Contacts of the helix formed by residues 278 - 289 (chain A) in PDB entry 3N51
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 SER 278 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148A GLU* 3.0 29.3 + - - -
277A VAL* 1.3 78.2 - - - +
279A GLU* 1.3 64.3 + - - +
280A SER* 3.5 10.8 + - - -
281A ALA* 3.0 21.7 + - - +
282A LYS* 3.3 13.0 + - - +
307A TRP* 3.7 3.6 - - - -
311A TYR* 3.6 16.8 - - - -
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Residues in contact with GLU 279 (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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277A VAL 3.6 2.2 + - - -
278A SER* 1.3 72.4 - - - +
280A SER* 1.3 52.0 + - - +
282A LYS* 3.3 25.5 + - - +
283A ASP* 2.8 34.4 + - + +
286A ARG* 3.3 35.4 + - - +
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Residues in contact with SER 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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278A SER* 3.6 10.7 - - - -
279A GLU* 1.3 75.9 - - - +
281A ALA* 1.3 64.9 + - - +
283A ASP* 3.3 6.8 + - - +
284A LEU 3.2 17.0 + - - -
305A HIS* 3.4 14.5 - - - -
306A GLU* 4.2 17.8 + - - +
307A TRP* 3.4 30.9 + - - +
311A TYR* 5.2 3.8 - - - -
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Residues in contact with ALA 281 (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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148A GLU* 3.8 1.1 - - - +
240A LEU* 4.7 1.0 - - - +
244A LEU* 3.9 12.1 - - + -
277A VAL* 3.6 22.9 - - + -
278A SER* 3.0 13.7 + - - +
280A SER* 1.3 72.7 - - - +
282A LYS* 1.3 63.2 + - - +
284A LEU* 3.2 5.5 + - - +
285A ILE* 3.1 27.1 + - - +
307A TRP* 3.4 39.7 - - + +
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Residues in contact with LYS 282 (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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269A PHE* 3.8 39.0 + - + +
274A TRP* 3.2 55.9 + - + +
275A LYS* 5.2 9.1 - - - +
277A VAL* 3.6 14.4 + - + -
278A SER 3.3 9.4 + - - +
279A GLU* 3.3 29.3 + - - +
280A SER 3.2 0.8 - - - -
281A ALA* 1.3 75.8 - - - +
283A ASP* 1.3 58.2 + - - +
285A ILE* 3.2 6.2 + - - +
286A ARG* 2.9 40.4 + - - +
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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
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279A GLU* 2.8 17.7 + - + +
280A SER* 3.3 13.0 + - - +
282A LYS* 1.3 74.2 - - - +
284A LEU* 1.3 61.3 + - - +
286A ARG* 3.2 21.4 + - - +
287A LYS* 2.6 56.4 + - - +
305A HIS* 2.7 18.8 + - + +
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Residues in contact with LEU 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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155A ILE* 5.2 0.2 - - + -
159A LEU* 4.9 3.8 - - + -
240A LEU* 4.1 10.8 - - + -
280A SER 3.2 4.9 + - - +
281A ALA 3.6 8.1 - - - +
283A ASP* 1.3 76.0 + - - +
285A ILE* 1.3 61.3 + - - +
287A LYS* 3.2 3.6 + - + -
288A MET* 2.8 56.4 + - + +
297A ILE* 4.5 7.4 - - + -
302A ALA* 4.0 16.8 - - + +
305A HIS* 3.6 42.0 - - + +
307A TRP* 3.8 27.4 - - + -
308A ILE* 4.0 19.7 - - + -
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Residues in contact with ILE 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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237A GLY 4.6 3.6 - - - +
240A LEU* 3.8 19.5 - - + -
241A TYR* 4.0 17.0 - - + +
244A LEU* 4.0 14.6 - - + -
267A TYR* 4.1 2.2 - - + -
269A PHE* 3.8 20.4 - - + -
274A TRP* 3.5 35.4 - - + -
281A ALA 3.1 16.3 + - - +
282A LYS 3.2 7.2 + - - +
284A LEU* 1.3 75.4 - - - +
286A ARG* 1.3 56.9 + - - +
288A MET* 4.6 5.6 - - - -
289A LEU* 2.9 52.5 + - + +
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Residues in contact with ARG 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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267A TYR* 3.3 16.1 + - - +
269A PHE* 3.7 24.6 - - + -
279A GLU* 3.3 27.5 + - - +
282A LYS* 2.9 14.7 + - - +
283A ASP* 3.5 34.9 + - - +
284A LEU 3.2 0.2 - - - -
285A ILE* 1.3 76.4 - - - +
287A LYS* 1.3 53.0 + - + +
289A LEU 3.6 2.1 + - - -
290A THR* 2.7 34.7 + - - -
705A DMS 2.5 34.0 + - + +
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Residues in contact with LYS 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 ASP* 2.6 42.6 + - - +
284A LEU* 3.2 7.4 + - - +
286A ARG* 1.3 79.3 - - + +
288A MET* 1.3 61.1 + - - +
290A THR* 3.3 15.4 + - - +
296A ARG* 3.4 13.7 - - - +
297A ILE* 3.4 42.8 + - + +
305A HIS* 3.9 12.8 + - + -
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Residues in contact with MET 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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155A ILE* 5.2 0.7 - - - -
159A LEU* 3.8 19.7 - - + -
233A VAL* 3.4 39.9 - - + +
234A TRP* 3.5 13.2 - - - -
236A THR* 3.6 29.2 - - + -
237A GLY* 3.6 17.5 - - - +
240A LEU* 4.5 10.5 - - - -
284A LEU* 2.8 54.4 + - + +
285A ILE* 4.1 2.2 - - - +
287A LYS* 1.3 74.3 - - - +
289A LEU* 1.3 58.0 + - - +
290A THR 3.3 0.9 - - - -
296A ARG* 3.2 22.3 + - - -
297A ILE* 4.1 4.0 - - + -
302A ALA* 4.6 2.7 - - + -
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Residues in contact with LEU 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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234A TRP* 3.2 56.9 - - + +
237A GLY* 3.9 11.7 - - - +
238A VAL* 3.8 17.7 - - + +
241A TYR* 4.6 1.3 - - + -
249A PRO* 4.5 16.4 - - + -
250A PHE* 4.5 2.2 - - + -
265A GLY 5.1 2.3 - - - +
267A TYR* 3.7 40.4 - - + +
285A ILE* 2.9 39.0 + - + +
286A ARG 3.6 4.0 - - - -
288A MET* 1.3 76.3 - - - +
290A THR* 1.3 63.3 + - - +
291A TYR* 3.5 1.9 + - - +
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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