Contacts of the helix formed by residues 281 - 296 (chain B) in PDB entry 3GG0
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 CYS 281 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B PRO* 3.9 26.7 - - - -
246B TYR* 5.9 7.0 - - - -
277B GLU 3.3 19.5 - - - +
278B VAL* 3.5 5.2 - - - +
279B ILE 3.2 0.8 + - - -
280B THR* 1.3 77.0 - - - +
282B PHE* 1.3 68.3 + - - +
283B ASP* 3.6 2.8 + - - -
284B GLN* 3.2 29.0 + - - +
285B PHE* 3.1 30.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 282 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B VAL* 2.9 21.0 + - + +
279B ILE* 3.9 10.2 + - - +
281B CYS* 1.3 76.7 - - - +
283B ASP* 1.3 65.1 + - + +
285B PHE* 2.7 26.7 + - - +
286B ARG* 3.0 50.9 + - + +
289B LEU* 3.7 20.4 - - + -
313B LEU* 5.0 4.9 - - + -
316B ARG* 3.7 37.0 - - + -
317B PHE* 3.6 42.0 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 283 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B ILE 5.8 0.3 - - - +
281B CYS 5.6 0.3 + - - -
282B PHE* 1.3 84.6 + - + +
284B GLN* 1.3 83.2 + - - +
286B ARG* 3.5 30.0 + - - +
287B LYS* 4.4 9.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 284 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B TYR* 3.4 47.5 + - + +
280B THR 4.3 4.0 + - - -
281B CYS* 3.5 35.8 + - - +
282B PHE 3.1 0.2 - - - -
283B ASP* 1.3 90.6 + - - +
285B PHE* 1.3 59.9 + - - +
287B LYS* 3.5 20.9 - - - +
288B VAL* 5.2 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 285 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B PRO* 3.3 49.6 - - + -
245B LEU* 3.9 28.9 - - + -
246B TYR* 4.4 9.0 - - + -
273B VAL* 4.3 15.3 - - + -
278B VAL* 4.6 18.8 - - + -
281B CYS* 3.1 22.8 + - - +
282B PHE* 2.7 11.8 + - - +
284B GLN* 1.3 77.2 - - - +
286B ARG* 1.3 64.3 + - - +
287B LYS 3.3 2.0 - - - -
288B VAL* 3.2 27.4 + - + -
289B LEU* 3.2 41.9 + - + +
292B LEU* 6.2 0.2 - - + -
299B LEU* 5.8 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 286 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A TYR* 6.1 2.8 - - - -
282B PHE* 3.0 53.0 + - + +
283B ASP* 3.5 22.2 - - - +
284B GLN 3.3 1.4 - - - -
285B PHE* 1.3 78.8 - - - +
287B LYS* 1.3 59.8 + - + +
289B LEU* 3.2 12.9 + - + +
290B LYS* 3.0 32.5 + - - +
316B ARG 5.2 5.9 + - - -
317B PHE* 5.6 3.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 287 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B TYR* 4.8 11.7 - - + -
283B ASP 4.4 8.1 + - - -
284B GLN* 3.5 25.7 - - - +
285B PHE 3.3 0.4 - - - -
286B ARG* 1.3 77.1 - - + +
288B VAL* 1.3 60.0 + - + +
290B LYS* 3.7 10.7 + - - +
291B ALA* 3.2 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 288 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B LEU* 3.6 47.8 - - + +
246B TYR* 4.3 16.4 - - + +
252B VAL* 4.3 15.3 - - + -
284B GLN 5.2 0.4 - - - +
285B PHE* 3.6 28.5 - - + +
286B ARG 3.2 0.4 - - - -
287B LYS* 1.3 81.3 - - + +
289B LEU* 1.3 64.6 + - - +
290B LYS 3.2 0.2 - - - -
291B ALA* 3.3 6.1 + - - +
292B LEU* 3.0 27.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 289 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B VAL* 5.5 0.7 - - + -
278B VAL* 5.7 1.6 - - + -
282B PHE* 3.7 32.8 - - + -
285B PHE* 3.2 45.8 - - + +
286B ARG* 3.2 12.3 + - - +
288B VAL* 1.3 75.6 - - - +
290B LYS* 1.3 62.0 + - - +
292B LEU* 3.4 10.0 + - + +
293B ARG* 3.2 27.2 + - - +
299B LEU* 3.7 28.2 - - + +
317B PHE* 4.5 26.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 290 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 3.5 24.7 - - - +
81A TYR* 3.6 54.7 - - + +
286B ARG* 3.0 19.5 + - - +
287B LYS* 3.7 10.3 - - - +
289B LEU* 1.3 77.4 - - - +
291B ALA* 1.3 62.5 + - - +
293B ARG* 3.2 9.1 + - - +
294B VAL* 3.1 30.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 291 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250B ASP* 5.9 0.4 - - - +
252B VAL* 3.7 26.8 - - + +
287B LYS 3.2 15.6 + - - +
288B VAL* 3.3 2.0 + - - +
290B LYS* 1.3 81.0 - - - +
292B LEU* 1.3 57.4 + - - +
294B VAL* 3.5 7.2 + - - +
295B ALA* 2.9 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 292 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B LEU* 4.5 18.2 - - + -
252B VAL* 3.9 18.8 - - + -
255B LEU* 4.6 8.3 - - + -
271B ILE* 4.2 21.5 - - + -
285B PHE* 6.2 0.4 - - + -
288B VAL* 3.0 24.2 + - + +
289B LEU* 3.7 5.8 - - + +
290B LYS 3.3 0.2 - - - -
291B ALA* 1.3 74.7 - - - +
293B ARG* 1.3 64.1 + - + +
295B ALA* 3.4 1.1 + - - +
296B GLY 3.1 17.0 + - - -
297B MET* 3.1 54.3 + - + +
298B LYS 5.6 1.1 - - - +
299B LEU* 3.9 28.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 293 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A ASP* 2.8 36.9 + - - +
81A TYR* 4.1 25.1 - - + +
82A SER 4.9 0.4 - - - -
83A ALA* 3.4 16.2 + - - +
124A ARG* 5.7 3.2 - - - +
289B LEU 3.2 15.5 + - - +
290B LYS* 3.2 11.4 + - - +
292B LEU* 1.3 76.7 - - - +
294B VAL* 1.3 62.5 + - - +
296B GLY* 3.0 12.8 + - - -
297B MET 4.3 8.3 + - - +
298B LYS* 5.8 2.1 - - - +
299B LEU* 4.5 8.9 - - - +
317B PHE* 4.9 9.4 - - - +
318B GLN 3.0 26.8 + - - +
319B PRO* 3.7 3.4 - - - +
320B ASP* 3.0 44.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 294 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 3.7 34.8 - - + -
2A LEU 6.4 0.4 - - - +
81A TYR* 4.2 12.3 - - + -
82A SER 4.2 16.2 - - - +
83A ALA* 3.5 15.6 - - - +
290B LYS* 3.1 21.7 + - + +
291B ALA* 3.9 6.7 - - - +
293B ARG* 1.3 74.2 - - - +
295B ALA* 1.3 63.3 + - - +
296B GLY 3.4 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 295 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A ALA* 4.5 1.3 - - - +
252B VAL* 3.7 20.0 - - + -
256B MET* 3.8 23.5 - - + +
266B PRO* 3.5 18.3 - - - +
291B ALA 2.9 18.8 + - - +
292B LEU 3.6 5.2 - - - +
294B VAL* 1.3 78.2 - - - +
296B GLY* 1.3 58.0 + - - +
297B MET* 3.6 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 296 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A ALA* 3.6 15.5 - - - -
84A TYR* 6.1 0.7 - - - -
266B PRO* 3.7 10.5 - - - -
267B ASP* 3.3 25.0 - - - +
292B LEU 3.1 0.6 + - - -
293B ARG 3.0 15.1 + - - -
295B ALA* 1.3 79.5 - - - +
297B MET* 1.3 64.8 + - - +
298B LYS* 3.9 8.7 + - - +
----------------------------------------------------------
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