Contacts of the helix formed by residues 280 - 291 (chain A) in PDB entry 6DWM
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 ASP 280 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A PHE* 3.4 24.1 - - - -
200A ALA 4.2 2.7 - - - +
201A ILE 3.6 9.9 - - - +
202A CYS 3.3 15.9 - - - +
203A PHE 2.9 15.4 - - - +
204A GLY* 3.1 9.8 + - - +
269A HIS* 2.8 31.2 + - - -
279A ARG* 1.3 84.0 - - - +
281A ILE* 1.3 64.4 + - - +
282A THR 3.2 1.6 + - - -
283A ASP* 3.0 27.4 + - - +
284A SER 3.3 9.2 + - - -
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Residues in contact with ILE 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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137A LEU 5.9 0.7 - - - +
138A ALA* 6.2 0.9 - - - -
141A GLY* 3.4 36.8 - - - +
142A LEU* 4.0 16.2 - - + +
145A PHE* 4.1 4.3 - - + -
201A ILE* 3.1 37.0 + - + +
202A CYS* 4.2 12.3 - - - -
280A ASP* 1.3 76.3 - - - +
282A THR* 1.3 63.5 + - - +
284A SER* 2.9 25.5 + - - +
285A LEU* 3.1 26.6 + - + +
311A VAL* 4.3 9.0 - - + -
314A LEU* 4.1 18.2 - - + -
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Residues in contact with THR 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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202A CYS 2.7 24.4 + - - -
203A PHE* 3.2 20.4 - - - -
265A MET 4.4 1.8 - - - +
266A VAL* 4.2 21.1 - - + -
269A HIS* 3.8 32.1 - - + -
280A ASP* 3.2 4.7 + - - -
281A ILE* 1.3 77.7 - - - +
283A ASP* 1.3 57.5 + - - +
285A LEU* 3.4 8.2 + - - +
286A ILE* 3.0 33.3 + - + +
308A ILE* 5.0 1.5 - - + +
311A VAL* 3.7 9.6 - - + +
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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
----------------------------------------------------------
269A HIS* 3.2 17.0 - - - +
273A PHE* 3.9 19.5 - - + -
274A GLU 5.4 0.2 + - - -
277A HIS 3.8 5.9 - - - +
278A ILE* 3.7 15.7 - - + -
279A ARG* 2.7 56.0 + - - +
280A ASP* 3.0 20.5 + - - +
282A THR* 1.3 71.4 - - - +
284A SER* 1.3 54.9 + - - +
285A LEU 3.0 2.2 - - - -
286A ILE* 3.1 7.1 + - - +
287A GLU* 2.7 36.3 + - - +
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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
----------------------------------------------------------
137A LEU* 5.9 0.9 - - - +
141A GLY* 4.5 9.1 - - - -
145A PHE* 4.3 11.0 - - - -
278A ILE* 3.5 18.3 - - - +
280A ASP 3.3 5.5 + - - -
281A ILE* 2.9 25.4 + - - +
283A ASP* 1.3 77.6 - - - +
285A LEU* 1.3 61.9 + - - +
287A GLU* 3.9 13.3 - - - +
288A HIS* 3.4 19.6 + - - +
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Residues in contact with LEU 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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137A LEU* 4.5 28.3 - - + +
281A ILE* 3.1 27.7 + - + +
282A THR* 3.7 5.8 - - - +
283A ASP 3.0 0.4 - - - -
284A SER* 1.3 80.0 - - - +
286A ILE* 1.3 60.3 + - - +
287A GLU 3.2 1.1 - - - -
288A HIS* 3.0 5.6 + - + +
289A CYS* 2.9 30.3 + - - -
307A ILE* 3.3 40.0 - - + +
308A ILE* 3.8 24.9 - - + +
310A ILE* 4.4 7.0 - - + -
311A VAL* 3.9 24.0 - - + +
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Residues in contact with ILE 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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266A VAL* 3.8 16.2 - - + +
269A HIS* 3.8 30.3 - - + +
270A TYR* 3.9 33.9 - - + +
273A PHE* 4.2 20.6 - - + -
282A THR* 3.0 22.5 + - + +
283A ASP* 3.6 10.1 - - - +
285A LEU* 1.3 74.2 - - - +
287A GLU* 1.3 63.3 + - - +
289A CYS* 3.1 15.3 + - + +
290A GLN* 3.2 14.3 + - + +
308A ILE* 4.0 18.4 - - + -
603A CPS 4.2 9.4 - - + -
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Residues in contact with GLU 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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273A PHE* 4.0 19.5 - - + -
275A LYS* 3.6 21.9 + - + +
278A ILE* 3.6 29.5 - - + +
283A ASP 2.7 20.7 + - - +
284A SER* 3.9 12.4 - - - +
286A ILE* 1.3 73.5 - - - +
288A HIS* 1.3 62.2 + - - +
290A GLN* 3.3 8.7 + - - +
291A GLU* 3.2 45.9 + - + +
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Residues in contact with HIS 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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137A LEU* 3.8 39.7 - - + +
284A SER 3.4 13.0 + - - +
285A LEU* 3.0 12.1 + - - +
287A GLU* 1.3 78.7 - - - +
289A CYS* 1.3 62.7 + - - +
290A GLN 3.5 0.2 + - - -
291A GLU* 3.5 40.0 + - + +
292A LYS* 3.7 9.3 - - + +
302A LEU* 4.5 7.2 - - + -
307A ILE* 3.6 24.3 - - + +
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Residues in contact with CYS 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 LEU 2.9 16.3 + - - -
286A ILE* 3.1 10.3 + - - +
288A HIS* 1.3 77.6 - - - +
290A GLN* 1.3 59.9 + - + +
292A LYS* 3.1 21.8 - - - +
304A ASP* 3.9 32.8 - - - +
307A ILE* 4.1 16.2 - - - -
308A ILE* 3.8 30.7 - - - -
603A CPS 4.6 14.1 - - + -
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Residues in contact with GLN 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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270A TYR* 3.7 30.3 + - + +
273A PHE* 3.5 34.9 - - - -
275A LYS* 4.9 14.8 - - - +
286A ILE* 3.2 12.2 + - + +
287A GLU* 3.7 8.6 - - - +
288A HIS 3.2 0.2 - - - -
289A CYS* 1.3 75.8 - - + +
291A GLU* 1.3 52.6 + - + +
292A LYS 2.5 27.9 + - - +
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Residues in contact with GLU 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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275A LYS* 5.7 7.5 + - - -
287A GLU* 3.2 38.1 + - + +
288A HIS* 3.5 28.6 + - + +
290A GLN* 1.3 71.4 - - + +
292A LYS* 1.3 62.0 + - - +
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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