Contacts of the helix formed by residues 278 - 292 (chain C) in PDB entry 1AIH
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 LEU 278 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259C TYR* 3.2 29.4 - - + +
262C PHE* 3.4 40.7 - - + -
263C GLU* 3.6 31.6 - - + +
266C VAL* 3.7 24.5 - - + -
273C LEU* 3.9 20.4 - - + +
274C PRO 4.9 1.2 + - - -
276C GLY* 3.5 2.5 - - - +
277C GLN* 1.3 78.4 - - - +
279C THR* 1.3 62.3 + - + +
280C HIS 3.2 0.9 + - - -
281C VAL* 3.2 20.2 - - + +
282C LEU* 4.8 0.7 + - - +
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Residues in contact with THR 279 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201C CYS* 5.9 0.3 - - - -
206C ALA 4.7 1.6 - - - +
207C ARG* 3.9 4.1 - - - -
208C TRP* 3.2 42.7 + - + +
259C TYR* 4.1 25.4 - - + +
262C PHE* 5.3 0.2 - - - -
276C GLY 4.3 10.5 + - - +
278C LEU* 1.3 74.4 - - + +
280C HIS* 1.3 88.2 + - - +
282C LEU* 5.4 2.4 + - - +
283C ARG* 4.9 0.7 + - - +
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Residues in contact with HIS 280 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107C SO4 3.1 42.7 + - - -
207C ARG* 3.9 20.2 - - + +
276C GLY 5.3 1.9 + - - -
277C GLN* 3.0 9.6 + - - +
279C THR* 1.3 108.9 + - - +
281C VAL* 1.3 66.6 + - - +
282C LEU 3.2 3.1 - - - -
283C ARG* 2.7 17.2 + - + +
284C HIS* 2.7 47.1 + + + +
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Residues in contact with VAL 281 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172C ALA* 3.8 19.6 - - + +
174C LEU* 3.4 36.6 - - + -
182C LEU* 6.1 1.8 - - + -
262C PHE* 4.3 15.3 - - + -
266C VAL* 6.0 0.9 - - + -
271C ILE* 5.6 0.2 - - + -
273C LEU* 3.8 30.1 - - + -
277C GLN 2.7 17.2 + - - +
278C LEU* 3.2 20.6 - - + +
280C HIS* 1.3 69.3 - - - +
282C LEU* 1.3 59.9 + - + +
284C HIS* 3.3 3.0 + - - +
285C THR* 2.5 39.6 + - - +
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Residues in contact with LEU 282 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174C LEU* 4.9 8.1 - - + -
182C LEU* 4.3 15.7 - - + -
198C VAL* 3.9 28.0 - - + -
201C CYS* 3.5 38.2 - - + +
202C LEU* 3.5 32.5 - - + +
208C TRP* 4.4 5.8 - - + -
262C PHE* 3.6 31.6 - - + -
278C LEU 4.8 0.8 + - - +
279C THR 5.8 2.2 - - - +
280C HIS 3.2 0.8 - - - -
281C VAL* 1.3 78.6 - - + +
283C ARG* 1.3 62.6 + - - +
285C THR* 3.3 7.0 - - - -
286C PHE* 3.1 21.8 + - - +
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Residues in contact with ARG 283 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107C SO4 3.0 41.2 + - - +
205C GLY* 2.7 50.8 + - - +
206C ALA 3.9 12.6 + - - +
207C ARG* 3.5 38.4 - - - +
235C ARG* 3.5 20.0 - - - +
279C THR 5.2 0.2 + - - -
280C HIS* 2.7 25.5 + - - +
282C LEU* 1.3 72.3 - - - +
284C HIS* 1.3 68.1 + - - +
286C PHE* 3.0 14.0 + - - +
287C ALA* 3.1 12.7 + - + +
304C LEU* 2.9 45.6 + - + +
306C HIS* 3.6 3.8 + - - -
315C TYR* 5.2 3.0 + - - +
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Residues in contact with HIS 284 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107C SO4 4.1 4.7 + - - -
171C LEU* 3.4 41.9 - - + +
172C ALA 3.2 32.3 - - - +
173C PHE* 3.9 4.5 - - + -
277C GLN* 4.3 10.3 + - - -
280C HIS* 2.7 52.0 + + + +
281C VAL 3.6 2.7 - - - +
283C ARG* 1.3 72.5 - - - +
285C THR* 1.3 52.6 + - - +
287C ALA* 3.2 2.4 + - - +
288C SER* 2.8 41.2 + - - +
314C ARG* 4.9 0.7 - - - -
315C TYR* 2.9 37.2 + - + -
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Residues in contact with THR 285 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173C PHE* 3.7 9.2 - - - +
174C LEU* 2.9 48.9 + - + +
179C ILE* 4.0 7.6 - - + -
202C LEU* 3.8 20.8 - - + +
281C VAL* 2.5 23.0 + - - +
282C LEU* 3.3 11.5 - - - -
284C HIS* 1.3 77.2 - - - +
286C PHE* 1.3 56.2 + - - +
288C SER* 3.8 0.4 - - - -
289C HIS* 3.0 43.3 + - + +
331D PRO* 3.6 1.7 - - + +
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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
----------------------------------------------------------
201C CYS 3.9 0.4 - - - +
202C LEU 3.1 24.9 - - - +
203C ALA 3.4 15.0 - - - -
204C THR* 3.6 12.6 - - - -
205C GLY* 3.4 26.0 - - - -
282C LEU 3.1 8.6 + - - +
283C ARG 3.0 9.2 + - - +
285C THR* 1.3 77.4 - - - +
287C ALA* 1.3 55.1 + - - +
289C HIS* 3.7 0.3 - - - -
290C PHE* 2.7 53.6 + + - +
300C LEU* 4.2 13.7 - - + -
303C ILE* 3.8 19.5 - - + -
304C LEU* 4.0 7.6 - - + -
326D ALA* 4.3 12.8 - - + -
330D ASN* 3.4 26.7 - - + -
331D PRO* 3.5 15.3 - - + +
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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
----------------------------------------------------------
283C ARG 3.1 7.3 + - - +
284C HIS 3.7 2.0 - - - +
286C PHE* 1.3 79.6 - - - +
288C SER* 1.3 64.0 + - - +
290C PHE* 3.2 2.3 + - - +
291C MET* 3.1 28.8 + - - +
300C LEU* 3.8 14.1 - - + -
304C LEU* 4.0 16.8 - - + -
315C TYR* 3.5 45.3 - - + -
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Residues in contact with SER 288 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171C LEU 5.4 0.3 + - - -
173C PHE* 3.4 38.7 - - - +
284C HIS* 2.8 27.9 + - - +
285C THR 3.8 2.5 - - - -
287C ALA* 1.3 74.3 - - - +
289C HIS* 1.3 63.2 + - - +
291C MET 3.6 0.2 + - - -
292C MET* 3.2 28.1 + - - +
315C TYR* 4.1 4.5 - - - -
318C PHE* 3.5 36.4 - - - +
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Residues in contact with HIS 289 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173C PHE* 4.7 2.4 - + - -
174C LEU 2.8 29.1 + - - -
175C TYR* 3.8 7.3 - + - -
176C GLU 4.1 4.5 - - - -
179C ILE* 3.7 15.6 - - + +
285C THR* 3.0 35.3 + - + +
288C SER* 1.3 79.2 - - - +
290C PHE* 1.3 67.4 + - - +
292C MET* 3.2 9.1 + - - +
293C ASN* 2.8 28.3 + - - +
329D PHE 4.0 4.0 - - - +
331D PRO* 3.5 22.7 - - + -
335D PRO* 3.8 4.8 - - + +
336D ALA* 3.0 25.2 + - + +
337D GLN* 3.4 26.4 + - - -
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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
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286C PHE* 2.7 41.4 + + + +
287C ALA* 3.2 9.4 + - - +
289C HIS* 1.3 75.3 - - - +
291C MET* 1.3 63.4 - - - +
293C ASN* 3.1 7.4 + - - +
294C GLY 3.4 0.2 + - - -
295C GLY* 2.8 46.8 + - - -
296C ASN 3.4 24.2 - - - -
299C VAL* 4.2 10.3 - - + -
300C LEU* 3.5 35.9 - - + -
303C ILE* 3.9 18.2 - - + -
325D SER* 4.3 6.1 - - - -
326D ALA* 4.4 4.9 - - - -
329D PHE* 3.7 37.3 + + + +
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Residues in contact with MET 291 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287C ALA 3.1 15.0 + - - +
290C PHE* 1.3 83.5 - - - +
292C MET* 1.3 56.3 + - - +
294C GLY* 2.9 18.4 + - - -
295C GLY 3.1 27.7 + - - +
297C ILE* 4.0 27.6 - - + +
300C LEU* 3.6 26.2 - - + -
315C TYR* 3.4 19.7 - - + +
316C ALA 5.0 0.2 - - - +
318C PHE* 3.6 22.0 - - + -
319C ALA* 3.7 26.7 - - + +
320C PRO* 3.3 15.4 - - + +
296D ASN* 4.5 7.0 - - - +
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Residues in contact with MET 292 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173C PHE* 5.2 2.7 - - - -
175C TYR* 4.3 17.9 - - + +
288C SER 3.2 20.6 + - - +
289C HIS* 3.2 9.3 + - - +
291C MET* 1.3 76.6 - - - +
293C ASN* 1.3 57.5 + - - +
294C GLY 3.1 3.9 + - - -
318C PHE* 3.6 39.7 - - + +
320C PRO* 4.3 11.4 - - - +
336D ALA* 3.7 25.2 - - + +
337D GLN 3.4 26.0 - - - +
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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
------------------------------------------------------------
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