Contacts of the helix formed by residues 276 - 297 (chain C) in PDB entry 1HHS
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 PRO 276 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151C THR 4.1 0.4 - - - +
153C ILE* 3.3 27.8 - - + +
194C GLN 4.3 8.7 - - - +
196C GLY 3.5 26.5 - - - +
198C ALA 3.5 20.6 - - - +
199C TYR* 4.4 4.0 - - + -
275C GLY* 1.3 79.4 - - - +
277C PHE* 1.3 65.6 + - - +
278C ALA 3.3 2.2 - - - -
279C LEU* 3.0 28.1 + - + -
280C ASN* 3.1 11.4 + - - +
363C LEU* 3.8 20.2 - - + -
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Residues in contact with PHE 277 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143C LEU* 4.7 2.0 - - + -
145C ILE* 3.9 27.1 - - + -
150C SER 4.9 3.8 - - - +
151C THR* 3.1 34.3 + - + +
153C ILE 4.0 1.6 + - - -
163C LYS* 3.5 42.4 - - + -
166C ILE* 3.7 20.0 - - + -
167C ALA* 3.7 17.0 - - + -
275C GLY 3.1 7.0 + - - +
276C PRO* 1.3 72.0 - - - +
278C ALA* 1.3 62.1 + - - +
280C ASN* 4.3 11.0 - - + -
281C ALA* 2.9 31.2 + - + +
284C MET* 3.8 28.5 - - + -
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Residues in contact with ALA 278 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153C ILE 5.3 1.2 + - - +
166C ILE* 4.3 15.6 - - + +
170C ALA* 3.4 21.5 - - + +
193C HIS 3.3 26.2 - - - +
194C GLN* 3.5 20.6 - - + +
195C MET* 3.5 7.1 - - + +
276C PRO 3.3 1.0 - - - -
277C PHE* 1.3 77.5 - - - +
279C LEU* 1.3 56.9 + - - +
281C ALA* 4.9 0.2 - - - -
282C PRO* 3.0 24.6 - - - +
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Residues in contact with LEU 279 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181C MET* 4.6 4.5 - - + -
194C GLN 4.3 1.2 + - - -
195C MET* 4.0 20.3 - - + +
196C GLY* 4.3 9.2 - - - +
199C TYR* 5.5 0.9 - - - +
276C PRO* 3.0 19.6 + - + +
278C ALA* 1.3 79.5 - - - +
280C ASN* 1.3 64.6 + - - +
282C PRO* 3.2 16.3 - - - +
283C ILE* 3.6 10.3 - - + +
356C LEU* 3.8 45.1 - - + +
359C THR* 4.8 3.1 - - + -
360C SER* 3.9 34.8 - - - +
363C LEU* 4.2 22.0 - - + -
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Residues in contact with ASN 280 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199C TYR* 4.8 2.4 + - - -
275C GLY* 3.7 21.5 + - - +
276C PRO* 3.1 11.4 + - - +
277C PHE* 3.2 13.2 + - + +
279C LEU* 1.3 79.2 - - - +
281C ALA* 1.3 55.8 + - - +
283C ILE* 2.9 11.2 + - - +
284C MET* 2.7 49.3 + - - +
360C SER* 5.2 1.2 - - - -
394C GLY 2.8 23.7 + - - +
395C GLN* 3.6 4.0 - - - +
396C GLY* 2.8 28.8 + - - +
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Residues in contact with ALA 281 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143C LEU* 3.6 19.2 - - + +
167C ALA* 4.1 26.0 - - + +
170C ALA* 4.1 14.1 - - + -
171C LEU* 4.1 3.4 - - + -
277C PHE* 2.9 23.9 + - + +
280C ASN* 1.3 72.8 - - - +
282C PRO* 1.3 71.2 - - + +
284C MET* 3.2 9.1 + - - +
285C ALA* 3.0 20.3 + - - +
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Residues in contact with PRO 282 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170C ALA* 4.1 6.7 - - + -
171C LEU* 3.7 13.0 - - + -
174C ALA* 3.9 22.2 - - + -
195C MET* 4.5 3.1 - - + -
278C ALA 3.0 25.6 - - - +
279C LEU* 3.2 16.2 - - - +
281C ALA* 1.3 88.4 - - + +
283C ILE* 1.3 59.9 + - + +
285C ALA* 3.7 3.9 + - - +
286C VAL* 3.9 1.7 - - - +
353C TRP* 2.9 23.5 + - - +
356C LEU* 4.4 12.3 - - + -
657C PHE* 3.5 29.5 - - + -
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Residues in contact with ILE 283 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279C LEU* 3.6 20.0 - - + +
280C ASN* 2.9 14.8 + - - +
282C PRO* 1.3 77.0 - - + +
284C MET* 1.3 61.9 + - - +
285C ALA 3.1 0.2 - - - -
286C VAL* 3.1 5.9 + - - +
287C ALA* 2.9 23.8 + - + +
353C TRP* 4.1 11.3 - - + +
356C LEU* 4.2 6.5 - - + +
357C PHE* 4.0 39.7 - - + +
360C SER* 3.4 36.6 - - - +
395C GLN* 4.0 5.8 - - - +
396C GLY* 3.9 25.1 - - - -
397C ALA* 4.1 3.4 - - + +
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Residues in contact with MET 284 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143C LEU* 4.0 18.1 - - + +
144C LYS 3.6 24.2 - - - +
145C ILE* 5.2 2.9 - - + -
277C PHE* 3.8 27.6 - - + -
280C ASN* 2.7 31.5 + - - +
281C ALA* 3.7 6.3 - - - +
283C ILE* 1.3 74.5 - - - +
285C ALA* 1.3 61.5 + - - +
287C ALA* 4.1 9.0 - - - -
288C GLN* 3.1 28.2 + - - +
291C ARG* 5.1 2.2 + - - +
396C GLY* 4.2 19.7 - - - +
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Residues in contact with ALA 285 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141C VAL 5.5 3.0 - - - +
143C LEU* 4.3 13.9 - - + +
171C LEU* 4.1 10.3 - - + -
281C ALA 3.0 15.9 + - - +
282C PRO 3.8 0.4 - - - +
283C ILE 3.1 0.4 - - - -
284C MET* 1.3 77.8 - - - +
286C VAL* 1.3 56.9 + - - +
288C GLN* 5.8 0.2 - - - -
289C PRO* 3.3 16.1 - - - +
654C THR* 5.1 9.1 - - - -
657C PHE* 3.6 33.9 - - + -
658C LEU* 3.1 17.9 - - + +
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Residues in contact with VAL 286 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135C PHE* 4.2 17.7 - - + -
138C LEU* 4.2 18.4 - - + -
282C PRO 3.9 1.8 - - - +
283C ILE 3.1 1.4 + - - +
284C MET 3.1 0.4 - - - -
285C ALA* 1.3 78.1 - - - +
287C ALA* 1.3 67.8 + - - +
288C GLN 3.4 0.7 - - - -
289C PRO* 3.1 14.2 - - - +
290C VAL* 3.1 13.3 + - - +
349C TYR* 4.3 7.0 - - + +
353C TRP* 3.4 53.2 - - + +
657C PHE* 4.5 2.5 - - + -
658C LEU* 4.0 15.9 - - + -
661C VAL* 4.2 12.6 - - + -
662C MET* 5.9 1.3 - - + -
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Residues in contact with ALA 287 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135C PHE* 6.1 0.7 - - - -
283C ILE* 2.9 15.7 + - + +
284C MET* 3.2 4.2 + - - +
286C VAL* 1.3 78.8 - - - +
288C GLN* 1.3 64.6 + - - +
290C VAL* 3.1 6.2 + - - +
291C ARG* 2.9 39.5 + - - +
396C GLY 3.6 22.4 - - - +
397C ALA* 4.1 7.9 - - + -
400C LEU* 3.7 17.3 - - + +
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Residues in contact with GLN 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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141C VAL* 3.7 20.2 - - + -
142C PRO 4.9 7.2 - - - +
143C LEU* 6.2 1.6 - - - -
144C LYS* 6.2 2.5 - - + +
284C MET 3.1 13.2 + - - +
287C ALA* 1.3 76.2 - - - +
289C PRO* 1.4 72.9 - - + +
291C ARG* 3.0 39.2 + - - +
292C ASN* 2.9 46.5 + - - +
295C TYR* 6.0 0.2 - - - -
633C THR* 4.5 10.7 + - - -
634C GLU* 4.2 22.1 + - - +
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Residues in contact with PRO 289 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138C LEU* 3.9 25.3 - - + +
139C GLU 3.5 27.2 + - - +
141C VAL* 4.0 13.5 - - + +
285C ALA* 3.3 24.5 - - - +
286C VAL* 3.1 11.7 - - - +
288C GLN* 1.4 94.6 - - + +
290C VAL* 1.3 56.9 + - - +
292C ASN* 3.2 11.7 + - + +
293C LYS* 2.9 28.2 + - - +
658C LEU* 4.2 10.5 - - + -
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Residues in contact with VAL 290 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134C MET* 3.5 34.3 - - + +
135C PHE* 3.7 25.8 - - + -
138C LEU* 3.5 26.0 - - + -
286C VAL* 3.1 18.9 + - + +
287C ALA* 3.5 8.1 - - - +
289C PRO* 1.3 77.0 - - - +
291C ARG* 1.3 61.8 + - - +
293C LYS* 3.1 2.4 + - - +
294C ILE* 2.9 25.7 + - + +
400C LEU* 3.7 26.5 - - + -
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Residues in contact with ARG 291 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284C MET* 5.1 2.2 + - - +
287C ALA* 2.9 21.4 + - - +
288C GLN* 3.1 56.7 + - - +
290C VAL* 1.3 76.9 - - - +
292C ASN* 1.3 58.4 + - - +
294C ILE* 4.0 9.2 - - - -
295C TYR* 2.8 60.9 + - + -
396C GLY 3.6 19.8 + - - -
399C ASP* 2.8 39.9 + - - +
400C LEU* 4.1 14.4 - - + -
633C THR* 4.7 5.6 - - - -
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Residues in contact with ASN 292 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139C GLU 5.1 0.8 + - - +
141C VAL* 3.5 37.0 - - - +
288C GLN* 2.9 38.2 + - - +
289C PRO* 3.2 9.3 + - + +
291C ARG* 1.3 75.3 - - - +
293C LYS* 1.3 60.5 + - - +
295C TYR* 4.0 5.0 - - - +
296C SER* 2.7 29.0 + - - -
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Residues in contact with LYS 293 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133C LEU* 2.8 30.9 + - - +
134C MET 4.2 3.6 - - - +
136C SER* 2.8 25.1 + - - +
137C ASP* 3.9 21.6 + - - +
138C LEU* 4.1 22.2 - - + -
289C PRO 2.9 14.3 + - - +
290C VAL* 3.6 6.7 - - - +
292C ASN* 1.3 76.1 - - - +
294C ILE* 1.3 61.1 + - + +
296C SER* 3.0 5.2 + - - +
297C LYS* 2.9 61.4 + - + +
298C TYR* 4.5 6.2 + - + -
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Residues in contact with ILE 294 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134C MET* 3.7 45.5 - - + +
290C VAL* 2.9 19.8 + - + +
291C ARG* 3.5 9.9 - - - +
293C LYS* 1.3 73.3 - - + +
295C TYR* 1.3 81.5 + - + +
298C TYR* 3.0 46.6 - - + +
302C PHE* 3.9 29.2 - - + +
400C LEU* 3.9 24.7 - - + -
403C THR* 4.7 5.6 - - + -
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Residues in contact with TYR 295 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288C GLN* 6.0 0.2 - - - -
291C ARG* 2.8 43.2 + - + +
292C ASN* 4.0 6.1 - - - +
294C ILE* 1.3 98.5 - - + +
296C SER* 1.3 56.8 + - - +
299C ALA* 3.1 19.8 - - - +
302C PHE* 3.2 32.1 - - + -
303C HIS* 3.5 28.7 + + + +
399C ASP* 4.2 13.2 + - - -
400C LEU* 5.5 0.9 - - - +
451C LYS* 3.9 26.3 + - + +
633C THR* 3.9 36.1 - - + -
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Residues in contact with SER 296 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292C ASN 2.7 22.6 + - - -
293C LYS* 3.0 7.4 + - - +
295C TYR* 1.3 75.8 - - - +
297C LYS* 1.3 74.7 + - - +
298C TYR 3.3 1.0 + - - -
299C ALA* 3.3 15.4 + - - +
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Residues in contact with LYS 297 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133C LEU* 6.0 1.2 - - - +
293C LYS* 2.9 32.4 + - + +
296C SER* 1.3 82.5 + - - +
298C TYR* 1.3 88.4 + - + +
299C ALA 3.7 0.7 + - - -
437C ASP* 3.4 23.9 + - - -
441C GLN* 3.8 21.6 - - - +
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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