Contacts of the helix formed by residues 275 - 289 (chain D) in PDB entry 1XS2
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 GLY 275 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108D ALA* 3.8 2.6 - - - +
111D GLU* 3.3 10.8 - - - -
112D MET* 3.9 9.6 - - - -
270D VAL* 2.9 22.4 + - - -
273D VAL* 3.6 0.5 - - - +
274D GLY* 1.3 79.5 - - - +
276D HIS* 1.3 56.9 + - - -
277D ALA 3.5 1.8 - - - -
278D GLU 3.7 1.7 + - - -
279D SER* 2.5 36.3 + - - -
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Residues in contact with HIS 276 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111D GLU* 2.9 8.9 + - - -
112D MET* 4.0 11.5 - - + +
115D TRP* 3.6 30.5 - + + +
126D LEU* 3.3 20.0 - - + +
130D LEU* 3.8 27.0 - - + +
270D VAL* 3.7 18.2 - - + +
275D GLY* 1.3 70.7 - - - -
277D ALA* 1.3 59.4 + - - +
279D SER* 3.2 3.5 + - - -
280D ARG* 2.8 30.3 + - - +
307D HIS* 2.9 56.2 + - + -
311D LEU* 4.0 16.2 - - + +
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Residues in contact with ALA 277 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91D GLU* 4.1 20.9 - - + +
94D SER* 5.9 0.4 - - - +
111D GLU* 3.1 18.5 + - - +
115D TRP* 3.7 7.3 - - + +
276D HIS* 1.3 78.6 - - - +
278D GLU* 1.3 62.8 + - - +
280D ARG* 3.3 17.6 + - - +
281D ARG* 3.1 49.8 + - - +
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Residues in contact with GLU 278 (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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104D ARG* 4.1 14.1 + - - +
111D GLU* 4.6 0.6 + - - -
250D SER* 3.6 9.2 - - - -
251D ALA* 2.8 33.7 + - - +
252D SER 4.7 0.3 + - - -
273D VAL* 3.2 33.7 - - + +
274D GLY 4.7 5.6 - - - +
275D GLY 3.7 4.8 + - - +
276D HIS 3.3 0.4 - - - -
277D ALA* 1.3 79.3 - - - +
279D SER* 1.3 57.8 + - - +
281D ARG* 2.9 41.7 + - - +
282D VAL* 2.9 26.3 + - - +
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Residues in contact with SER 279 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268D LEU* 3.6 14.5 - - - +
270D VAL* 3.2 16.3 - - - +
273D VAL* 3.2 20.6 - - - +
275D GLY 2.5 26.5 + - - -
276D HIS* 3.5 3.8 - - - -
278D GLU* 1.3 74.5 - - - +
280D ARG* 1.3 65.7 + - - +
282D VAL* 3.3 0.8 + - - -
283D HIS* 2.9 25.2 + - - +
311D LEU* 3.5 27.1 - - - -
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Residues in contact with ARG 280 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91D GLU* 3.5 22.8 + - - -
115D TRP* 4.3 12.5 - - - -
129D LEU 3.8 7.7 + - - -
130D LEU* 3.4 41.8 + - + +
276D HIS 2.8 16.1 + - - +
277D ALA* 3.3 16.6 + - - +
279D SER* 1.3 74.3 - - - +
281D ARG* 1.3 59.0 + - - +
283D HIS* 3.3 7.4 + - - +
284D ASP* 2.8 48.8 + - - +
311D LEU* 4.6 1.8 - - + +
314D LEU* 3.8 25.6 - - + -
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Residues in contact with ARG 281 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91D GLU* 4.1 17.4 + - - +
251D ALA* 3.7 18.4 - - + -
277D ALA* 3.1 33.0 + - - +
278D GLU* 2.9 54.3 + - - +
280D ARG* 1.3 76.2 - - + +
282D VAL* 1.3 62.3 + - - +
284D ASP* 3.1 8.3 + - - +
285D VAL* 2.8 35.5 + - + +
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Residues in contact with VAL 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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248D VAL* 4.4 9.6 - - + -
250D SER* 3.7 8.1 - - - +
251D ALA* 3.6 28.7 - - - +
254D ALA* 4.0 15.3 - - + +
266D ILE* 4.5 14.1 - - + -
268D LEU* 4.1 21.1 - - + -
272D ARG* 6.0 0.2 - - - +
273D VAL* 4.3 17.7 - - + -
278D GLU* 2.9 18.7 + - + +
279D SER 3.7 5.8 - - - +
281D ARG* 1.3 74.7 - - - +
283D HIS* 1.3 55.0 + - - +
285D VAL* 3.1 4.7 + - - +
286D ALA* 2.8 34.5 + - - +
293D VAL* 5.0 1.8 - - + -
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Residues in contact with HIS 283 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268D LEU* 4.1 13.6 - - + +
279D SER 2.9 18.5 + - - +
280D ARG* 3.3 6.6 + - + +
282D VAL* 1.3 77.2 - - - +
284D ASP* 1.3 83.1 + - - +
286D ALA* 3.8 0.3 - - - +
287D GLN* 3.1 36.1 + - - +
293D VAL* 4.0 10.8 - - + -
314D LEU* 3.5 35.3 - - + +
315D SER* 4.3 4.5 - - - -
316D ASN* 2.8 53.2 + - + +
317D PHE* 3.8 14.8 - + + -
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Residues in contact with ASP 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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280D ARG* 2.8 40.6 + - - +
281D ARG* 3.1 7.3 + - - +
283D HIS* 1.3 101.2 + - - +
285D VAL* 1.3 66.0 + - + +
287D GLN* 3.4 11.9 + - - +
288D SER* 3.0 24.1 + - - -
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Residues in contact with VAL 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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251D ALA* 4.1 18.6 - - + +
254D ALA* 4.2 4.5 - - + -
255D ARG* 3.8 39.0 - - + +
258D LEU* 4.8 0.2 - - + -
281D ARG* 2.8 28.5 + - + +
282D VAL* 3.6 5.4 - - - +
284D ASP* 1.3 68.8 - - + +
286D ALA* 1.3 67.8 + - - +
288D SER* 2.6 26.2 + - - +
289D PHE* 3.3 16.8 + - + -
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Residues in contact with ALA 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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254D ALA* 5.4 0.2 - - - +
258D LEU* 3.7 21.5 - - + -
266D ILE* 4.3 7.9 - - + -
282D VAL 2.8 16.2 + - - +
283D HIS 3.8 1.8 - - - +
285D VAL* 1.3 77.3 - - - +
287D GLN* 1.3 55.4 + - - +
289D PHE* 3.0 13.9 + - - +
291D ALA* 2.9 41.0 + - + +
293D VAL* 3.8 22.0 - - + -
316D ASN* 3.9 0.2 - - - +
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Residues in contact with GLN 287 (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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283D HIS* 3.1 25.3 + - - +
284D ASP* 3.7 12.6 - - - +
285D VAL 3.3 0.2 - - - -
286D ALA* 1.3 79.5 - - - +
288D SER* 1.3 57.6 + - - +
290D GLY* 3.0 18.5 + - - +
291D ALA 4.0 1.8 - - - +
315D SER* 3.3 19.5 + - - -
316D ASN* 3.4 28.8 + - - +
318D ARG* 3.1 28.2 - - - +
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Residues in contact with SER 288 (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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284D ASP 3.0 14.4 + - - -
285D VAL* 2.6 24.1 + - - +
287D GLN* 1.3 75.2 - - - +
289D PHE* 1.3 66.3 + - - +
290D GLY 3.3 0.6 + - - -
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Residues in contact with PHE 289 (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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255D ARG* 3.8 26.0 - - + -
258D LEU* 3.8 35.0 - - + -
259D ALA* 3.7 34.5 - - + -
285D VAL* 3.3 25.6 - - + -
286D ALA 3.0 9.5 + - - +
288D SER* 1.3 85.7 + - - +
290D GLY* 1.3 61.6 + - - +
291D ALA* 4.4 3.4 - - + +
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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
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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