Contacts of the helix formed by residues 280 - 296 (chain C) in PDB entry 3HU1
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 GLY 280 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278C LEU 3.2 1.6 + - - -
279C ALA* 1.3 69.1 - - - +
281C GLU* 1.3 52.7 + - - +
282C SER* 3.2 1.5 + - - -
283C GLU* 3.1 32.4 + - - +
284C SER* 2.8 34.2 + - - -
287C ARG* 5.0 0.9 + - - -
320C VAL* 4.6 0.4 - - - +
323C ARG* 4.7 3.4 - - - +
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Residues in contact with GLU 281 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277C LYS* 3.3 31.3 + - - +
278C LEU* 3.2 35.4 + - + +
279C ALA 3.2 3.8 + - - +
280C GLY* 1.3 70.6 - - - +
282C SER* 1.3 59.6 + - - +
284C SER* 3.7 9.6 - - - -
285C ASN* 3.1 44.5 + - - +
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Residues in contact with SER 282 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274C ILE* 3.4 43.3 - - - +
275C MET* 5.4 0.9 - - - -
277C LYS* 4.1 10.7 + - - +
278C LEU 3.1 15.6 + - - -
279C ALA* 4.7 1.2 - - - -
280C GLY 4.1 0.3 + - - -
281C GLU* 1.3 73.2 - - - +
283C GLU* 1.3 76.5 + - - -
284C SER 3.1 1.1 - - - -
285C ASN* 3.1 16.5 + - - +
286C LEU* 3.1 13.2 + - - +
320C VAL* 4.8 0.9 - - - +
324C ILE* 3.5 13.7 - - - +
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Residues in contact with GLU 283 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B SER 4.5 1.0 - - - +
280C GLY* 3.1 31.2 + - - +
282C SER* 1.3 80.5 + - - +
284C SER* 1.3 56.4 + - - +
286C LEU* 3.3 6.6 + - - +
287C ARG* 3.0 37.6 + - - +
320C VAL* 3.8 4.2 - - - +
323C ARG* 2.9 43.9 + - - +
324C ILE* 3.3 36.0 - - + +
327C GLN* 3.4 39.2 + - + +
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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 GLY 2.8 15.1 + - - -
281C GLU* 3.7 14.2 - - - +
283C GLU* 1.3 75.3 - - - +
285C ASN* 1.3 62.9 + - - +
287C ARG* 3.4 27.0 + - - +
288C LYS* 2.9 39.2 + - - +
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Residues in contact with ASN 285 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267C PHE* 5.3 1.6 - - - -
269C ILE* 5.7 0.2 - - - +
273C GLU* 6.0 0.7 - - - +
274C ILE* 3.7 16.7 - - + +
277C LYS* 3.3 32.8 - - - +
281C GLU* 3.1 23.2 + - - +
282C SER* 3.1 8.5 + - - +
284C SER* 1.3 78.4 + - - +
286C LEU* 1.4 60.5 + - - +
288C LYS* 3.4 10.6 + - - +
289C ALA* 3.0 27.7 + - - +
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Residues in contact with LEU 286 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269C ILE* 4.3 24.7 - - + -
274C ILE* 4.2 14.2 - - + +
282C SER 3.1 12.4 + - - +
283C GLU* 3.4 11.0 - - - +
285C ASN* 1.4 73.6 - - - +
287C ARG* 1.3 64.6 + - - +
289C ALA* 3.3 4.6 + - - +
290C PHE* 3.3 42.8 + - + -
303C ILE* 5.3 1.1 - - + -
309C ILE* 4.6 13.0 - - + -
324C ILE* 4.3 24.9 - - + +
327C GLN* 3.8 22.2 - - + -
328C LEU* 4.3 20.4 - - + +
331C LEU* 4.1 7.0 - - + -
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Residues in contact with ARG 287 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280C GLY 5.0 1.0 + - - -
283C GLU* 3.0 24.6 + - - +
284C SER* 3.7 26.7 + - - +
285C ASN 3.4 0.2 - - - -
286C LEU* 1.3 73.4 - - - +
288C LYS* 1.3 59.7 + - - +
290C PHE* 3.0 4.3 + - - +
291C GLU* 2.9 54.4 + - - +
327C GLN* 3.6 33.4 - - - +
331C LEU* 4.3 16.8 - - + -
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Residues in contact with LYS 288 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267C PHE* 4.9 4.0 - - + -
284C SER* 2.9 27.0 + - - +
285C ASN* 3.6 13.4 - - - +
286C LEU 3.3 0.2 - - - -
287C ARG* 1.3 73.8 - - - +
289C ALA* 1.3 55.8 + - - +
291C GLU* 4.0 19.3 + - + +
292C GLU* 3.0 45.3 + - + +
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Residues in contact with ALA 289 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267C PHE* 3.5 36.7 - - + -
269C ILE* 3.6 24.9 - - + -
285C ASN 3.0 12.6 + - - +
286C LEU 3.4 10.3 - - - +
288C LYS* 1.3 78.2 - - - +
290C PHE* 1.3 58.6 - - + +
292C GLU* 3.6 2.3 - - - +
293C ALA* 3.0 28.8 + - - +
301C ILE* 4.2 3.2 - - + +
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Residues in contact with PHE 290 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269C ILE* 4.7 2.2 - - + -
286C LEU* 3.3 23.5 + - + +
287C ARG 3.0 7.2 + - - +
289C ALA* 1.3 80.7 - - + +
291C GLU* 1.3 55.7 + - + +
293C ALA* 3.3 1.7 + - - +
294C GLU* 2.8 43.3 + - - +
301C ILE* 3.9 35.1 - - + +
303C ILE* 4.8 1.6 - - + -
328C LEU* 4.1 21.5 - - + -
331C LEU* 3.7 59.9 - - + -
332C MET* 4.1 7.0 - - - -
335C LEU* 4.2 18.1 - - + +
343C VAL* 4.2 22.9 - - + -
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Residues in contact with GLU 291 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287C ARG* 2.9 46.7 + - + +
288C LYS* 4.0 25.3 - - + +
290C PHE* 1.3 71.2 - - + +
292C GLU* 1.3 57.8 + - - +
294C GLU* 3.5 12.8 + - - +
295C LYS* 3.0 29.5 + - - +
331C LEU* 6.3 1.1 - - + -
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Residues in contact with GLU 292 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265C PHE* 4.1 10.3 - - + -
267C PHE* 3.8 23.4 - - + -
288C LYS* 3.0 32.1 + - + +
289C ALA 3.6 4.5 - - - +
291C GLU* 1.3 76.2 - - - +
293C ALA* 1.3 62.4 + - - +
295C LYS* 3.0 14.6 + - - +
296C ASN* 3.0 42.0 + - - +
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Residues in contact with ALA 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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265C PHE* 4.0 16.0 - - + -
267C PHE* 5.0 2.0 - - + -
289C ALA 3.0 18.3 + - - +
290C PHE 3.7 1.6 - - - +
292C GLU* 1.3 75.1 - - - +
294C GLU* 1.3 57.7 - - - +
296C ASN 3.0 23.9 - - - +
297C ALA 4.0 0.9 - - - +
299C ALA* 3.3 17.6 - - + +
300C ILE 5.3 0.2 - - - +
301C ILE* 3.6 32.1 - - + -
341C VAL* 3.8 9.5 - - + +
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Residues in contact with GLU 294 (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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290C PHE* 2.8 28.2 + - - +
291C GLU* 3.6 11.7 + - - +
293C ALA* 1.3 72.4 - - - +
295C LYS* 1.3 62.5 + - - +
296C ASN 3.5 0.2 + - - -
297C ALA 4.5 6.4 + - - +
334C GLY 4.3 5.5 - - - +
335C LEU* 3.6 38.2 + - + +
336C LYS 5.2 0.7 + - - -
339C ALA* 4.3 20.4 - - + +
341C VAL* 4.1 7.3 - - + +
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Residues in contact with LYS 295 (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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291C GLU 3.0 18.3 + - - +
292C GLU* 3.0 16.5 + - - +
294C GLU* 1.3 77.0 - - - +
296C ASN* 1.3 72.2 + - - +
297C ALA 3.5 5.0 + - - -
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Residues in contact with ASN 296 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265C PHE* 3.7 33.6 - - + +
292C GLU* 3.0 38.2 + - - +
293C ALA 3.0 10.2 - - - +
294C GLU 3.3 0.2 - - - -
295C LYS* 1.3 88.2 + - - +
297C ALA* 1.3 75.5 + - + +
298C PRO 3.7 0.2 - - - +
299C ALA* 3.5 9.2 - - - +
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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
------------------------------------------------------------
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