Contacts of the helix formed by residues 278 - 286 (chain D) in PDB entry 3SRF
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 ARG 278 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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245D ARG 3.6 11.0 - - - +
246D LYS* 3.5 27.5 - - - +
274D GLU* 2.8 52.2 + - - +
275D GLY 3.7 4.3 - - - -
277D ARG* 1.3 90.5 - - + +
279D PHE* 1.3 62.0 + - - +
280D ASP* 3.4 2.7 - - - -
281D GLU* 2.9 51.5 + - + +
282D ILE* 3.1 17.1 - - - +
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Residues in contact with PHE 279 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270D ILE* 4.2 12.1 - - + -
275D GLY 3.3 9.5 + - - +
276D VAL* 3.4 18.2 - - - +
277D ARG 3.3 4.2 + - - -
278D ARG* 1.3 74.1 - - - +
280D ASP* 1.3 58.8 + - - +
282D ILE* 3.1 4.9 + - - +
283D LEU* 2.7 46.7 + - + +
289D ILE* 3.6 28.9 - - + -
311D MET* 4.2 7.6 - - - -
312D MET* 3.5 49.1 - - + -
315D ARG* 3.6 45.5 - - + +
316D CYS* 4.0 13.7 - - - -
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Residues in contact with ASP 280 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277D ARG 5.1 0.8 + - - -
278D ARG 3.4 0.8 - - - -
279D PHE* 1.3 78.6 - - - +
281D GLU* 1.3 58.8 + - - +
283D LEU* 3.2 8.6 + - - +
284D GLU* 3.0 31.5 + - - +
315D ARG* 2.7 41.5 + - - -
318D ARG* 5.3 1.6 + - - -
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Residues in contact with GLU 281 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246D LYS* 3.5 1.0 - - - +
247D ALA* 3.2 37.6 + - + +
278D ARG* 2.9 62.0 + - + +
280D ASP* 1.3 78.1 - - - +
282D ILE* 1.3 59.7 + - - +
284D GLU* 3.4 26.8 - - + +
285D ALA* 3.4 11.4 + - - +
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Residues in contact with ILE 282 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244D ILE* 3.7 26.2 - - + +
245D ARG 3.8 20.0 - - - +
246D LYS* 3.9 19.5 - - - +
247D ALA* 4.7 2.9 - - - +
250D VAL* 4.0 2.0 - - + -
268D SER* 3.7 19.7 - - - +
270D ILE* 3.9 12.1 - - + -
275D GLY 3.5 20.6 - - - +
278D ARG 3.1 17.5 + - - +
279D PHE* 3.1 6.8 + - - +
281D GLU* 1.3 76.5 - - - +
283D LEU* 1.3 59.1 + - - +
285D ALA* 3.2 4.1 + - - +
286D SER* 2.6 47.0 + - - +
289D ILE* 4.2 2.5 - - + -
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Residues in contact with LEU 283 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279D PHE* 2.7 43.7 + - + +
280D ASP* 3.6 8.5 - - - +
282D ILE* 1.3 73.8 - - - +
284D GLU* 1.3 50.2 + - - +
286D SER* 3.0 12.3 + - - +
288D GLY 5.3 1.3 - - - -
289D ILE* 3.8 16.5 - - + +
315D ARG* 4.1 12.1 - - + +
316D CYS* 3.7 26.0 - - - -
319D ALA* 3.8 22.4 - - + -
321D LYS* 2.7 52.8 + - + +
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Residues in contact with GLU 284 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247D ALA* 4.9 2.6 - - - +
251D HIS* 4.7 7.6 + - - -
280D ASP 3.0 16.5 + - - +
281D GLU* 3.4 26.8 - - - +
283D LEU* 1.3 78.2 - - - +
285D ALA* 1.3 69.4 + - - +
321D LYS* 3.4 16.3 + - - +
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Residues in contact with ALA 285 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247D ALA 4.4 3.1 - - - +
250D VAL* 3.6 23.8 - - + +
251D HIS* 3.8 27.9 - - + +
254D ARG* 3.5 17.2 + - - -
281D GLU 3.4 17.0 + - - +
282D ILE 3.2 4.2 + - - +
283D LEU 3.2 0.2 - - - -
284D GLU* 1.3 86.3 - - - +
286D SER* 1.3 59.8 + - - +
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Residues in contact with SER 286 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250D VAL* 3.6 10.4 - - - +
254D ARG* 4.6 1.3 - - - +
266D ILE 4.0 4.0 - - - -
268D SER* 2.9 27.3 + - - -
282D ILE* 2.6 23.8 + - - +
283D LEU* 3.0 5.1 + - - +
285D ALA* 1.3 79.5 - - - +
287D ASP* 1.3 60.5 + - - +
288D GLY 3.4 21.3 - - - -
289D ILE* 4.4 2.9 - - - -
321D LYS* 2.7 32.1 + - - +
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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