Contacts of the helix formed by residues 273 - 292 (chain A) in PDB entry 1HU9
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 273 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266A HIS* 5.3 0.2 + - - -
270A SER 3.9 19.3 - - - +
271A ASP* 2.8 18.2 + - - +
272A PHE* 1.3 69.8 - - - +
274A THR* 1.3 66.5 + - + +
276A GLY* 2.9 12.6 + - - +
277A LEU* 2.9 18.3 + - - +
330A VAL* 4.7 4.3 - - + -
334A ILE* 5.0 7.0 - - + -
772A ILE* 3.9 19.9 - - + +
775A ARG* 3.7 38.4 - - + +
777A ALA* 4.3 20.4 - - + +
856A SER 5.7 0.9 - - - +
857A ILE* 3.6 31.2 - - + -
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Residues in contact with THR 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A PHE* 4.9 5.2 - - - +
273A LEU* 1.3 76.6 - - + +
275A TYR* 1.3 59.4 + - - +
277A LEU* 3.5 3.1 + - - +
278A LYS* 3.0 29.5 + - - +
553A ASP* 5.1 6.5 - - - +
556A ASN* 3.9 25.6 + - - +
557A ILE* 4.2 24.9 - - + -
560A LEU* 3.9 31.5 - - + +
856A SER 5.2 3.4 - - - +
857A ILE* 5.3 2.7 - - + -
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Residues in contact with TYR 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A VAL* 4.0 32.8 - - + -
27A ASN* 4.3 12.2 + - - -
272A PHE* 3.1 25.8 + + + +
273A LEU 3.0 0.2 - - - -
274A THR* 1.3 80.8 + - - +
276A GLY* 1.3 62.1 + - - +
278A LYS* 3.5 14.8 + - + +
279A SER* 3.1 37.6 + - - -
329A PRO* 3.4 38.9 - - + +
330A VAL* 3.7 17.3 - - + -
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Residues in contact with GLY 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A PHE 3.1 7.1 + - - -
273A LEU 2.9 6.7 + - - -
275A TYR* 1.3 77.1 - - - +
277A LEU* 1.3 56.3 + - - +
279A SER* 3.0 5.9 + - - -
280A VAL* 3.0 29.1 + - - +
330A VAL* 3.9 13.6 - - - +
331A LEU* 3.7 22.4 - - - +
334A ILE* 6.2 0.2 - - - -
772A ILE* 3.9 10.8 - - - -
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Residues in contact with LEU 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A LEU 2.9 14.4 + - - +
274A THR 3.8 4.3 - - - +
276A GLY* 1.3 73.6 - - - +
278A LYS* 1.3 64.1 + - - +
280A VAL* 3.4 4.5 + - - +
281A SER* 3.3 23.0 + - - -
557A ILE* 5.3 2.2 - - + -
560A LEU* 3.8 25.1 - - + -
564A SER* 4.7 0.9 + - - -
565A LEU* 4.7 14.8 - - + +
769A VAL* 4.0 30.1 - - + +
772A ILE* 3.6 29.6 - - + +
773A LEU* 3.6 34.8 - - + -
857A ILE* 3.8 14.8 - - + +
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Residues in contact with LYS 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254A ASN* 3.5 30.0 + - - +
255A ASP* 4.4 10.7 + - - -
274A THR 3.0 18.1 + - - +
275A TYR* 3.7 16.4 - - + +
277A LEU* 1.3 75.3 - - - +
279A SER* 1.3 58.8 + - - +
281A SER* 3.2 9.1 + - - -
282A GLN* 3.0 58.8 + - + +
560A LEU* 4.0 17.4 - - + +
563A LEU* 3.9 17.3 - - + -
564A SER* 5.0 1.8 - - - +
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Residues in contact with SER 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A TYR* 3.1 28.5 + - - -
276A GLY 3.0 9.5 + - - -
278A LYS* 1.3 75.7 - - - +
280A VAL* 1.3 59.1 + - - +
281A SER 3.4 0.2 - - - -
282A GLN* 4.6 1.6 - - - +
283A ASN* 2.7 50.5 + - - +
284A VAL* 3.0 10.1 + - - +
328A LEU* 5.0 4.5 - - - +
329A PRO* 4.8 1.2 + - - +
331A LEU* 3.5 20.5 - - - +
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Residues in contact with VAL 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A GLY 3.0 15.4 + - - +
277A LEU* 3.8 9.4 - - - +
278A LYS 3.3 0.4 - - - -
279A SER* 1.3 76.2 - - - +
281A SER* 1.3 60.9 + - - +
284A VAL* 3.3 12.0 + - + +
285A LEU* 2.6 35.3 + - + +
331A LEU* 3.8 20.6 - - + -
335A PHE* 4.0 14.8 - - + -
571A VAL* 5.6 0.4 - - + -
765A ILE* 5.1 7.9 - - + +
768A SER* 4.3 17.0 - - - -
769A VAL* 4.0 26.0 - - + -
772A ILE* 3.9 14.1 - - + -
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Residues in contact with SER 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A LEU 3.3 10.7 + - - -
278A LYS 3.2 11.4 + - - -
280A VAL* 1.3 79.5 - - - +
282A GLN* 1.3 61.0 + - - +
285A LEU* 4.0 18.8 - - - +
286A PRO* 4.0 9.2 - - - +
564A SER* 3.3 31.9 + - - -
565A LEU* 5.8 1.8 - - - -
571A VAL* 4.1 22.0 - - - -
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Residues in contact with GLN 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A ASN* 2.9 32.1 - - - +
278A LYS* 3.0 46.0 + - + +
279A SER* 4.4 1.2 - - - +
281A SER* 1.3 85.7 - - - +
283A ASN* 1.3 73.3 + - - +
286A PRO* 3.2 21.0 - - - +
563A LEU* 4.9 3.1 - - - +
564A SER* 5.7 4.6 - - - -
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Residues in contact with ASN 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A SER* 2.7 39.9 + - - +
282A GLN* 1.3 88.0 + - - +
284A VAL* 1.3 59.7 - - - +
285A LEU 3.6 0.2 - - - -
286A PRO* 3.9 1.8 - - - +
287A LEU* 3.2 42.6 + - + +
325A ILE* 4.7 0.2 - - - -
328A LEU* 4.2 23.6 - - + +
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Residues in contact with VAL 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A SER 3.0 13.1 + - - +
280A VAL* 3.3 23.3 - - + +
283A ASN* 1.3 77.3 - - + +
285A LEU* 1.3 60.6 + - - +
287A LEU* 4.0 0.5 - - - +
288A LEU* 2.8 47.7 + - + +
325A ILE* 4.2 29.0 - - + +
328A LEU* 4.9 3.1 - - + -
331A LEU* 4.7 5.6 - - + -
335A PHE* 3.9 35.2 - - + -
343A LEU* 5.8 3.1 - - + -
768A SER* 5.2 5.8 - - - +
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Residues in contact with LEU 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A VAL* 2.6 19.9 + - + +
281A SER* 4.0 18.2 - - - +
284A VAL* 1.3 72.9 - - - +
286A PRO* 1.4 76.3 - - + +
288A LEU* 3.1 8.9 + - - +
289A GLN* 3.1 42.2 + - - +
569A GLY 5.7 0.2 - - - +
570A GLY 5.9 0.2 - - - -
571A VAL* 4.3 19.3 - - + +
574A GLN* 3.8 24.2 - - - +
761A PHE* 4.1 5.6 - - + -
765A ILE* 4.3 24.5 - - + -
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Residues in contact with PRO 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281A SER 4.0 5.4 - - - +
282A GLN* 3.2 34.3 - - - +
283A ASN 3.9 1.8 - - - +
284A VAL 3.8 0.7 - - - -
285A LEU* 1.4 101.3 - - + +
287A LEU* 1.3 62.9 + - + +
289A GLN* 3.3 22.3 - - + +
290A SER* 3.3 16.6 + - - -
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Residues in contact with LEU 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283A ASN* 3.2 27.7 + - + +
284A VAL 4.0 2.0 - - - +
285A LEU 3.3 0.4 - - - -
286A PRO* 1.3 80.4 - - + +
288A LEU* 1.3 63.3 + - - +
290A SER* 3.7 16.8 + - - +
291A ALA* 4.0 4.2 + - - +
321A ILE* 3.9 35.6 - - + +
324A LYS* 4.0 34.1 - - + +
325A ILE* 3.5 23.6 - - + -
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Residues in contact with LEU 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284A VAL* 2.8 34.7 + - + +
285A LEU* 3.5 4.5 - - - +
287A LEU* 1.3 77.5 - - - +
289A GLN* 1.3 63.8 + - - +
291A ALA* 3.3 13.0 + - - +
292A PHE* 3.4 17.7 - - + -
315A ILE* 6.2 0.7 - - + -
317A LEU* 3.9 27.1 - - + -
321A ILE* 5.4 2.0 - - - -
325A ILE* 5.6 4.5 - - + +
343A LEU* 5.5 9.0 - - + -
761A PHE* 3.7 20.6 - - + -
764A LEU* 4.0 39.5 - - + +
765A ILE* 4.6 10.3 - - + -
768A SER* 5.6 1.6 - - - +
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Residues in contact with GLN 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285A LEU* 3.1 20.9 + - - +
286A PRO* 3.3 23.4 - - - +
288A LEU* 1.3 74.9 - - - +
290A SER* 1.3 61.8 + - - +
291A ALA 3.2 0.2 - - - -
292A PHE* 3.2 5.7 + - + +
293A ASP* 2.8 43.4 + - - +
574A GLN* 5.3 4.8 - - - +
761A PHE* 3.6 35.7 - - + -
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Residues in contact with SER 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286A PRO 3.3 13.5 + - - -
287A LEU* 3.7 12.6 + - - +
288A LEU 3.2 0.8 - - - -
289A GLN* 1.3 80.2 - - - +
291A ALA* 1.3 57.9 + - - +
292A PHE 3.1 0.4 - - - -
293A ASP* 3.4 9.0 + - - +
294A LEU* 3.1 30.1 + - - +
321A ILE* 5.7 5.2 - - - -
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Residues in contact with ALA 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287A LEU 4.0 5.3 + - - +
288A LEU 3.3 12.8 + - - +
289A GLN 3.2 0.8 - - - -
290A SER* 1.3 78.6 - - - +
292A PHE* 1.3 59.6 + - + +
294A LEU* 3.9 11.2 - - - -
295A ASN 3.8 1.9 + - - -
296A PHE* 3.7 20.1 + - + -
297A THR* 3.7 12.7 + - - +
317A LEU* 3.9 30.3 - - + -
318A PRO* 4.5 16.2 - - + -
321A ILE* 5.1 4.7 - - + +
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Residues in contact with PHE 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288A LEU* 3.4 24.9 - - + -
289A GLN* 3.2 9.1 + - + +
290A SER 3.1 0.4 - - - -
291A ALA* 1.3 78.3 - - + +
293A ASP* 1.3 60.0 + - - +
294A LEU 2.9 15.5 + - - +
295A ASN* 5.1 0.2 - - - -
297A THR* 4.0 19.8 - - - +
298A PRO 3.5 20.9 - - - -
299A ARG* 3.2 52.5 + - + +
315A ILE* 4.4 2.2 - - + -
317A LEU* 5.4 1.3 - - + -
760A LYS* 3.8 25.1 - - + -
761A PHE* 3.8 31.6 - + + -
764A LEU* 3.6 34.3 - - + -
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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