Contacts of the helix formed by residues 293 - 310 (chain D) in PDB entry 1SXG
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 PRO 293 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159D ILE* 4.5 5.6 - - + -
275D ASP 5.4 0.4 - - - +
291D VAL* 3.7 20.8 - - + +
292D GLN* 1.3 79.8 - - - +
294D MET* 1.3 66.6 + - - +
295D TYR* 3.2 2.7 - - + +
296D ASP* 3.1 31.3 + - + +
297D ILE* 3.0 20.9 + - + +
321D LEU* 4.4 12.3 - - + -
322D PRO 4.2 18.2 - - - +
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Residues in contact with MET 294 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74D PHE* 3.3 59.7 - - + +
75D TYR* 4.9 0.2 - - - -
77D GLU* 4.1 16.6 + - + +
78D LEU* 3.1 51.4 - - + +
123D MET* 3.8 14.4 - - + -
146D ALA* 4.1 7.0 - - + -
275D ASP* 5.2 2.9 - - + +
277D THR* 5.7 0.4 - - + -
292D GLN* 2.7 37.7 + - + +
293D PRO* 1.3 71.6 - - - +
295D TYR* 1.3 63.1 + - - +
297D ILE* 3.3 5.9 + - - -
298D GLY 3.0 19.4 + - - -
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Residues in contact with TYR 295 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77D GLU* 3.4 19.3 + - + +
80D ARG* 3.8 23.8 - - + -
81D GLY* 3.5 26.9 - - - +
84D ASP* 2.4 35.7 + - + +
85D ILE* 5.6 1.0 - - + +
293D PRO* 3.2 1.9 - - + +
294D MET* 1.3 79.0 - - - +
296D ASP* 1.3 69.9 + - - +
298D GLY 3.4 0.2 + - - -
299D ALA* 2.9 32.9 + - + +
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Residues in contact with ASP 296 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293D PRO* 3.1 27.0 + - + +
295D TYR* 1.3 85.4 - - - +
297D ILE* 1.3 58.7 + - - +
299D ALA* 3.0 5.1 + - - +
300D VAL* 2.7 43.1 + - + +
321D LEU* 3.6 18.2 - - + -
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Residues in contact with ILE 297 (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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78D LEU* 3.8 11.2 - - + -
145D ALA* 4.3 4.9 - - + -
146D ALA* 3.8 21.1 - - + +
157D VAL* 3.4 34.1 - - + +
158D THR* 4.5 8.3 - - - -
159D ILE* 4.4 18.6 - - + -
292D GLN* 3.9 22.9 - - + +
293D PRO* 3.0 16.1 + - + +
294D MET* 3.4 14.1 - - - +
296D ASP* 1.3 75.7 - - - +
298D GLY* 1.3 52.5 - - - +
300D VAL* 3.3 2.6 + - - +
301D ALA* 2.6 36.4 + - - +
321D LEU* 3.5 15.4 - - + +
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Residues in contact with GLY 298 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78D LEU* 3.4 12.9 - - - +
81D GLY 4.0 2.9 - - - -
82D ILE* 3.4 32.9 - - - +
294D MET 3.0 11.3 + - - -
295D TYR 3.8 2.7 - - - -
297D ILE* 1.3 75.1 - - - +
299D ALA* 1.3 66.6 + - - +
301D ALA* 4.1 3.1 - - - -
302D MET* 3.0 22.2 + - - +
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Residues in contact with ALA 299 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81D GLY* 3.5 11.7 - - - +
85D ILE* 3.1 37.3 - - + +
295D TYR* 2.9 27.2 + - + +
296D ASP* 3.5 8.1 - - - +
298D GLY* 1.3 76.1 - - - +
300D VAL* 1.3 65.4 + - + +
302D MET* 3.1 4.0 + - - +
303D ARG* 3.1 23.4 + - - +
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Residues in contact with VAL 300 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157D VAL* 4.1 21.1 - - + -
296D ASP* 2.7 30.5 + - + +
297D ILE 3.4 4.0 - - - +
299D ALA* 1.3 74.0 - - + +
301D ALA* 1.3 62.4 + - - +
303D ARG* 3.1 26.8 + - + +
304D LEU* 2.9 23.3 + - + +
319D VAL* 4.3 20.4 - - + -
321D LEU* 4.3 14.1 - - + -
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Residues in contact with ALA 301 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121D ILE* 4.4 11.0 - - + -
143D VAL* 3.6 16.2 - - + +
145D ALA* 4.3 16.4 - - + -
157D VAL* 3.5 22.2 - - + -
297D ILE 2.6 21.4 + - - +
298D GLY* 3.2 10.3 + - - +
300D VAL* 1.3 72.4 - - - +
302D MET* 1.3 57.0 + - - +
304D LEU* 3.7 1.8 - - - +
305D LEU* 3.0 28.9 + - - +
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Residues in contact with MET 302 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63D VAL* 3.6 26.2 - - + -
82D ILE* 3.6 29.6 - - + +
85D ILE* 3.3 24.5 - - + -
86D ALA* 4.7 5.6 - - - -
91D TYR* 4.9 4.5 - - - -
93D ILE* 4.2 6.3 - - - -
121D ILE* 3.4 19.7 - - + +
298D GLY 3.0 8.0 + - - +
299D ALA 3.4 5.8 - - - +
301D ALA* 1.3 75.6 - - - +
303D ARG* 1.3 61.3 + - - +
305D LEU* 3.1 37.2 + - + +
306D THR* 2.8 40.3 + - - +
309D MET* 5.0 3.1 - - + -
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Residues in contact with ARG 303 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85D ILE* 3.7 23.1 - - + -
88D MET* 6.4 1.1 - - - -
89D TYR* 3.5 23.4 + - - +
299D ALA* 3.1 16.9 + - - +
300D VAL* 3.1 29.6 + - + +
302D MET* 1.3 75.8 - - - +
304D LEU* 1.3 60.7 + - - +
306D THR* 3.4 8.5 + - - -
307D LYS* 3.2 28.0 + - - +
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Residues in contact with LEU 304 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143D VAL* 3.9 21.1 - - + -
155D PRO* 4.1 4.7 - - + -
156D SER 4.5 3.1 - - - +
157D VAL* 4.7 5.6 - - + -
300D VAL* 2.9 18.2 + - + +
301D ALA* 3.7 4.7 - - - +
303D ARG* 1.3 74.0 - - - +
305D LEU* 1.3 67.9 + - - +
307D LYS* 3.4 14.5 + - + +
308D TYR* 3.1 27.3 + - + -
314D VAL* 3.4 36.8 - - + -
316D SER 4.0 5.2 - - - +
317D SER 3.6 20.2 - - - +
319D VAL* 4.2 16.8 - - + -
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Residues in contact with LEU 305 (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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63D VAL* 3.7 13.2 - - + -
119D GLY* 3.8 5.6 - - - -
120D ILE 3.6 24.7 - - - +
121D ILE* 3.9 8.7 - - + -
141D PRO* 3.5 44.4 - - + +
142D VAL 4.0 1.3 - - - +
143D VAL* 3.8 11.4 - - + +
301D ALA 3.0 18.6 + - - +
302D MET* 3.3 28.0 - - + +
304D LEU* 1.3 77.7 - - - +
306D THR* 1.3 63.2 + - - +
308D TYR* 3.0 11.4 + - + +
309D MET* 3.0 32.3 + - + +
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Residues in contact with THR 306 (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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85D ILE* 4.8 0.2 - - - +
89D TYR* 3.3 39.6 - - + -
91D TYR* 3.9 20.1 - - + +
302D MET* 2.8 26.7 + - - +
303D ARG 3.6 6.1 - - - -
304D LEU 3.3 0.2 - - - -
305D LEU* 1.3 76.6 - - - +
307D LYS* 1.3 63.7 + - - +
309D MET* 3.3 12.2 + - + +
310D ASN* 2.9 39.2 + - - +
312D GLU* 5.7 1.6 - - - +
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Residues in contact with LYS 307 (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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89D TYR* 5.9 0.8 + - - -
303D ARG* 3.2 18.2 + - - +
304D LEU* 3.6 11.0 - - + +
305D LEU 3.2 0.2 - - - -
306D THR* 1.3 78.3 - - - +
308D TYR* 1.3 66.6 + - - +
310D ASN* 3.0 5.5 + - - -
312D GLU* 2.9 66.7 + - + +
313D THR 4.0 14.1 - - - +
314D VAL* 3.8 16.8 - - + -
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Residues in contact with TYR 308 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141D PRO* 3.6 25.5 - - + +
143D VAL* 5.8 0.9 - - + -
155D PRO* 3.7 36.1 - - + +
304D LEU* 3.1 39.7 + - + -
305D LEU* 3.0 11.1 + - + +
307D LYS* 1.3 78.7 - - - +
309D MET* 1.3 56.4 + - - +
311D LYS* 2.5 32.2 + - - +
312D GLU 4.7 5.6 - - - +
314D VAL* 3.2 34.9 + - + +
317D SER* 3.8 10.6 + - - -
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Residues in contact with MET 309 (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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61D THR* 4.0 11.4 - - + -
63D VAL* 4.9 4.7 - - + -
91D TYR* 3.5 36.6 - - + +
118D ASP* 3.5 42.8 - - + +
119D GLY* 3.8 8.3 - - - -
141D PRO* 4.0 13.2 - - + -
302D MET* 5.0 2.9 - - + -
305D LEU* 3.0 31.5 + - + +
306D THR* 3.7 19.7 - - - +
308D TYR* 1.3 75.6 - - - +
310D ASN* 1.3 64.9 + - - +
311D LYS* 3.5 12.6 + - - +
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Residues in contact with ASN 310 (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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61D THR* 6.2 1.4 - - - +
91D TYR* 3.7 13.6 + - - -
306D THR* 2.9 34.0 + - - +
307D LYS 3.7 0.7 - - - +
308D TYR 3.0 0.2 - - - -
309D MET* 1.3 84.5 + - - +
311D LYS* 1.3 72.1 + - - +
312D GLU* 3.2 30.6 + - - +
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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) + - + + + + + -
------------------------------------------------------------
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