Contacts of the helix formed by residues 276 - 296 (chain A) in PDB entry 4PE5
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 ASN 276 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A THR* 5.5 0.9 - - - -
273A ASN* 3.1 13.2 + - - +
275A LYS* 1.3 74.2 - - - +
277A GLU* 1.3 63.2 + - - +
278A SER* 3.0 22.6 + - - -
279A ALA* 3.2 20.7 + - + -
280A HIS* 3.2 18.9 + - - -
943A NAG 1.4 73.1 + - - +
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Residues in contact with GLU 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A LEU* 3.7 13.7 - - + +
34A SER* 3.3 25.5 + - - -
38A HIS* 3.3 38.3 + - + +
93A SER* 2.8 38.6 + - - -
94A HIS 6.1 1.1 - - - -
121A LEU* 4.6 3.8 - - + +
122A THR* 4.7 15.7 - - + -
275A LYS 3.1 11.2 + - - +
276A ASN* 1.3 71.8 + - - +
278A SER* 1.3 56.7 + - - +
280A HIS* 3.4 3.6 + - - +
281A ILE* 2.9 29.1 + - + +
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Residues in contact with SER 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A HIS* 4.0 14.5 + - - -
41A MET* 3.3 43.1 - - - +
276A ASN* 3.0 12.2 + - - -
277A GLU* 1.3 79.1 - - - +
279A ALA* 1.3 57.2 + - - +
281A ILE* 3.2 3.3 + - - +
282A SER 2.9 24.1 + - - -
943A NAG 5.0 6.1 + - - -
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Residues in contact with ALA 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A MET* 5.4 0.2 - - - -
273A ASN* 5.4 2.2 - - - -
276A ASN* 3.2 29.1 + - + +
278A SER* 1.3 78.9 - - - +
280A HIS* 1.3 60.0 + - - +
282A SER* 3.2 8.8 + - - -
283A ASP* 2.9 31.2 + - - +
334A VAL* 3.8 18.5 - - + +
335A THR* 3.8 22.0 - - + -
943A NAG 4.7 7.4 + - - +
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Residues in contact with HIS 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A LEU* 3.2 36.9 - - + +
122A THR* 5.4 2.2 - - + -
140A THR* 3.3 27.4 + - - +
141A VAL* 3.3 21.4 - - + +
271A LEU* 5.3 0.8 - - - +
272A ILE 5.1 1.5 + - - -
273A ASN* 2.9 31.3 - - + -
274A GLY* 4.4 3.0 - - - -
276A ASN 3.2 13.4 + - - +
277A GLU* 3.9 8.1 - - - +
278A SER 3.2 0.4 - - - -
279A ALA* 1.3 74.4 - - - +
281A ILE* 1.3 61.2 + - - +
283A ASP* 4.1 6.0 - - + +
284A ALA* 2.9 32.1 + - - +
335A THR* 3.7 27.6 - - + +
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Residues in contact with ILE 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A LEU* 5.2 7.4 - - + -
38A HIS* 5.4 3.1 - - + +
41A MET* 4.5 11.4 - - + -
42A PHE* 4.9 13.9 - - + +
45A ALA* 4.8 0.7 - - - -
91A LEU* 4.6 5.2 - - + -
121A LEU* 4.0 17.4 - - + +
277A GLU* 2.9 19.1 + - + +
278A SER* 3.5 8.3 - - - +
280A HIS* 1.3 77.2 - - - +
282A SER* 1.3 57.9 + - - +
284A ALA* 3.4 2.0 + - - +
285A VAL* 2.9 37.4 + - + +
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Residues in contact with SER 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A MET* 3.7 15.8 - - - +
45A ALA* 4.1 13.7 - - - +
278A SER 2.9 13.4 + - - -
279A ALA* 3.2 12.5 + - - -
281A ILE* 1.3 78.4 - - - +
283A ASP* 1.3 64.4 + - - +
285A VAL* 3.3 3.3 + - - +
286A GLY* 3.0 23.4 + - - -
334A VAL* 4.4 12.8 - - - +
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Residues in contact with ASP 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A THR* 5.3 7.2 - - + -
279A ALA 2.9 15.5 + - - +
280A HIS* 4.1 4.7 - - - +
282A SER* 1.3 78.3 + - - +
284A ALA* 1.3 66.8 + - - +
286A GLY* 3.1 2.1 + - - -
287A VAL* 2.9 25.6 + - - +
333A GLY* 3.9 9.8 - - - -
334A VAL* 3.2 26.8 + - - +
335A THR* 2.5 42.5 + - - +
336A GLY 5.1 0.2 - - - +
338A VAL* 5.4 16.0 - - + +
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Residues in contact with ALA 284 (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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91A LEU* 3.7 17.7 - - + -
119A LEU* 4.1 15.5 - - + -
121A LEU* 3.5 22.7 - - + -
140A THR* 4.4 9.3 - - + +
280A HIS 2.9 20.2 + - - +
283A ASP* 1.3 76.3 - - - +
285A VAL* 1.3 57.9 + - - +
287A VAL* 3.8 2.9 - - - +
288A VAL* 2.9 36.3 + - - +
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Residues in contact with VAL 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A ILE* 4.9 6.0 - - + +
42A PHE* 3.5 38.4 - - + -
45A ALA* 3.4 40.2 - - + +
46A VAL* 3.7 14.4 - - + +
49A ALA* 4.1 7.0 - - + -
91A LEU* 3.8 5.6 - - + -
281A ILE 2.9 24.7 + - - +
282A SER 3.7 3.8 - - - +
284A ALA* 1.3 73.2 - - - +
286A GLY* 1.3 62.0 + - - +
288A VAL* 4.0 5.0 - - - +
289A ALA* 2.9 28.8 + - - +
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Residues in contact with GLY 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A ALA* 5.3 3.1 - - - -
282A SER 3.0 14.3 + - - -
283A ASP* 3.1 4.0 + - - -
285A VAL* 1.3 80.5 - - - +
287A VAL* 1.3 55.3 + - - +
289A ALA* 3.7 4.8 - - - +
290A GLN* 3.0 30.6 + - - +
330A TYR* 5.8 3.1 - - - -
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Residues in contact with VAL 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A LEU* 5.0 7.6 - - + -
140A THR* 6.1 0.4 - - + -
283A ASP 2.9 16.2 + - - +
284A ALA* 3.8 7.0 - - - +
286A GLY* 1.3 75.8 - - - +
288A VAL* 1.3 56.5 + - - +
290A GLN* 3.4 7.3 + - - +
291A ALA* 2.9 29.5 + - - +
325A LEU* 4.3 3.8 - - + +
328A SER* 4.2 12.8 + - - -
330A TYR* 5.3 9.3 - - + +
338A VAL* 5.2 14.6 - - + -
340A PHE* 5.1 13.9 - - + -
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Residues in contact with VAL 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A ILE* 3.6 31.4 - - + -
89A ALA* 4.2 18.6 - - + -
91A LEU* 3.9 14.4 - - + -
119A LEU* 3.6 27.6 - - + -
284A ALA 2.9 25.1 + - - +
285A VAL* 4.1 3.6 - - - +
287A VAL* 1.3 73.8 - - - +
289A ALA* 1.3 59.9 + - - +
291A ALA* 3.6 1.0 - - - +
292A VAL* 2.8 35.6 + - + +
321A PHE* 4.6 3.1 - - + -
325A LEU* 4.1 13.9 - - + -
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Residues in contact with ALA 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A ILE* 4.7 0.4 - - - +
49A ALA* 3.7 16.2 - - + -
60A LEU* 3.6 31.2 - - + -
285A VAL 2.9 19.0 + - - +
286A GLY* 3.7 3.8 - - - +
288A VAL* 1.3 77.9 - - - +
290A GLN* 1.3 59.3 + - - +
292A VAL* 3.2 4.8 + - - +
293A HIS* 2.7 40.9 + - + +
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Residues in contact with GLN 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A GLY 3.0 18.2 + - - +
287A VAL* 3.6 6.5 - - - +
289A ALA* 1.3 75.3 - - - +
291A ALA* 1.3 57.6 + - - +
293A HIS* 3.4 6.6 + - - +
294A GLU* 2.9 38.3 + - - +
328A SER* 4.5 9.0 + - - +
329A LYS 3.2 39.7 + - - +
330A TYR* 4.1 13.6 - - - +
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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 VAL 2.9 17.5 + - - +
288A VAL 3.6 4.3 - - - +
290A GLN* 1.3 73.2 - - - +
292A VAL* 1.3 61.6 + - - +
294A GLU* 3.5 0.4 + - - -
295A LEU* 2.9 30.5 + - - +
321A PHE* 3.5 2.8 - - + -
324A VAL* 3.4 18.1 - - + +
325A LEU* 3.6 33.2 - - + -
328A SER* 3.7 16.1 + - - +
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Residues in contact with VAL 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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27A VAL* 3.7 39.5 - - + -
29A ILE* 5.1 0.9 - - + -
58A ILE* 3.8 23.3 - - + -
60A LEU* 4.1 9.0 - - + -
88A TYR* 4.6 5.2 - - + -
288A VAL* 2.8 29.7 + - + +
289A ALA* 3.2 8.5 + - - +
291A ALA* 1.3 76.5 - - - +
293A HIS* 1.3 57.9 + - - +
295A LEU* 3.2 4.6 + - + +
296A LEU* 2.9 29.9 + - + +
321A PHE* 3.5 24.2 - - + -
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Residues in contact with HIS 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A ALA 5.1 8.1 - - - -
50A ASN* 5.7 2.7 - - - -
58A ILE* 3.4 40.7 + - + +
60A LEU* 4.8 12.1 - - + -
289A ALA* 2.7 40.9 + - + +
290A GLN* 3.8 6.6 - - - +
292A VAL* 1.3 76.0 - - - +
294A GLU* 1.3 64.9 + - - +
296A LEU* 3.2 7.2 + - - +
297A GLU* 3.0 22.1 + - - +
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Residues in contact with GLU 294 (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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290A GLN* 2.9 27.9 + - + +
291A ALA* 3.8 3.9 - - - +
293A HIS* 1.3 75.8 - - - +
295A LEU* 1.3 62.6 + - - +
297A GLU* 3.1 21.4 + - + +
298A LYS* 3.9 9.6 + - + +
324A VAL* 3.8 26.9 - - + +
327A SER* 4.7 11.2 + - - +
328A SER* 5.1 6.6 + - - -
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Residues in contact with LEU 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A TYR* 4.4 15.7 - - + -
291A ALA 2.9 18.4 + - - +
292A VAL* 3.4 4.9 - - - +
294A GLU* 1.3 77.3 - - - +
296A LEU* 1.3 66.7 + - + +
298A LYS* 3.1 27.0 + - + +
301A ILE* 3.6 44.5 - - + +
317A THR* 3.7 17.7 - - + -
320A LEU* 3.8 21.5 - - + -
321A PHE* 3.8 26.9 - - + -
324A VAL* 4.5 8.7 - - + -
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Residues in contact with LEU 296 (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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25A LYS* 5.2 1.1 - - - +
27A VAL* 3.8 20.6 - - + -
58A ILE* 3.6 46.7 - - + -
88A TYR* 5.1 5.8 - - + +
292A VAL* 2.9 18.0 + - + +
293A HIS* 3.2 7.6 + - - +
295A LEU* 1.3 79.1 - - + +
297A GLU* 1.3 57.8 + - - +
298A LYS 3.1 11.8 - - - +
301A ILE* 3.7 33.0 - - + -
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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