Contacts of the helix formed by residues 278 - 293 (chain C) 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 ASP 278 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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273C TYR* 3.5 13.7 + - + -
276C ILE* 3.5 18.9 - - + -
277C ARG* 1.3 72.7 - - - +
279C ILE* 1.3 55.7 + - - +
280C ASP* 4.0 5.7 + - - +
281C LYS* 3.4 25.6 + - - +
282C ALA* 3.0 27.9 + - - +
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Residues in contact with ILE 279 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274C HIS* 6.3 0.9 - - - +
277C ARG* 2.6 30.1 - - - +
278C ASP* 1.3 70.6 + - - +
280C ASP* 1.3 53.6 + - - +
282C ALA* 4.3 5.4 - - - -
283C LEU* 2.7 39.7 + - + +
306C LEU* 4.0 38.4 - - + +
309C VAL* 4.7 9.4 - - + -
310C ARG* 3.4 34.1 - - + +
73R LYS 5.7 1.8 - - - +
75R GLY* 3.1 21.1 - - - +
77R ASP* 3.1 19.7 - - - +
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Residues in contact with ASP 280 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278C ASP* 3.4 5.9 + - - +
279C ILE* 1.3 78.9 - - - +
281C LYS* 1.3 61.7 + - - +
283C LEU* 3.9 2.2 - - - +
284C SER* 3.4 21.0 + - - -
310C ARG* 2.9 38.0 + - - +
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Residues in contact with LYS 281 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273C TYR* 4.0 23.8 - - + -
278C ASP* 3.4 21.0 + - - +
280C ASP* 1.3 75.2 - - - +
282C ALA* 1.3 59.1 + - - +
284C SER* 3.1 10.8 + - - -
285C ILE* 3.0 29.9 - - + +
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Residues in contact with ALA 282 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270C ALA* 4.3 5.9 - - - +
273C TYR* 3.4 37.4 - - + -
274C HIS* 4.1 2.5 - - - +
278C ASP 3.0 16.6 + - - +
279C ILE* 3.8 3.4 - - - +
281C LYS* 1.3 74.7 - - - +
283C LEU* 1.3 59.9 + - - +
285C ILE* 3.3 10.0 + - - +
286C PHE* 3.1 28.2 + - - +
306C LEU* 3.9 19.7 - - + -
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Residues in contact with LEU 283 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279C ILE* 2.7 21.8 + - + +
280C ASP 3.9 3.6 - - - +
282C ALA* 1.3 71.2 - - - +
284C SER* 1.3 65.4 + - - +
286C PHE* 3.0 7.6 + - + +
287C ASN* 3.0 31.6 + - - +
303C PHE* 4.3 20.2 - - + -
306C LEU* 2.8 35.6 - - + +
307C LEU* 4.8 8.3 - - + -
310C ARG* 3.6 31.9 - - + +
312C MET* 4.3 23.8 - - + -
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Residues in contact with SER 284 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280C ASP 3.4 11.2 + - - -
281C LYS* 3.1 16.0 + - - -
283C LEU* 1.3 77.7 - - - +
285C ILE* 1.4 66.2 + - - +
287C ASN* 3.2 23.0 + - - +
288C GLU* 3.2 18.1 + - - +
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Residues in contact with ILE 285 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266C VAL* 3.6 28.6 - - + +
269C ILE* 4.4 16.6 - - + -
270C ALA* 3.7 20.2 - - + +
273C TYR* 5.6 7.0 - - + -
281C LYS* 3.0 24.9 - - + +
282C ALA* 3.3 8.7 + - - +
283C LEU 3.2 0.4 - - - -
284C SER* 1.4 82.0 + - - +
286C PHE* 1.3 62.4 + - - +
288C GLU* 2.0 41.0 - - - +
289C LEU* 3.0 9.4 + - - +
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Residues in contact with PHE 286 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267C SER 5.1 0.4 - - - -
270C ALA* 3.6 29.4 - - + -
271C VAL* 4.5 1.3 - - + -
274C HIS* 5.2 0.2 - - + -
282C ALA 3.1 12.5 + - - -
283C LEU* 3.0 10.8 + - - +
285C ILE* 1.3 76.1 - - - +
287C ASN* 1.3 62.5 + - - +
289C LEU* 3.0 40.9 + - + +
290C ARG 3.1 6.2 + - - -
299C ASN* 4.1 14.1 - - + -
300C MET* 4.9 0.2 - - - -
302C THR* 3.8 16.2 - - + -
303C PHE* 3.4 76.6 - + + -
306C LEU* 3.7 32.5 - - + -
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Residues in contact with ASN 287 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283C LEU* 3.0 24.4 + - - +
284C SER* 3.2 13.3 + - - +
286C PHE* 1.3 76.1 - - - +
288C GLU* 1.3 62.0 + - - +
290C ARG* 3.4 8.4 + - - +
291C LYS* 3.4 21.3 + - - +
303C PHE* 3.7 22.8 - - - -
315C GLU* 5.4 11.0 + - - +
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Residues in contact with GLU 288 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266C VAL* 4.1 10.9 - - - +
284C SER 3.6 6.5 - - - +
285C ILE* 2.0 61.5 - - - +
287C ASN* 1.3 73.5 - - - +
289C LEU* 1.3 65.4 + - - -
291C LYS* 3.0 12.6 + - + +
292C GLN* 2.7 43.6 + - + +
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Residues in contact with LEU 289 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263C SER* 3.9 19.3 - - - +
266C VAL* 3.9 11.7 - - + -
267C SER* 3.6 45.1 - - - +
270C ALA* 4.7 1.3 - - + -
285C ILE 3.3 9.4 - - - +
286C PHE* 3.0 41.8 + - + +
288C GLU* 1.3 83.5 + - - +
290C ARG* 1.3 55.0 + - + +
292C GLN* 3.0 11.2 + - + +
293C ASP* 2.8 27.8 + - - +
296C ARG* 4.8 13.0 - - - +
299C ASN* 5.3 0.9 - - + -
300C MET* 4.9 14.1 - - + -
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Residues in contact with ARG 290 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286C PHE 3.1 5.6 + - - +
287C ASN* 3.4 9.4 + - - +
288C GLU 3.2 0.2 - - - -
289C LEU* 1.3 76.0 - - - +
291C LYS* 1.3 67.3 + - - +
293C ASP 3.3 20.9 - - - +
294C PRO* 3.7 24.5 + - + +
296C ARG 4.9 0.4 + - - -
300C MET* 3.4 27.6 - - + +
303C PHE* 3.8 24.7 - - + -
318C TYR* 4.9 13.1 - - - -
319C LEU* 3.4 45.6 + - - +
322C ASN* 3.7 27.1 - - - +
323C LEU* 3.7 23.4 - - - +
326C ILE* 4.5 0.2 - - - +
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Residues in contact with LYS 291 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287C ASN 3.4 14.1 + - - +
288C GLU* 3.0 16.0 + - + +
290C ARG* 1.3 82.6 + - - +
292C GLN* 1.3 63.5 + - - +
293C ASP 5.1 0.2 - - - -
294C PRO* 5.5 2.3 - - - +
259J GLU* 3.9 38.6 - - + +
104P HIS* 5.8 1.9 - - - -
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Residues in contact with GLN 292 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260C SER 5.0 4.6 + - - -
261C LYS* 3.4 51.2 + - - +
263C SER* 5.0 8.5 + - - -
266C VAL* 4.6 17.7 - - + +
288C GLU* 2.7 25.8 + - + +
289C LEU* 3.0 17.5 + - + +
291C LYS* 1.3 75.7 - - - +
293C ASP* 1.3 60.9 + - + +
294C PRO* 4.6 0.7 - - - -
104P HIS* 3.9 13.3 + - - -
105P PHE* 5.0 5.5 - - - -
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Residues in contact with ASP 293 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263C SER* 4.2 11.1 + - - +
289C LEU 2.8 11.6 + - - +
290C ARG* 3.3 18.5 - - - +
291C LYS 3.5 0.2 - - - -
292C GLN* 1.3 76.6 - - + +
294C PRO* 1.3 74.1 - - - +
295C TYR 3.3 1.7 + - - -
296C ARG* 3.0 44.3 + - + +
300C MET* 5.0 0.2 - - - +
93P TYR* 4.3 1.7 + - - -
101P ARG* 3.0 39.0 + - - +
104P HIS* 4.0 3.7 - - - -
105P PHE* 3.8 18.0 - - + -
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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