Contacts of the helix formed by residues 298 - 311 (chain K) in PDB entry 4UJ3
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 ASP 298 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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331E PRO 4.5 2.6 - - - +
334E THR* 3.9 11.3 - - - +
406E PHE* 4.7 5.4 - - + -
410E ARG* 3.2 42.6 + - - +
452E LYS 4.2 10.8 - - - +
454E GLY* 5.1 1.5 - - - +
296K GLU 3.5 3.4 + - - -
297K ALA* 1.3 69.4 - - - +
299K LEU* 1.3 63.6 + - - +
300K SER* 3.6 16.2 + - - -
301K LEU* 2.9 29.0 + - + +
302K TYR* 2.9 23.6 + - - +
438K PHE* 4.6 4.5 - - - -
442K MET* 5.0 4.4 - - + +
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Residues in contact with LEU 299 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336E SER* 4.5 15.9 - - - +
382E THR* 5.3 6.7 - - + -
383E GLY 6.2 0.2 - - - +
384E GLN* 3.5 37.0 - - + +
297K ALA* 3.4 10.3 + - + +
298K ASP* 1.3 75.1 + - - +
300K SER* 1.3 56.9 + - - +
302K TYR* 3.8 19.7 - - + -
303K ASN* 2.8 47.9 + - - +
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Residues in contact with SER 300 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334E THR* 3.7 30.4 - - - +
298K ASP* 3.1 11.5 + - - -
299K LEU* 1.3 78.0 - - - +
301K LEU* 1.3 58.8 + - - +
303K ASN* 4.6 2.7 - - - +
304K GLU* 3.2 25.8 + - - +
323K LYS* 3.9 16.5 + - - -
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Residues in contact with LEU 301 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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452E LYS* 4.0 22.2 - - + +
453E LEU* 4.3 3.4 - - + -
298K ASP* 2.9 19.0 + - + +
300K SER* 1.3 79.3 - - - +
302K TYR* 1.3 60.3 + - - +
304K GLU* 3.5 12.1 - - - +
305K PHE* 3.0 30.3 + - - +
320K PHE* 5.3 0.7 - - - -
323K LYS* 3.5 35.0 - - + +
324K ILE* 6.1 0.7 - - + -
327K GLU* 6.1 0.2 - - - +
438K PHE* 4.0 3.2 - - + -
442K MET* 3.7 29.6 - - + -
445K ARG* 3.6 26.9 - - - +
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Residues in contact with TYR 302 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297K ALA* 4.4 11.9 - - + -
298K ASP 2.9 16.8 + - - +
299K LEU* 3.1 19.5 + - + +
301K LEU* 1.3 74.6 - - - +
303K ASN* 1.3 73.6 + - - +
305K PHE* 3.3 3.0 + + - +
306K ARG* 2.9 67.5 + - + +
434K VAL* 4.5 7.8 - - + +
435K ASP* 2.6 30.4 + - - -
438K PHE* 3.6 45.7 - + + -
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Residues in contact with ASN 303 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299K LEU* 2.8 33.5 + - - +
300K SER* 4.6 2.4 - - - +
302K TYR* 1.3 85.8 - - - +
304K GLU* 1.3 66.4 + - - +
306K ARG* 3.3 6.8 + - - +
307K LEU* 3.2 35.1 + - + +
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Residues in contact with GLU 304 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300K SER 3.2 16.8 + - - +
301K LEU* 3.5 27.2 - - - +
303K ASN* 1.3 81.5 - - - +
305K PHE* 1.3 61.8 + - - +
307K LEU* 3.9 8.3 + - - +
308K TRP* 3.6 16.1 + - - +
319K PRO* 3.1 38.0 - - + +
320K PHE* 3.9 25.8 - - - +
323K LYS* 3.2 28.6 + - - +
324K ILE* 6.0 0.3 - - - +
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Residues in contact with PHE 305 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301K LEU 3.0 19.0 + - - +
302K TYR* 3.7 3.8 - + - +
304K GLU* 1.3 74.0 - - - +
306K ARG* 1.3 64.1 + - + +
307K LEU 3.1 2.0 - - - -
308K TRP* 2.9 38.9 + + - +
309K LYS* 2.9 25.4 + - + -
320K PHE* 3.2 40.4 - + + -
424K ILE* 4.7 1.8 - - + -
434K VAL* 3.9 18.4 - - + -
437K MET* 4.1 15.7 - - + -
438K PHE* 3.7 43.5 - + + -
441K VAL* 3.5 30.1 - - + -
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Residues in contact with ARG 306 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302K TYR* 2.9 53.0 + - + +
303K ASN* 3.3 7.5 + - - +
305K PHE* 1.3 83.3 - - + +
307K LEU* 1.3 63.9 + - + +
309K LYS* 3.7 8.0 + - + +
310K ASP* 3.6 27.1 + - - +
434K VAL* 3.7 29.4 - - + +
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Residues in contact with LEU 307 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303K ASN* 3.2 21.8 + - + +
304K GLU* 4.1 7.9 - - - +
305K PHE 3.1 0.6 - - - -
306K ARG* 1.3 77.8 - - + +
308K TRP* 1.3 66.0 + - - +
310K ASP* 3.1 19.4 + - - +
311K GLU* 3.2 13.2 + - - +
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Residues in contact with TRP 308 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304K GLU 3.6 11.2 + - - +
305K PHE* 2.9 23.1 + + - +
307K LEU* 1.3 77.7 - - - +
309K LYS* 1.3 66.3 + - - +
311K GLU* 3.1 4.6 - - - +
312K PRO* 2.9 41.4 - - + +
313K THR* 3.0 40.8 + - + +
314K MET* 5.5 0.4 - - - -
318K CYS* 4.0 13.2 - - - -
320K PHE* 3.6 37.4 - + + -
321K LEU* 4.1 3.8 - - + +
421K ILE* 3.3 59.2 - - + -
424K ILE* 3.6 30.1 - - + -
425K GLN* 5.5 0.9 - - + -
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Residues in contact with LYS 309 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305K PHE* 2.9 23.9 + - + +
306K ARG* 3.9 9.2 - - + +
307K LEU 3.2 0.4 - - - -
308K TRP* 1.3 93.2 - - + +
310K ASP* 1.3 75.2 + - - +
312K PRO* 3.2 16.7 - - - +
424K ILE* 5.0 5.8 - - + +
434K VAL* 3.0 47.6 - - + +
437K MET* 4.3 24.3 - - + +
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Residues in contact with ASP 310 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306K ARG* 3.6 17.5 + - - +
307K LEU* 3.1 15.0 + - - +
309K LYS* 1.3 95.8 + - - +
311K GLU* 1.3 71.1 + - + +
312K PRO* 3.5 3.3 - - - +
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Residues in contact with GLU 311 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307K LEU 3.2 8.0 + - - +
308K TRP* 3.1 9.8 + - - +
310K ASP* 1.3 94.4 - - + +
312K PRO* 1.3 67.5 - - - +
313K THR* 3.6 8.7 + - - +
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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