Contacts of the helix formed by residues 281 - 296 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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246A TYR* 4.0 9.4 + - + +
277A GLU 4.6 0.6 + - - -
278A VAL 3.6 7.8 + - - +
280A THR* 1.3 85.6 - - + +
282A PHE* 1.3 61.5 + - - +
283A ASP* 3.3 19.1 - - - -
284A GLN* 3.3 54.5 - - + +
285A PHE* 3.4 20.6 + - - +
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Residues in contact with PHE 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278A VAL* 4.0 15.0 - - + -
279A ILE* 3.7 32.1 - - + -
280A THR 5.6 0.4 - - - -
281A CYS* 1.3 73.0 - - - +
283A ASP* 1.3 65.6 + - - +
284A GLN 3.5 0.4 - - - -
285A PHE* 4.1 6.5 - + - -
286A ARG* 2.9 47.8 + - - +
313A LEU* 3.7 28.5 - - + -
316A ARG* 4.2 35.4 - - + -
317A PHE* 4.6 9.6 - + - -
307B GLY 5.9 1.3 - - - -
308B TYR* 5.2 12.8 - + + -
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Residues in contact with ASP 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281A CYS* 3.3 18.5 - - - -
282A PHE* 1.3 85.9 + - - +
284A GLN* 1.3 62.1 + - + +
286A ARG* 3.3 31.8 + - - +
287A LYS* 3.4 17.7 - - - +
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Residues in contact with GLN 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246A TYR* 3.6 39.6 - - + +
281A CYS* 3.3 27.3 - - - +
283A ASP* 1.3 79.7 - - + +
285A PHE* 1.3 64.8 + - - +
286A ARG 3.3 0.7 - - - -
287A LYS* 3.6 32.7 + - + +
288A VAL* 3.7 8.5 + - - +
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Residues in contact with PHE 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242A PRO* 4.5 8.7 - - + -
245A LEU* 4.7 11.2 - - + -
246A TYR* 3.3 28.9 + + - +
273A VAL* 4.1 27.8 - - + -
278A VAL* 3.7 35.2 - - + +
281A CYS 3.4 15.9 + - - +
282A PHE* 4.5 6.1 - + - +
283A ASP 3.5 0.4 - - - -
284A GLN* 1.3 77.7 - - - +
286A ARG* 1.3 55.5 + - - +
288A VAL* 3.1 11.1 + - + +
289A LEU* 2.8 43.8 + - + -
292A LEU* 5.7 1.1 - - + -
299A LEU* 4.1 24.5 - - + -
317A PHE* 4.1 20.2 - + - -
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Residues in contact with ARG 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282A PHE* 2.9 38.0 + - - +
283A ASP* 3.3 24.2 + - - +
285A PHE* 1.3 78.1 - - - +
287A LYS* 1.3 64.0 + - + +
289A LEU* 3.6 15.2 - - + +
290A LYS* 3.0 29.1 + - - +
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Residues in contact with LYS 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283A ASP* 3.4 24.3 + - - +
284A GLN* 3.7 24.6 - - + +
285A PHE 3.2 0.4 - - - -
286A ARG* 1.3 80.5 - - + +
288A VAL* 1.3 64.5 + - + +
290A LYS* 3.6 7.6 + - - +
291A ALA* 3.2 21.3 + - - +
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Residues in contact with VAL 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245A LEU* 3.9 41.7 - - + +
246A TYR* 3.8 31.4 - - + -
252A VAL* 4.2 7.6 - - + -
284A GLN 3.7 2.9 + - - +
285A PHE* 3.1 15.3 + - + +
287A LYS* 1.3 76.1 - - + +
289A LEU* 1.3 60.8 + - - +
291A ALA* 3.1 7.7 + - - +
292A LEU* 2.8 47.9 + - + +
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Residues in contact with LEU 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285A PHE* 2.8 30.5 + - + +
286A ARG* 3.6 15.0 - - + +
288A VAL* 1.3 72.2 - - - +
290A LYS* 1.3 63.0 + - + +
292A LEU* 3.2 12.1 + - - +
293A ARG* 2.9 51.2 + - + +
299A LEU* 4.2 13.9 - - + -
317A PHE* 3.7 42.6 - - + -
318A GLN 5.3 0.2 - - - +
80B ASP* 4.7 12.8 - - - +
81B TYR* 6.2 1.3 - - + -
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Residues in contact with LYS 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286A ARG 3.0 17.8 + - - +
287A LYS* 3.8 7.6 - - - +
289A LEU* 1.3 82.2 - - + +
291A ALA* 1.3 58.0 + - - +
293A ARG* 3.5 4.9 + - - +
294A VAL* 3.0 39.0 + - + +
1B MET* 3.6 30.0 - - - +
81B TYR* 3.6 48.2 - - + +
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Residues in contact with ALA 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252A VAL* 3.6 26.9 - - + +
287A LYS 3.2 11.2 + - - +
288A VAL* 3.1 9.9 + - - +
290A LYS* 1.3 78.2 - - - +
292A LEU* 1.3 58.9 + - - +
294A VAL* 4.0 5.2 - - - +
295A ALA* 3.0 30.0 + - - +
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Residues in contact with LEU 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245A LEU* 5.0 7.2 - - + -
252A VAL* 3.8 16.8 - - + -
255A LEU* 4.8 4.5 - - + -
271A ILE* 4.1 27.1 - - + -
285A PHE* 5.7 1.6 - - + -
288A VAL* 2.8 33.8 + - + +
289A LEU* 3.2 9.6 + - - +
291A ALA* 1.3 74.0 - - - +
293A ARG* 1.3 62.0 + - + +
295A ALA* 3.9 1.5 - - - -
296A GLY 3.0 7.1 + - - -
297A MET* 3.0 65.6 + - + +
298A LYS 5.5 0.7 - - - +
299A LEU* 4.3 27.4 - - + -
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Residues in contact with ARG 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289A LEU* 2.9 35.9 + - + +
290A LYS* 3.9 5.2 - - - +
292A LEU* 1.3 78.1 - - - +
294A VAL* 1.3 62.4 + - - +
296A GLY* 3.4 9.9 + - - -
297A MET 3.9 13.1 + - - -
299A LEU* 3.8 23.0 - - - +
318A GLN 2.8 29.1 + - - -
319A PRO* 3.8 10.3 - - - +
320A ASP* 3.0 30.7 + - - +
78B MET* 6.3 1.0 - - - +
80B ASP* 3.3 28.7 + - - +
81B TYR* 3.7 28.9 - - + +
82B SER* 4.5 0.2 - - - -
83B ALA* 3.7 14.9 + - - +
124B ARG* 6.2 0.6 - - - +
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Residues in contact with VAL 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290A LYS* 3.0 27.6 + - + +
291A ALA* 4.0 5.8 - - - +
293A ARG* 1.3 72.2 - - - +
295A ALA* 1.3 67.0 + - - +
1B MET* 4.6 23.8 - - + -
2B LEU 5.8 0.2 - - - +
81B TYR* 4.0 23.6 - - + -
82B SER 4.6 9.0 - - - +
83B ALA* 3.3 17.2 - - - +
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Residues in contact with ALA 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252A VAL* 4.2 3.6 - - + -
256A MET* 3.8 36.5 - - + +
266A PRO* 3.4 19.6 - - - +
291A ALA 3.0 19.5 + - - +
292A LEU 4.0 1.1 - - - +
294A VAL* 1.3 78.9 - - - +
296A GLY* 1.3 59.5 + - - +
297A MET* 3.6 13.2 - - + -
83B ALA* 4.0 3.9 - - - +
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Residues in contact with GLY 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266A PRO* 3.9 8.7 - - - -
267A ASP* 3.3 25.0 - - - +
292A LEU 3.0 5.5 + - - -
293A ARG* 3.4 5.1 + - - -
294A VAL 3.3 2.4 - - - -
295A ALA* 1.3 78.2 - - - +
297A MET* 1.3 65.7 + - - +
298A LYS* 3.7 4.7 + - - +
83B ALA* 3.6 18.8 - - - -
84B TYR* 6.0 2.0 - - - -
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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