Contacts of the helix formed by residues 280 - 292 (chain A) in PDB entry 3G73
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 280 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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278A LYS* 3.0 6.0 + - - +
279A PRO* 1.3 73.9 - - - +
281A TRP* 1.3 64.9 + - - +
282A LYS 3.1 1.1 - - - -
283A ASN* 3.1 17.2 + - - +
284A SER* 3.0 23.6 + - - -
11C T 5.6 2.2 - - - +
12C A 4.3 17.6 + - - -
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Residues in contact with TRP 281 (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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241A TYR* 3.5 26.3 - + - +
263A TYR* 3.7 38.1 - + - -
266A ILE* 4.0 19.7 - - + -
267A GLU* 3.6 29.3 + - + -
273A PHE* 3.4 41.3 + + + -
277A ALA* 3.8 16.3 + - + -
278A LYS 3.2 25.9 + - - +
279A PRO* 3.0 9.5 + - + +
280A GLY* 1.3 77.5 - - - +
282A LYS* 1.3 77.3 + - + +
284A SER* 3.1 7.0 + - - -
285A ILE* 3.0 50.1 + - + +
11C T 5.4 0.7 - - - -
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Residues in contact with LYS 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A TYR* 3.6 50.5 + - + +
267A GLU* 4.1 11.9 + - - -
279A PRO* 3.3 10.1 + - + +
280A GLY 3.1 0.4 - - - -
281A TRP* 1.3 111.1 - - + +
283A ASN* 1.3 65.3 + - - +
285A ILE* 3.2 4.6 + - - +
286A ARG* 3.1 33.2 + - - +
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Residues in contact with ASN 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A PRO 4.5 0.4 + - - -
280A GLY* 3.1 19.0 + - - +
282A LYS* 1.3 76.5 - - - +
284A SER* 1.3 58.4 + - - +
286A ARG* 3.1 28.9 + - - +
287A HIS* 2.9 26.9 + - - +
12C A 4.1 15.8 + - + +
13C A 2.9 51.2 + - - -
14C A 5.0 2.3 - - - +
10D T 4.5 3.3 - - - +
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Residues in contact with SER 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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241A TYR* 3.6 28.5 - - - -
280A GLY 3.0 12.3 + - - -
281A TRP* 3.1 10.5 + - - -
283A ASN* 1.3 74.2 - - - +
285A ILE* 1.3 64.1 + - - +
287A HIS* 3.5 7.6 + - - +
288A ASN* 2.8 32.0 + - - -
11C T 3.4 38.7 + - - +
12C A 5.4 1.3 + - - -
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Residues in contact with ILE 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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241A TYR* 3.7 23.8 - - + +
245A ILE* 3.8 21.4 - - + +
259A LEU* 3.8 24.7 - - + -
262A ILE* 4.3 10.3 - - + -
263A TYR* 4.0 8.5 - - + -
266A ILE* 3.6 27.8 - - + -
281A TRP* 3.0 37.5 + - + +
282A LYS 3.2 7.8 + - - +
284A SER* 1.3 75.9 - - - +
286A ARG* 1.3 63.0 + - - +
288A ASN* 3.2 4.0 + - - +
289A LEU* 3.0 28.8 + - + +
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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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259A LEU* 3.7 23.8 - - + -
263A TYR* 3.0 31.2 + - - +
282A LYS* 3.1 22.2 + - - +
283A ASN* 3.1 30.4 + - - +
285A ILE* 1.3 75.5 - - - +
287A HIS* 1.3 62.9 + - - +
289A LEU* 3.3 10.6 + - + +
290A SER* 3.1 19.2 + - - -
14C A 5.7 1.0 - - - +
15C C 5.8 0.4 - - - +
8D T 3.7 31.8 - - - +
9D G 3.3 36.0 + - + +
10D T 3.5 21.4 + - + +
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Residues in contact with HIS 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A ASN* 2.9 19.1 + - - +
284A SER* 3.5 7.4 - - - +
286A ARG* 1.3 76.2 - - - +
288A ASN* 1.3 65.8 + - - +
290A SER* 3.4 3.1 + - - -
291A LEU* 2.8 58.7 + - + +
10C A 4.8 5.6 + + - -
11C T 3.2 36.4 + - + +
12C A 3.4 6.8 + - - +
10D T 4.0 9.9 - - - +
11D T 3.0 26.7 + - + +
12D T 3.1 28.6 + + + -
13D A 4.0 5.3 + - - -
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Residues in contact with ASN 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A TYR* 3.7 26.5 - - + +
242A MET* 4.0 10.3 + - - +
245A ILE* 3.7 15.7 - - + -
284A SER* 2.8 30.7 + - - +
285A ILE 3.2 4.2 + - - +
287A HIS* 1.3 84.9 - - - +
289A LEU* 1.3 65.2 + - - +
291A LEU* 4.2 2.4 - - - +
292A HIS* 3.1 56.9 + - + -
295A PHE* 3.6 6.3 - - - -
9C T 5.9 1.6 - - - +
10C A 4.7 7.0 + - - -
11C T 4.7 3.4 - - - +
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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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245A ILE* 3.7 32.8 - - + -
259A LEU* 3.5 32.3 - - + -
262A ILE* 4.6 3.6 - - + -
285A ILE* 3.0 22.1 + - + +
286A ARG* 3.5 11.0 - - + +
288A ASN* 1.3 77.0 - - - +
290A SER* 1.3 50.3 + - - +
292A HIS 3.5 2.3 - - - +
295A PHE* 3.6 19.1 - - + +
308A TRP* 3.6 57.2 - - + +
996A MG 2.3 30.1 - - - -
9D G 5.0 0.2 - - - +
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Residues in contact with SER 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 3.1 8.5 + - - -
289A LEU* 1.3 74.4 - - - +
291A LEU* 1.3 66.0 + - - +
292A HIS 4.6 0.3 - - - -
293A ASP* 4.9 3.8 - - - +
308A TRP* 4.7 0.3 - - - -
996A MG 3.5 7.7 - - - -
9D G 3.4 17.3 - - - +
10D T 2.7 45.4 + - - +
11D T 3.7 28.5 + - - -
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Residues in contact with LEU 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A HIS* 2.8 52.7 + - + +
288A ASN* 3.4 5.1 + - - +
290A SER* 1.3 76.4 - - - +
292A HIS* 1.3 82.7 + - + +
293A ASP* 3.7 8.0 + - - +
291B LEU* 4.3 36.8 - - + -
9C T 5.1 10.1 - - + -
10C A 6.3 0.4 - - - +
11D T 4.6 4.9 - - + +
12D T 5.4 6.7 - - + -
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Residues in contact with HIS 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A MET* 4.1 32.3 - - + +
288A ASN* 3.1 51.5 + - + +
289A LEU 3.5 1.9 - - - +
291A LEU* 1.3 95.3 - - + +
293A ASP* 1.3 56.5 + - - +
294A MET* 4.1 10.8 - - + -
295A PHE* 3.1 24.6 + + + -
996A MG 2.5 25.0 - - - -
9C T 4.2 15.4 + - + -
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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