Contacts of the helix formed by residues 283 - 296 (chain A) in PDB entry 3NNJ
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 ASP 283 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99A HIS* 5.3 0.7 - - - -
119A GLY 4.7 6.9 - - - +
120A SER* 4.4 1.8 - - - +
123A PHE* 4.4 3.8 - - - -
247A ARG* 2.7 40.1 + - - -
280A TYR* 3.6 13.4 + - - +
281A ASN 3.1 2.1 - - - -
282A LYS* 1.3 76.2 - - - +
284A SER* 1.3 67.2 + - - +
285A VAL* 3.1 9.2 + - - +
286A LEU* 3.2 23.3 + - + +
287A VAL* 3.1 23.9 + - - +
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Residues in contact with SER 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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66A HIS* 5.7 0.7 + - - -
67A ALA* 4.4 13.0 + - - -
69A ASP* 3.7 14.3 + - - -
70A LEU* 3.2 44.0 + - - +
99A HIS* 3.5 15.6 + - - -
282A LYS 3.3 6.3 + - - -
283A ASP* 1.3 73.9 + - - +
285A VAL* 1.3 59.7 + - - +
287A VAL* 3.5 9.4 + - - +
288A MSE 2.9 28.6 + - - +
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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
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70A LEU* 3.9 11.0 - - + -
98A MSE 4.1 15.9 - - + +
99A HIS* 3.4 43.1 - - + -
123A PHE* 3.6 35.9 - - + -
247A ARG* 3.8 12.1 - - - +
283A ASP* 3.1 6.1 + - - +
284A SER* 1.3 75.2 + - - +
286A LEU* 1.3 65.0 + - - +
288A MSE 3.3 9.2 + - + +
289A VAL* 3.0 35.7 + - + +
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Residues in contact with LEU 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 SER* 3.9 18.2 - - - +
123A PHE* 4.3 13.7 - - + -
260A LEU* 3.5 32.1 - - + -
263A PHE* 3.9 13.5 - - + -
280A TYR* 3.2 44.9 - - + +
281A ASN* 4.7 5.8 - - - +
283A ASP* 3.2 25.0 + - + +
285A VAL* 1.3 80.4 - - - +
287A VAL* 1.3 63.5 + - - +
289A VAL* 3.5 0.7 + - - -
290A SER* 2.9 34.7 + - - +
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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
----------------------------------------------------------
66A HIS 4.9 11.4 - - - +
67A ALA* 6.2 3.6 - - + -
281A ASN* 3.3 37.7 - - + +
283A ASP 3.1 10.3 + - - +
284A SER* 3.6 11.0 - - - +
285A VAL 3.3 0.2 - - - -
286A LEU* 1.3 77.8 - - + +
288A MSE 1.3 65.5 + - - +
290A SER* 3.1 7.7 + - - -
291A ARG* 3.0 24.3 + - + +
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Residues in contact with MSE 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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66A HIS* 4.7 11.6 - - + +
70A LEU* 3.9 20.9 - - + -
98A MSE 5.5 4.5 - - - +
284A SER 2.9 18.6 + - - +
285A VAL* 3.6 11.7 - - + +
287A VAL* 1.3 78.3 - - - +
289A VAL* 1.3 76.7 + - + +
291A ARG* 3.3 7.0 + - - +
292A ALA* 3.1 20.3 + - - +
302A LEU* 6.2 0.2 - - + -
305A ILE* 4.7 10.3 - - + -
307A HIS* 2.9 50.9 - - + -
308A VAL* 3.8 26.2 - - + -
315A ARG* 5.1 7.0 - - - +
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Residues in contact with VAL 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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98A MSE 6.5 0.2 - - - -
123A PHE* 4.1 22.0 - - + -
255A VAL* 3.8 29.2 - - + -
260A LEU* 3.6 18.6 - - + -
285A VAL* 3.0 22.7 + - + +
286A LEU 4.0 2.5 - - - +
288A MSE 1.3 81.1 - - + +
290A SER* 1.3 60.3 + - - +
292A ALA* 3.3 6.5 + - - +
293A VAL* 2.9 34.2 + - + +
302A LEU* 4.0 19.5 - - + -
305A ILE* 4.1 9.0 - - + -
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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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260A LEU* 3.7 26.0 + - - +
263A PHE* 5.6 2.8 - - - +
264A SER* 5.4 4.7 + - - -
286A LEU* 2.9 31.4 + - - +
287A VAL* 3.4 7.4 - - - -
289A VAL* 1.3 75.3 - - - +
291A ARG* 1.3 65.4 + - - +
293A VAL* 3.2 5.3 + - - +
294A GLN* 2.9 30.0 + - - +
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Residues in contact with ARG 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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66A HIS* 3.4 36.5 + - - +
287A VAL* 3.0 15.3 + - + +
288A MSE 3.6 9.4 - - - +
290A SER* 1.3 77.3 - - - +
292A ALA* 1.3 57.5 + - - +
294A GLN* 2.8 32.6 + - + +
295A LYS* 2.8 47.8 + - + +
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Residues in contact with ALA 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 MSE 3.1 13.0 + - - +
289A VAL* 3.7 7.6 - - - +
291A ARG* 1.3 75.9 - - - +
293A VAL* 1.3 65.3 + - - +
295A LYS* 3.4 9.7 + - - +
296A GLY 3.2 25.6 + - - +
297A LEU* 3.7 7.9 - - + +
305A ILE* 3.8 37.0 - - + -
306A PRO* 5.4 3.8 - - + -
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Residues in contact with VAL 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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255A VAL* 3.8 20.4 - - + -
257A GLU* 3.8 29.5 - - + +
260A LEU* 3.7 26.7 - - + -
289A VAL* 2.9 25.6 + - + +
290A SER* 3.4 7.9 - - - +
292A ALA* 1.3 74.9 - - - +
294A GLN* 1.3 66.2 + - + +
296A GLY* 3.0 15.1 + - - -
297A LEU* 4.2 12.8 + - + +
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Residues in contact with GLN 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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264A SER* 4.4 16.6 + - - -
290A SER* 2.9 18.8 + - - +
291A ARG* 2.8 20.0 + - + +
293A VAL* 1.3 81.6 - - + +
295A LYS* 1.3 60.7 + - + +
296A GLY* 3.1 1.8 + - - -
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Residues in contact with LYS 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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291A ARG* 2.8 51.2 + - + +
292A ALA* 4.0 7.6 - - - +
293A VAL 3.3 0.2 - - - -
294A GLN* 1.3 72.1 - - + +
296A GLY* 1.3 61.2 + - - +
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Residues in contact with GLY 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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292A ALA 3.2 9.0 + - - +
293A VAL 3.0 13.4 + - - -
294A GLN 3.1 2.5 + - - -
295A LYS* 1.3 84.0 - - - +
297A LEU* 1.3 65.3 + - - +
298A LYS* 3.7 11.1 + - - +
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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
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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