - - +
264E MET* 3.8 35.7 - - + -
267E ILE* 3.9 15.5 - - + -
268E CYS* 4.1 7.0 - - - -
271E TRP* 4.2 14.1 - + + -
275E HIS 3.3 16.9 + - - -
276E CYS* 3.5 39.5 - - - -
278E LYS* 1.3 77.2 - - - +
280E LEU* 1.3 67.6 + - + +
281E LYS 3.2 0.2 - - - -
282E ASN* 3.3 3.9 + - - +
283E CYS* 3.0 30.5 + - - -
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Residues in contact with LEU 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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264E MET* 4.1 18.6 - - + -
268E CYS* 4.7 4.9 - - - -
276E CYS* 2.9 32.3 + - + +
277E LEU* 3.7 5.6 - - - +
279E PHE* 1.3 92.1 - - + +
281E LYS* 1.3 63.1 + - - +
283E CYS* 3.3 9.1 + - + +
284E TYR 3.1 16.1 + - - -
293E VAL* 4.7 5.4 - - + -
338E LEU* 4.2 25.6 - - + +
342E ALA* 3.8 15.3 - - + -
344E PHE* 3.6 13.7 - - + -
361E PHE* 4.1 33.2 - - + -
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Residues in contact with LYS 281 (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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277E LEU* 2.9 40.6 + - - +
278E LYS* 3.7 7.9 - - - +
280E LEU* 1.3 75.8 - - - +
282E ASN* 1.3 66.9 + - - +
284E TYR* 3.0 19.4 + - + +
285E GLU* 3.0 24.6 + - - +
341E GLY 2.9 29.3 + - - -
342E ALA* 4.1 16.5 - - - +
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Residues in contact with ASN 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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252E MET 2.9 20.2 + - - -
253E PHE* 3.0 25.9 + - - +
254E VAL 3.4 16.7 + - - +
255E SER* 4.3 4.0 - - - -
256E ILE* 3.3 23.6 + - + +
278E LYS* 3.4 14.3 + - - +
279E PHE 3.3 5.0 + - - +
280E LEU 3.3 0.2 - - - -
281E LYS* 1.3 79.9 - - - +
283E CYS* 1.3 60.9 + - - +
285E GLU* 3.3 20.3 + - - +
286E ALA* 3.0 23.4 + - - +
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Residues in contact with CYS 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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207E VAL* 4.5 1.3 - - - -
256E ILE* 4.4 15.9 - - - -
262E VAL* 4.0 20.6 - - + +
264E MET* 3.5 30.1 - - - -
279E PHE* 3.0 23.3 + - - -
280E LEU* 3.5 11.7 - - - +
281E LYS 3.2 0.2 - - - -
282E ASN* 1.3 72.5 - - - +
284E TYR* 1.3 68.0 + - - +
286E ALA* 3.3 12.9 + - - +
287E LEU* 3.2 23.7 + - - +
293E VAL* 3.8 20.9 - - + -
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Residues in contact with TYR 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 LEU 3.1 11.9 + - - +
281E LYS* 3.0 13.2 + - - +
283E CYS* 1.3 76.2 - - - +
285E GLU* 1.3 69.8 + - + +
287E LEU* 3.2 12.7 + - - +
342E ALA 4.0 17.0 - - - +
343E GLY* 3.5 21.7 + - - -
344E PHE* 3.9 28.2 - + + -
345E GLN* 3.4 18.2 + - - -
363E LYS* 3.2 59.8 + - + -
365E VAL* 4.5 7.1 + - - -
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Residues in contact with GLU 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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258E LYS* 3.3 18.1 + - - -
281E LYS* 3.0 20.3 + - - +
282E ASN* 3.7 21.1 - - - +
283E CYS 3.3 0.2 - - - -
284E TYR* 1.3 87.4 - - + +
286E ALA* 1.3 59.5 + - - +
287E LEU 3.1 5.6 + - - +
363E LYS* 5.3 0.4 - - - +
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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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256E ILE* 3.1 37.5 - - + +
257E PRO 3.4 11.0 - - - +
258E LYS* 3.4 25.7 - - - +
259E ALA 3.5 17.0 + - - +
262E VAL* 5.4 2.7 - - + -
282E ASN 3.0 15.9 + - - +
283E CYS 3.3 5.6 + - - +
285E GLU* 1.3 76.0 - - - +
287E LEU* 1.3 59.3 + - + +
288E PRO* 4.4 0.3 - - - +
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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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258E LYS* 5.0 3.6 + - - -
259E ALA 3.6 15.7 - - - +
260E ASP 3.7 7.4 - - - +
261E ALA* 3.6 26.0 - - - -
262E VAL* 4.0 13.0 - - + -
283E CYS 3.2 15.5 - - - +
284E TYR 3.2 8.3 + - - +
285E GLU 3.1 7.0 - - - +
286E ALA* 1.3 81.5 - - - +
288E PRO* 1.3 70.8 - - + +
291E GLY* 3.9 4.3 - - - -
292E LYS* 3.5 29.8 - - - +
293E VAL* 4.0 5.6 - - + -
344E PHE* 4.0 20.0 - - + -
363E LYS* 3.4 19.7 + - + -
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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
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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