Contacts of the helix formed by residues 276 - 295 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B MET* 4.1 25.8 - - + -
127B ARG* 3.8 41.5 - - + -
130B ASP* 3.2 43.7 - - + -
133B TYR* 4.2 10.3 - + - -
235B TYR* 4.9 6.3 - - - -
237B ILE* 4.3 12.1 - - + -
272B TRP 4.3 3.7 + - - +
273B GLN 4.0 2.6 + - - -
274B ARG 3.4 0.2 - - - -
275B ARG* 1.3 117.9 - - + +
277B VAL* 1.3 56.8 + - - +
278B ALA 3.1 3.4 - - - -
279B ALA* 2.8 38.1 + - + +
280B TYR* 3.2 14.9 + - + -
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Residues in contact with VAL 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B ARG* 4.8 10.5 - - - +
24B LYS* 4.6 17.5 - - - +
273B GLN 3.9 14.2 + - - +
274B ARG* 3.9 15.7 - - + +
275B ARG 3.7 0.4 - - - -
276B PHE* 1.3 76.3 - - - +
278B ALA* 1.3 66.6 + - + +
280B TYR* 3.4 20.8 + - + +
281B ASP* 3.5 15.9 + - - +
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Residues in contact with ALA 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B TYR 5.4 0.4 - - - -
276B PHE 3.1 0.8 - - - -
277B VAL* 1.3 83.6 - - + +
279B ALA* 1.3 66.0 + - - +
281B ASP* 3.3 8.4 + - - +
282B VAL* 3.1 34.1 + - + +
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Residues in contact with ALA 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B MET* 3.5 34.7 - - + +
129B TYR* 3.7 17.2 - - - +
130B ASP* 4.2 11.4 - - - +
276B PHE* 2.8 28.3 + - + +
278B ALA* 1.3 79.8 - - - +
280B TYR* 1.3 55.1 + - - +
283B GLU* 2.9 29.3 + - - +
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Residues in contact with TYR 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B ILE* 5.0 10.8 - - + -
17B HIS* 4.5 10.5 - + + -
20B ARG* 3.4 34.3 - - - +
96B GLU* 4.7 7.4 - - - -
124B GLY 5.8 0.2 - - - -
126B MET* 3.2 39.5 - - + +
272B TRP* 3.8 17.8 - + - -
273B GLN* 4.8 8.3 - - - -
276B PHE* 3.2 21.6 + - + +
277B VAL* 3.6 9.9 - - - +
278B ALA 3.2 0.2 - - - -
279B ALA* 1.3 75.1 - - - +
281B ASP* 1.3 65.6 + - - +
283B GLU* 3.0 15.8 + - - +
284B ILE* 3.0 27.5 + - - +
400B NAI 2.9 32.7 + - - -
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Residues in contact with ASP 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B ARG* 2.8 32.6 + - - +
24B LYS* 3.4 34.1 + - - +
25B LEU* 3.6 23.0 - - + +
277B VAL* 3.5 14.0 + - - +
278B ALA* 3.3 12.1 + - - +
280B TYR* 1.3 76.5 - - - +
282B VAL* 1.3 62.8 + - + +
285B GLN* 3.1 26.4 + - - +
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Residues in contact with VAL 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B TYR* 3.6 35.2 - - + +
278B ALA* 3.1 21.0 + - + +
279B ALA 3.9 4.3 - - - +
281B ASP* 1.3 77.7 - - + +
283B GLU* 1.3 62.6 + - - +
285B GLN* 3.9 5.3 - - - +
286B ASP* 3.1 23.9 + - + +
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Residues in contact with GLU 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B HIS* 4.6 3.5 - - - -
94B PHE* 3.5 28.5 - - + -
96B GLU* 4.9 1.0 - - - +
122B GLN* 3.8 9.1 + - - +
123B VAL 4.1 1.2 - - - +
124B GLY* 3.0 33.1 - - - +
125B PHE 3.3 2.1 + - - -
126B MET* 3.2 25.0 + - - +
129B TYR* 3.5 27.8 - - + -
279B ALA 2.9 17.6 + - - +
280B TYR* 3.0 18.5 + - - +
282B VAL* 1.3 80.8 - - - +
284B ILE* 1.3 63.3 + - + +
286B ASP* 3.3 4.7 + - - +
287B PHE* 3.2 14.7 + - - +
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Residues in contact with ILE 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B ILE* 5.8 0.2 - - + -
17B HIS* 3.7 28.7 - - + +
20B ARG* 3.8 6.5 - - - -
21B ILE* 3.6 26.9 - - + -
25B LEU* 3.4 23.3 - - + -
71B LEU* 5.0 5.8 - - + -
94B PHE* 3.8 41.3 - - + -
280B TYR 3.0 13.0 + - - +
283B GLU* 1.3 72.7 - - - +
285B GLN* 1.3 65.8 - - - +
287B PHE* 3.0 20.7 + - + +
288B ILE* 3.0 21.3 + - + +
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Residues in contact with GLN 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B LEU* 3.5 17.3 - - + +
26B SER* 3.0 49.0 + - - -
281B ASP 3.1 19.1 + - - +
282B VAL* 3.9 5.8 - - - +
284B ILE* 1.3 76.7 - - - +
286B ASP* 1.3 52.7 + - - +
288B ILE* 3.4 5.8 + - - +
289B ASP* 2.8 74.9 + - - +
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Residues in contact with ASP 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B GLN* 4.7 1.0 - - - +
129B TYR* 2.9 33.9 + - + +
282B VAL* 3.1 19.0 + - + +
283B GLU 3.6 4.9 - - - +
284B ILE 3.2 0.2 - - - -
285B GLN* 1.3 73.8 - - - +
287B PHE* 1.3 60.6 + - - +
289B ASP* 4.4 6.1 - - - +
290B SER* 2.8 39.9 + - - -
298B SER* 3.7 23.9 - - - -
299B GLY 4.1 1.0 + - - -
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Residues in contact with PHE 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B LEU* 4.6 3.4 - - + -
5B ILE* 4.6 12.3 - - + -
69B ALA* 3.8 18.6 - - + -
70B VAL 4.9 0.2 - - - -
71B LEU* 4.6 7.6 - - + -
92B TYR* 3.9 2.9 - - + -
93B VAL 3.7 25.4 - - - -
94B PHE* 3.6 36.8 - - + -
122B GLN* 3.6 26.8 + - + +
283B GLU 3.2 10.1 + - - +
284B ILE* 3.0 19.0 + - + +
286B ASP* 1.3 78.7 - - - +
288B ILE* 1.3 70.1 + - + +
290B SER* 3.8 2.3 - - - -
291B ILE* 3.2 38.8 + - + +
297B VAL* 3.3 27.4 - - + -
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Residues in contact with ILE 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B LEU* 4.2 16.6 - - + -
5B ILE* 4.6 4.9 - - + -
21B ILE* 4.8 4.7 - - + -
25B LEU* 4.7 10.3 - - + -
26B SER 3.7 19.7 - - - +
27B GLY 3.5 22.2 - - - +
28B ALA* 3.6 25.8 - - + +
284B ILE* 3.0 30.7 + - + +
285B GLN* 3.6 11.9 - - - +
287B PHE* 1.3 77.9 - - + +
289B ASP* 1.3 65.2 + - - +
291B ILE* 3.1 5.4 + - - +
292B GLN* 3.0 35.3 + - + +
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Residues in contact with ASP 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B SER 4.6 0.3 - - - +
285B GLN* 2.8 54.5 + - - +
286B ASP* 4.2 7.2 - - - +
288B ILE* 1.3 75.6 - - - +
290B SER* 1.3 62.9 + - - +
292B GLN* 3.4 9.3 + - - +
293B LYS* 3.0 42.4 + - + +
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Residues in contact with SER 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B ASP* 2.8 23.2 + - - -
287B PHE 3.8 2.9 - - - -
289B ASP* 1.3 76.6 - - - +
291B ILE* 1.3 58.7 + - - +
293B LYS* 5.0 0.4 - - - -
294B LYS* 2.9 39.8 + - - +
296B GLU 2.7 27.9 + - - +
297B VAL* 3.5 1.2 - - - -
298B SER* 2.6 38.1 + - - -
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Residues in contact with ILE 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B LEU* 3.9 28.9 - - + -
92B TYR* 3.4 60.8 - - + +
287B PHE* 3.3 32.8 - - + +
288B ILE 3.1 7.9 + - - +
290B SER* 1.3 75.4 - - - +
292B GLN* 1.3 65.3 + - + +
295B GLY* 2.9 24.4 + - - -
296B GLU 3.7 15.5 - - - +
297B VAL* 4.1 6.3 - - + -
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Residues in contact with GLN 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B MET 3.4 21.2 + - - +
3B LEU* 3.5 12.7 - - + +
26B SER 5.2 0.2 - - - +
27B GLY* 2.7 36.0 + - - -
288B ILE* 3.0 29.8 + - + +
289B ASP* 4.0 10.5 - - - +
291B ILE* 1.3 78.1 - - + +
293B LYS* 1.3 63.5 + - + +
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Residues in contact with LYS 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B ASP* 3.0 29.6 + - + +
290B SER* 5.0 0.2 - - - -
292B GLN* 1.3 86.6 - - + +
294B LYS* 1.3 69.9 + - + +
295B GLY 3.7 0.4 - - - -
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Residues in contact with LYS 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B SER* 2.9 24.0 + - - +
293B LYS* 1.3 85.7 - - + +
295B GLY* 1.3 64.1 + - - +
296B GLU* 3.4 29.8 + - + +
297B VAL 4.9 1.4 + - - -
298B SER* 2.7 28.1 + - - -
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Residues in contact with GLY 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B TYR* 3.0 26.6 + - - -
118B LYS* 3.4 21.4 + - - +
291B ILE 2.9 17.9 + - - -
293B LYS 3.7 0.4 - - - -
294B LYS* 1.3 78.4 - - - +
296B GLU* 1.3 61.4 + - - +
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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