Contacts of the helix formed by residues 315 - 330 (chain K) in PDB entry 5G04
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 LYS 315 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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308K TYR* 6.5 0.2 - - - -
309K TYR* 3.5 51.8 - - + +
312K VAL* 4.1 15.7 - - + +
313K GLY 2.9 6.0 + - - +
314K HIS* 1.3 77.6 - - + +
316K ASN* 1.3 62.5 + - - +
317K GLU 3.3 2.9 - - - -
318K HIS* 3.1 31.8 + - + +
319K ALA 3.2 9.0 + - - -
59M ASP* 5.0 7.9 - - - -
61M ALA* 6.3 1.3 - - - -
63M GLN* 4.7 20.4 - - - +
64M TYR* 4.4 16.2 + - - -
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Residues in contact with ASN 316 (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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309K TYR 3.8 2.2 + - - -
310K LEU* 3.3 42.4 + - - +
313K GLY* 4.9 1.6 - - - -
314K HIS* 3.2 16.7 + - - +
315K LYS* 1.3 75.2 - - - +
317K GLU* 1.3 67.0 + - - +
318K HIS 3.0 2.0 - - - -
319K ALA* 3.0 4.0 + - - +
320K ARG* 2.9 44.2 + - - +
343K SER* 4.5 6.8 - - - +
346K VAL* 3.1 29.8 - - - +
347K GLU* 5.0 2.2 + - + +
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Residues in contact with GLU 317 (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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314K HIS 5.0 1.2 + - - -
315K LYS 3.3 0.8 - - - -
316K ASN* 1.3 78.1 - - - +
318K HIS* 1.3 62.5 + - + +
320K ARG* 3.0 45.5 + - - +
321K ARG* 3.3 19.6 + - - +
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Residues in contact with HIS 318 (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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309K TYR* 3.7 24.7 - + + -
315K LYS* 3.1 29.7 + - + +
316K ASN 3.0 0.4 - - - -
317K GLU* 1.3 79.6 - - + +
319K ALA* 1.3 63.8 + - - +
320K ARG 3.3 0.2 - - - -
321K ARG* 3.0 48.6 + - - +
322K TYR* 3.0 28.9 + + + -
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Residues in contact with ALA 319 (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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306K GLY* 3.3 27.9 - - - +
309K TYR* 3.8 14.5 - - + +
310K LEU* 3.6 26.7 - - + +
315K LYS 3.2 4.8 + - - +
316K ASN* 3.0 9.1 + - - +
318K HIS* 1.3 76.8 - - - +
320K ARG* 1.3 63.7 + - - +
322K TYR* 3.3 1.9 + - - -
323K LEU* 2.9 30.7 + - + +
343K SER* 5.2 0.4 - - - +
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Residues in contact with ARG 320 (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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316K ASN* 2.9 26.2 + - - +
317K GLU* 3.0 44.7 + - - +
319K ALA* 1.3 76.2 - - - +
321K ARG* 1.3 58.8 + - - +
323K LEU* 3.8 1.8 - - - +
324K SER* 2.9 31.9 + - - -
340K TYR* 3.5 28.1 - - + +
343K SER* 3.5 38.8 + - - +
344K PHE* 3.7 34.4 - - - -
347K GLU* 3.9 18.4 + - - +
349K GLU* 4.1 10.9 + - - -
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Residues in contact with ARG 321 (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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317K GLU 3.3 15.2 + - - +
318K HIS* 3.0 35.4 + - - +
320K ARG* 1.3 77.6 - - - +
322K TYR* 1.3 97.0 + - + +
324K SER* 3.4 7.9 - - - -
325K LYS* 3.2 23.4 + - - +
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Residues in contact with TYR 322 (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 TRP* 3.6 53.2 - + + +
305K VAL* 3.6 11.4 - - + -
306K GLY* 3.9 9.6 - - - +
309K TYR* 3.4 30.9 + + - -
318K HIS* 3.0 30.3 + + + -
319K ALA* 4.8 0.2 - - - -
321K ARG* 1.3 113.0 + - + +
323K LEU* 1.3 60.3 + - - +
324K SER 3.1 1.6 - - - -
325K LYS* 3.3 13.8 + - + +
326K ALA* 3.0 26.7 + - - +
57M TRP* 3.3 26.2 + + - -
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Residues in contact with LEU 323 (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 PHE* 3.9 35.2 - - + +
306K GLY* 3.9 16.8 - - - +
310K LEU* 4.3 3.6 - - + -
319K ALA* 2.9 32.3 + - + +
320K ARG* 3.9 3.6 - - - +
322K TYR* 1.3 72.7 - - - +
324K SER* 1.3 56.1 + - - +
326K ALA* 3.1 3.4 + - - +
327K THR* 2.8 40.2 + - - +
336K ALA* 3.8 17.7 - - - +
339K ALA* 3.4 46.7 - - + +
340K TYR* 3.8 12.3 - - + +
343K SER* 4.3 2.7 - - - +
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Residues in contact with SER 324 (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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320K ARG 2.9 19.1 + - - -
321K ARG* 3.4 9.4 - - - -
323K LEU* 1.3 78.2 - - - +
325K LYS* 1.3 57.1 + - - +
327K THR* 3.3 8.9 + - - +
328K THR* 2.9 46.1 + - - +
340K TYR* 4.9 14.5 + - - -
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Residues in contact with LYS 325 (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 TRP* 3.4 53.4 - - + -
321K ARG 3.2 10.6 + - - +
322K TYR* 3.5 18.2 - - + +
324K SER* 1.3 80.4 - - - +
326K ALA* 1.3 56.1 + - - +
328K THR* 3.5 7.0 + - - -
329K LEU* 3.1 30.0 + - + +
54M GLU* 2.5 36.8 + - - +
55M MET* 3.8 15.9 - - - -
56M LYS 5.6 0.2 + - - -
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Residues in contact with ALA 326 (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 PRO* 3.5 33.9 - - + +
302K TRP* 3.6 12.1 - - + -
303K PHE* 3.7 8.3 - - - +
322K TYR 3.0 13.3 + - - +
323K LEU* 3.1 7.8 + - - +
325K LYS* 1.3 74.3 - - - +
327K THR* 1.3 66.7 + - - +
329K LEU* 3.5 5.3 + - - +
330K GLU 3.1 18.9 + - - +
333K TYR* 4.7 0.9 - - - +
336K ALA* 4.0 15.3 - - + -
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Residues in contact with THR 327 (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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323K LEU 2.8 22.3 + - - +
324K SER* 3.3 16.2 - - - +
326K ALA* 1.3 75.0 - - - +
328K THR* 1.3 62.1 + - + +
330K GLU 3.0 4.2 - - - -
331K LYS* 2.8 38.6 + - - +
333K TYR* 4.1 1.9 + - - -
336K ALA* 4.2 15.2 - - - +
337K TRP* 2.7 58.8 + - + -
340K TYR* 4.8 4.9 - - + -
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Residues in contact with THR 328 (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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324K SER* 2.9 37.3 + - - +
325K LYS* 3.5 8.7 + - - +
327K THR* 1.3 80.5 - - + +
329K LEU* 1.3 68.0 + - - +
331K LYS* 4.4 24.3 + - - +
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Residues in contact with LEU 329 (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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296K PRO 4.3 2.0 - - - +
297K SER* 3.0 31.4 - - - +
299K PRO* 3.8 22.9 - - + -
302K TRP* 4.4 11.7 - - + -
325K LYS* 3.1 21.3 + - + +
326K ALA* 3.7 6.3 - - - +
328K THR* 1.3 81.0 + - - +
330K GLU* 1.3 63.1 + - + +
331K LYS 4.2 0.3 + - - -
55M MET* 4.1 24.9 - - + -
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Residues in contact with GLU 330 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299K PRO* 3.7 32.3 - - + +
326K ALA 3.1 4.9 + - - -
327K THR* 3.0 7.1 - - - +
329K LEU* 1.3 84.4 - - + +
331K LYS* 1.3 51.8 + - - +
332K THR* 3.0 29.3 + - - +
333K TYR* 2.8 40.5 + - + +
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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