Contacts of the helix formed by residues 276 - 295 (chain A) in PDB entry 3NT2
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 PHE 276 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A MET* 3.6 28.5 - - + -
127A ARG* 3.8 37.5 - - + -
130A ASP* 3.5 33.2 - - + -
133A TYR* 4.5 5.6 - + - -
235A TYR* 4.5 9.9 - - - -
237A ILE* 4.3 14.1 - - + -
272A TRP* 4.2 6.2 + + - +
273A GLN 4.5 1.0 + - - -
274A ARG 3.4 0.2 - - - -
275A ARG* 1.3 123.2 - - + +
277A VAL* 1.3 67.5 + - - +
278A ALA 3.1 3.4 - - - -
279A ALA* 2.8 22.6 + - + +
280A TYR* 3.1 23.7 + - + -
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Residues in contact with VAL 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A ARG* 4.5 11.0 - - - +
24A LYS* 4.7 11.9 - - - +
273A GLN 4.2 10.4 + - - +
274A ARG* 3.5 28.3 - - + +
275A ARG 3.8 0.4 - - - -
276A PHE* 1.3 73.7 - - - +
278A ALA* 1.3 64.8 + - + +
280A TYR* 3.4 12.6 + - - +
281A ASP* 3.2 31.8 + - - +
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Residues in contact with ALA 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A TYR 5.4 0.2 - - - -
276A PHE 3.0 1.2 + - - -
277A VAL* 1.3 84.3 - - + +
279A ALA* 1.3 56.8 + - - +
281A ASP* 3.4 7.0 + - - +
282A VAL* 3.1 36.7 + - + +
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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
----------------------------------------------------------
126A MET* 3.4 31.6 - - + +
129A TYR* 3.7 13.7 - - - +
130A ASP* 3.8 25.9 + - + +
276A PHE* 2.8 16.0 + - + +
278A ALA* 1.3 78.0 - - - +
280A TYR* 1.3 59.5 + - - +
282A VAL* 4.5 0.4 - - - +
283A GLU* 2.8 31.2 + - - +
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Residues in contact with TYR 280 (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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13A ILE* 5.5 7.0 - - + -
17A HIS* 4.3 11.4 - + + -
20A ARG* 3.5 30.7 - - - +
96A GLU* 4.3 5.4 - - - -
126A MET* 3.5 27.1 - - + +
272A TRP* 4.2 15.7 - + - -
273A GLN* 5.5 5.4 - - - -
276A PHE* 3.1 37.2 + - + -
277A VAL* 3.7 6.3 - - - +
279A ALA* 1.3 75.0 - - - +
281A ASP* 1.3 64.6 + - - +
283A GLU* 3.2 18.8 + - - +
284A ILE* 3.0 30.1 + - - +
400A NAD 2.6 47.6 + + - -
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Residues in contact with ASP 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A ARG* 2.7 37.0 + - - +
24A LYS* 3.8 28.0 + - - +
25A LEU* 3.5 24.2 - - + +
277A VAL* 3.2 13.9 + - - +
278A ALA* 3.6 10.6 - - - +
279A ALA 3.3 0.2 - - - -
280A TYR* 1.3 76.6 - - - +
282A VAL* 1.3 59.7 + - + +
285A GLN* 3.0 32.2 + - - +
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Residues in contact with VAL 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A TYR* 4.1 28.7 - - + +
278A ALA* 3.1 20.6 + - + +
279A ALA* 4.1 3.8 - - - +
281A ASP* 1.3 75.5 - - + +
283A GLU* 1.3 65.7 + - - +
285A GLN* 4.1 6.3 - - + +
286A ASP* 3.2 24.4 + - + +
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Residues in contact with GLU 283 (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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17A HIS* 4.7 1.0 - - - -
94A PHE* 3.4 27.8 - - + -
96A GLU* 4.8 0.5 - - - +
122A GLN* 3.6 11.5 + - - +
123A VAL 4.1 1.4 - - - +
124A GLY* 3.1 33.7 - - - +
125A PHE 3.5 1.6 + - - -
126A MET* 3.3 24.3 + - - +
129A TYR* 3.7 29.0 - - + -
279A ALA 2.8 19.7 + - - +
280A TYR* 3.2 20.5 + - - +
282A VAL* 1.3 77.8 - - - +
284A ILE* 1.3 62.2 - - - +
286A ASP* 3.6 2.1 - - - +
287A PHE* 3.2 15.6 + - - +
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Residues in contact with ILE 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A HIS* 4.0 19.3 - - + +
20A ARG* 3.8 14.4 - - + -
21A ILE* 3.8 26.5 - - + -
25A LEU* 3.5 23.1 - - + -
71A LEU* 5.3 6.1 - - + -
94A PHE* 3.8 43.5 - - + -
280A TYR 3.0 17.7 + - - +
283A GLU* 1.3 74.2 - - - +
285A GLN* 1.3 65.3 + - - +
286A ASP 3.0 1.6 - - - -
287A PHE* 2.9 23.9 + - + +
288A ILE* 3.1 18.3 + - + +
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Residues in contact with GLN 285 (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 LEU* 3.3 20.7 - - + +
26A SER* 2.9 47.8 + - - -
281A ASP 3.0 20.0 + - - +
282A VAL* 4.1 5.6 - - + +
284A ILE* 1.3 75.0 - - - +
286A ASP* 1.3 56.8 + - - +
288A ILE* 3.6 6.4 - - - +
289A ASP* 2.8 62.0 + - - +
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Residues in contact with ASP 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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122A GLN* 5.0 0.9 - - - +
129A TYR* 3.4 30.1 + - + -
282A VAL* 3.2 20.6 + - + +
283A GLU 3.6 4.9 - - - +
284A ILE 3.0 0.6 - - - -
285A GLN* 1.3 74.2 - - - +
287A PHE* 1.3 68.6 + - - +
288A ILE 3.2 0.2 - - - -
289A ASP* 4.5 5.7 - - - +
290A SER* 2.8 36.5 + - - -
298A SER* 4.1 17.9 - - - -
299A GLY 4.7 0.7 + - - -
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Residues in contact with PHE 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A LEU* 4.6 0.7 - - + -
5A ILE* 4.6 7.4 - - + -
69A ALA* 4.1 21.1 - - + -
70A VAL 4.4 1.1 - - - -
71A LEU* 4.1 20.4 - - + -
92A TYR* 4.2 2.9 - - + -
93A VAL 3.9 7.0 - - - -
94A PHE* 3.7 41.3 - + + -
122A GLN* 3.5 29.1 + - - +
283A GLU 3.2 9.9 + - - +
284A ILE* 2.9 17.9 + - + +
286A ASP* 1.3 79.3 - - - +
288A ILE* 1.3 72.2 + - + +
290A SER* 4.0 3.1 - - - -
291A ILE* 3.3 41.7 + - + +
297A VAL* 3.8 24.2 - - + +
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Residues in contact with ILE 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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3A LEU* 4.2 14.6 - - + -
5A ILE* 4.7 2.7 - - + -
21A ILE* 4.9 5.6 - - + -
25A LEU* 4.7 9.2 - - + -
26A SER 3.8 21.8 - - - +
27A GLY 3.6 21.1 - - - +
28A ALA* 3.6 26.0 - - + +
284A ILE* 3.1 24.9 + - + +
285A GLN* 3.6 13.0 - - - +
287A PHE* 1.3 80.0 - - + +
289A ASP* 1.3 71.7 + - - +
291A ILE* 2.9 16.3 + - - +
292A GLN* 3.2 25.5 + - + +
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Residues in contact with ASP 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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26A SER 4.4 0.7 - - - +
285A GLN* 2.8 49.6 + - - +
286A ASP* 4.2 7.1 - - - +
288A ILE* 1.3 82.1 - - - +
290A SER* 1.3 63.3 + - - +
292A GLN* 3.4 7.6 + - - +
293A LYS* 3.0 50.3 + - + +
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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 ASP* 2.8 24.8 + - - -
287A PHE* 4.0 3.6 - - - -
289A ASP* 1.3 77.7 - - - +
291A ILE* 1.3 56.8 + - - +
293A LYS* 4.8 2.0 - - - -
294A LYS* 2.8 44.9 + - - +
296A GLU 2.8 18.8 + - - +
297A VAL* 4.5 0.7 - - - -
298A SER* 2.5 39.1 + - - -
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Residues in contact with ILE 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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3A LEU* 3.7 35.7 - - + -
92A TYR* 3.4 62.6 - - + +
287A PHE* 3.3 32.9 + - + +
288A ILE 2.9 5.9 + - - +
290A SER* 1.3 75.2 - - - +
292A GLN* 1.3 61.4 + - + +
293A LYS 3.0 1.4 + - - -
295A GLY* 2.8 25.8 + - - -
296A GLU 3.7 13.9 - - - +
297A VAL* 4.3 4.0 - - + -
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Residues in contact with GLN 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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1A MET 4.0 8.3 + - - +
2A SER 3.7 2.3 - - - -
3A LEU* 2.9 27.3 + - + +
27A GLY* 2.7 34.8 + - - +
288A ILE* 3.2 25.4 + - + +
289A ASP* 4.1 7.9 + - - +
291A ILE* 1.3 80.5 - - + +
293A LYS* 1.3 64.3 + - + +
294A LYS 3.8 0.2 - - - -
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Residues in contact with LYS 293 (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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289A ASP* 3.0 41.5 + - + +
290A SER* 4.2 1.1 - - - +
292A GLN* 1.3 85.4 - - + +
294A LYS* 1.3 73.0 + - + +
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Residues in contact with LYS 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 SER* 2.8 22.1 + - - +
292A GLN 3.8 0.4 - - - -
293A LYS* 1.3 88.7 - - + +
295A GLY* 1.3 66.5 + - - +
296A GLU* 3.2 40.4 + - - +
297A VAL 4.9 2.0 + - - -
298A SER* 3.5 19.4 + - - +
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Residues in contact with GLY 295 (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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92A TYR* 3.1 24.1 + - - -
118A LYS* 3.3 19.5 + - - +
291A ILE* 2.8 16.1 + - - -
294A LYS* 1.3 79.3 - - - +
296A GLU* 1.3 61.3 + - - +
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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
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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