Contacts of the helix formed by residues 293 - 310 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B ILE* 5.1 4.5 - - + -
291B VAL* 4.0 14.8 - - + +
292B GLN* 1.3 81.8 - - + +
294B MET* 1.3 63.1 + - - +
295B TYR 3.3 2.7 - - - -
296B ASP* 3.3 21.9 + - - +
297B ILE* 2.9 31.6 + - + +
321B LEU* 4.0 23.8 - - + -
322B PRO* 3.7 24.9 - - + +
323B HIS* 4.8 1.1 - - - -
324B ARG* 6.0 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 294 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B PHE* 3.9 43.5 - - + +
77B GLU* 3.8 42.6 - - + +
78B LEU* 3.6 32.7 - - + +
81B GLY* 5.7 1.0 - - - -
275B ASP 4.4 1.6 - - - +
276B ASN 3.6 24.7 - - - +
277B THR* 4.5 2.2 - - - -
292B GLN* 2.8 18.2 + - + +
293B PRO* 1.3 68.8 - - - +
295B TYR* 1.3 66.6 + - - +
297B ILE* 3.4 3.3 + - - -
298B GLY* 3.0 19.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 295 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B GLY* 5.0 13.9 - - - -
84B ASP* 5.0 11.0 - - + -
85B ILE* 3.4 40.0 - - + +
88B MET* 4.4 10.9 - - - -
293B PRO 3.3 0.6 - - - -
294B MET* 1.3 80.5 - - - +
296B ASP* 1.3 71.9 + - - +
298B GLY 3.1 0.5 + - - -
299B ALA* 2.8 25.4 + - + -
5256B 171 2.9 42.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 296 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293B PRO* 3.3 21.3 + - + +
295B TYR* 1.3 87.1 - - - +
297B ILE* 1.3 56.4 + - - +
299B ALA* 3.0 6.5 + - - -
300B VAL* 2.7 42.9 + - + +
321B LEU* 3.7 30.6 - - + +
5256B 171 5.8 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 297 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B LEU* 4.3 7.0 - - + -
145B ALA* 4.1 11.4 - - + -
146B ALA* 3.7 22.0 - - + +
157B VAL* 3.6 38.4 - - + +
158B THR 5.1 2.7 - - - +
159B ILE* 4.9 5.8 - - + -
292B GLN* 3.7 35.2 - - + +
293B PRO* 2.9 31.8 + - + +
294B MET* 3.6 9.6 - - + +
296B ASP* 1.3 75.1 - - - +
298B GLY* 1.3 64.8 + - - +
301B ALA* 2.8 27.0 + - - +
321B LEU* 4.8 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 298 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B LEU* 4.7 2.6 - - - +
81B GLY* 6.1 0.2 - - - -
82B ILE* 4.0 28.9 - - - +
85B ILE* 3.7 8.3 - - - -
121B ILE* 5.5 1.1 - - - +
294B MET 3.0 9.8 + - - -
295B TYR 3.6 2.9 - - - -
297B ILE* 1.3 80.1 - - - +
299B ALA* 1.3 56.9 + - - +
301B ALA* 3.5 7.0 - - - +
302B MET* 2.8 30.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 299 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B ILE* 3.2 25.7 - - + +
89B TYR* 4.6 1.2 + - - -
295B TYR* 2.8 15.2 + - + +
296B ASP* 3.4 11.7 - - - +
298B GLY* 1.3 73.0 - - - +
300B VAL* 1.3 67.0 + - + +
302B MET* 2.9 12.8 + - - +
303B ARG* 2.9 14.9 + - - +
5256B 171 3.9 35.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 300 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B VAL* 4.0 7.9 - - + -
296B ASP* 2.7 31.0 + - + +
297B ILE 4.0 1.3 - - - +
299B ALA* 1.3 71.2 - - + +
301B ALA* 1.3 57.7 + - - +
303B ARG* 3.2 2.0 + - + +
304B LEU* 2.8 35.2 + - + +
319B VAL* 3.8 35.2 - - + -
321B LEU* 3.9 19.5 - - + -
5256B 171 4.0 28.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 301 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B ILE* 4.8 8.7 - - + -
143B VAL* 3.5 12.5 - - + +
144B LEU 4.5 6.7 - - - +
145B ALA* 4.5 10.1 - - + -
157B VAL* 3.4 24.6 - - + +
297B ILE 2.8 21.4 + - - +
298B GLY* 3.5 7.6 - - - +
300B VAL* 1.3 76.9 - - - +
302B MET* 1.3 57.1 + - - +
304B LEU* 3.2 5.3 - - - +
305B LEU* 2.9 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 302 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B VAL* 4.2 13.7 - - + -
82B ILE* 3.4 42.0 - - + +
85B ILE* 4.2 5.8 - - + -
86B ALA* 3.8 22.2 - - + +
89B TYR* 3.9 23.1 - - + -
91B TYR* 4.0 21.1 - - + -
121B ILE* 4.0 19.5 - - - -
298B GLY 2.8 15.3 + - - +
299B ALA* 2.9 12.7 + - - +
301B ALA* 1.3 73.8 - - - +
303B ARG* 1.3 54.7 + - - +
304B LEU 3.0 0.7 - - - -
305B LEU* 3.1 6.9 + - - +
306B THR* 2.7 36.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 303 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B MET* 5.8 1.4 - - - +
89B TYR* 2.7 38.9 + - - +
299B ALA 2.9 9.5 + - - -
300B VAL 3.9 4.5 - - - +
302B MET* 1.3 72.9 - - - +
304B LEU* 1.3 53.4 + - - +
306B THR* 3.2 7.4 - - - -
307B LYS* 2.7 60.0 + - + +
5256B 171 2.8 62.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 304 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B VAL* 3.4 27.1 - - + -
155B PRO* 4.3 11.4 - - + -
156B SER 4.6 1.6 - - - +
157B VAL* 4.2 13.7 - - + -
300B VAL* 2.8 18.2 + - + +
301B ALA 3.2 5.2 - - - +
303B ARG* 1.3 79.0 - - - +
305B LEU* 1.3 63.7 + - - +
307B LYS* 3.2 9.4 + - + +
308B TYR* 3.0 39.6 + - + +
314B VAL* 3.8 30.5 - - + -
316B SER 4.2 7.9 - - - +
317B SER 4.5 7.6 - - - +
319B VAL* 4.6 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 305 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B VAL* 3.6 28.7 - - + -
119B GLY* 3.9 3.8 - - - -
120B ILE 3.2 38.8 - - - +
121B ILE* 3.3 26.2 - - + -
141B PRO* 3.9 17.5 - - + +
142B VAL 4.1 0.2 - - - +
143B VAL* 3.5 15.2 - - + +
301B ALA 2.9 18.4 + - - +
302B MET* 3.4 8.5 - - - +
304B LEU* 1.3 77.0 - - - +
306B THR* 1.3 51.9 + - - +
308B TYR* 3.4 6.7 + - - +
309B MET* 2.7 48.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 306 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B TYR* 3.3 20.2 - - + -
91B TYR* 2.8 28.5 + - - +
302B MET 2.7 22.7 + - - -
303B ARG* 3.2 16.4 - - - +
304B LEU 3.1 0.2 - - - -
305B LEU* 1.3 68.5 - - - +
307B LYS* 1.3 70.0 + - + +
309B MET* 3.0 12.7 + - - +
310B ASN* 2.8 39.2 + - - +
312B GLU* 5.4 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 307 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B ARG* 2.7 46.6 + - + +
304B LEU* 3.6 8.5 - - + +
306B THR* 1.3 72.5 - - + +
308B TYR* 1.3 58.8 + - - +
310B ASN* 2.9 4.0 + - - +
311B LYS 2.9 23.2 + - - -
312B GLU* 3.0 43.6 + - + +
313B THR 4.0 10.3 + - - +
314B VAL* 3.7 30.2 - - + +
315B ASP* 5.5 4.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 308 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B PRO* 3.8 25.1 - - + +
142B VAL 6.1 0.7 - - - -
143B VAL* 5.4 3.6 - - + -
155B PRO* 3.8 24.0 - - + +
304B LEU* 3.0 47.3 + - + -
305B LEU* 3.6 8.1 - - + +
307B LYS* 1.3 72.4 - - - +
309B MET* 1.3 56.8 + - - +
310B ASN 2.8 10.2 + - - -
311B LYS* 2.9 24.4 + - - +
312B GLU 4.9 4.3 - - - -
314B VAL* 3.2 32.0 - - + +
317B SER* 3.1 31.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 309 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B THR* 4.2 7.6 - - + -
63B VAL* 3.8 13.5 - - + -
91B TYR* 3.9 25.4 - - + +
118B ASP* 3.4 49.1 - - + +
119B GLY* 3.4 9.9 - - - -
141B PRO* 3.9 14.1 - - + -
305B LEU* 2.7 50.1 + - + +
306B THR* 3.4 8.5 - - - +
308B TYR* 1.3 72.3 - - - +
310B ASN* 1.3 60.3 + - - +
311B LYS* 3.6 2.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 310 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B TYR* 5.8 0.2 + - - -
306B THR* 2.8 27.2 + - - +
307B LYS 3.4 2.7 - - - +
308B TYR 2.8 0.2 - - - -
309B MET* 1.3 82.5 + - - +
311B LYS* 1.3 68.0 + - - +
312B GLU* 3.1 32.0 + - - +
----------------------------------------------------------
Back to top of page
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