Contacts of the helix formed by residues 280 - 291 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145D PHE* 3.4 24.8 - - - -
200D ALA 4.3 2.0 - - - +
201D ILE 3.6 12.6 - - - +
202D CYS 3.6 12.3 - - - +
203D PHE 3.0 12.3 - - - +
204D GLY* 3.3 9.7 + - - +
269D HIS* 2.4 37.6 + - - -
279D ARG* 1.3 83.6 - - - +
281D ILE* 1.3 65.4 + - - +
282D THR 3.2 1.4 + - - -
283D ASP* 3.0 27.4 + - - +
284D SER 3.2 8.8 + - - -
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Residues in contact with ILE 281 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137D LEU 5.8 1.1 - - - +
138D ALA* 6.1 0.9 - - - -
141D GLY* 3.6 35.4 - - - +
142D LEU* 4.1 6.7 - - + -
145D PHE* 3.9 4.7 - - + -
201D ILE* 3.3 34.4 + - + +
202D CYS* 4.0 14.1 + - - -
280D ASP* 1.3 76.3 - - - +
282D THR* 1.3 62.9 + - - +
284D SER* 2.9 23.5 + - - +
285D LEU* 3.0 30.4 + - + +
310D ILE* 6.2 0.2 - - + -
311D VAL* 4.4 6.3 - - + -
314D LEU* 3.9 30.3 - - + -
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Residues in contact with THR 282 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202D CYS 2.7 23.1 + - - -
203D PHE* 3.4 17.0 - - - -
265D MET 4.4 1.1 - - - +
266D VAL* 4.2 23.1 - - + -
269D HIS* 3.8 29.2 - - + -
280D ASP* 3.2 6.6 + - - -
281D ILE* 1.3 79.0 - - - +
283D ASP* 1.3 56.5 + - - +
285D LEU* 3.3 9.7 + - - +
286D ILE* 2.9 36.7 + - + +
308D ILE* 5.1 1.9 - - + +
311D VAL* 3.7 7.9 - - + +
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Residues in contact with ASP 283 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269D HIS* 3.5 14.2 - - - +
273D PHE* 3.8 24.4 - - + -
277D HIS 3.8 4.9 - - - +
278D ILE* 3.5 18.6 - - + -
279D ARG* 2.6 57.7 + - - +
280D ASP* 3.0 16.9 + - - +
282D THR* 1.3 76.8 - - - +
284D SER* 1.3 52.2 + - - +
286D ILE* 3.0 5.5 + - - +
287D GLU* 2.7 35.7 + - - +
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Residues in contact with SER 284 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137D LEU* 5.7 1.0 + - - +
141D GLY* 4.6 9.3 - - - -
144D SER* 6.3 0.4 - - - -
145D PHE* 4.3 8.7 - - - -
278D ILE* 3.3 18.5 - - - +
280D ASP 3.2 5.4 + - - -
281D ILE* 2.9 24.8 + - - +
283D ASP* 1.3 78.4 - - - +
285D LEU* 1.3 62.5 + - - +
287D GLU* 3.9 12.6 - - - +
288D HIS* 3.3 22.5 + - - +
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Residues in contact with LEU 285 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137D LEU* 4.3 32.3 - - + +
138D ALA* 6.2 0.2 - - - -
281D ILE* 3.0 37.1 + - + +
282D THR* 3.7 5.2 - - - +
284D SER* 1.3 82.5 - - - +
286D ILE* 1.3 60.8 + - - +
287D GLU 3.3 0.2 - - - -
288D HIS* 3.2 4.3 + - + +
289D CYS* 2.9 31.9 + - - -
307D ILE* 3.4 36.1 - - + +
308D ILE* 4.0 14.1 - - + +
310D ILE* 4.3 8.7 - - + -
311D VAL* 4.0 25.4 - - + +
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Residues in contact with ILE 286 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266D VAL* 4.0 16.8 - - + +
269D HIS* 4.1 5.2 - - + +
270D TYR* 3.6 51.1 - - + +
273D PHE* 4.0 24.5 - - + -
282D THR* 2.9 34.2 + - + +
283D ASP* 3.5 12.6 - - - +
285D LEU* 1.3 76.2 - - - +
287D GLU* 1.3 62.6 + - - +
289D CYS* 3.1 15.0 + - - +
290D GLN* 3.3 16.0 + - - +
308D ILE* 4.2 18.8 - - + -
603D CPS 5.1 2.2 - - + -
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Residues in contact with GLU 287 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273D PHE* 4.1 16.4 - - + -
275D LYS* 3.5 27.9 - - + +
278D ILE* 3.7 24.0 - - + +
283D ASP 2.7 19.4 + - - +
284D SER* 3.9 10.5 - - - +
286D ILE* 1.3 73.4 - - - +
288D HIS* 1.3 60.2 + - - +
290D GLN* 3.3 10.4 + - - +
291D GLU* 3.2 43.7 + - + +
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Residues in contact with HIS 288 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137D LEU* 3.6 46.3 - - + +
284D SER 3.3 15.6 + - - +
285D LEU* 3.2 8.2 + - - +
286D ILE 3.2 0.8 - - - -
287D GLU* 1.3 77.4 - - - +
289D CYS* 1.3 65.3 + - - +
290D GLN 3.4 0.3 + - - -
291D GLU* 3.5 33.3 + - + +
302D LEU* 5.4 6.1 - - + -
307D ILE* 3.8 21.2 - - + +
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Residues in contact with CYS 289 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285D LEU 2.9 11.9 + - - -
286D ILE* 3.1 10.3 + - - +
288D HIS* 1.3 76.5 - - - +
290D GLN* 1.3 63.6 + - + +
291D GLU 4.6 1.7 - - - -
304D ASP* 3.8 31.4 - - - +
307D ILE* 3.5 38.6 - - - -
308D ILE* 3.9 22.9 - - - -
603D CPS 4.9 9.9 - - + -
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Residues in contact with GLN 290 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270D TYR* 4.0 21.2 + - + +
273D PHE* 3.9 27.8 - - - -
275D LYS* 3.8 32.4 + - - +
286D ILE* 3.3 16.2 + - + +
287D GLU* 3.6 9.7 - - - +
288D HIS 3.2 0.4 - - - -
289D CYS* 1.3 78.3 - - + +
291D GLU* 1.3 67.5 + - + +
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Residues in contact with GLU 291 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275D LYS* 5.6 8.2 - - - +
287D GLU* 3.2 39.3 + - + +
288D HIS* 3.5 30.3 + - + +
289D CYS 4.6 2.0 - - - -
290D GLN* 1.3 82.2 - - + +
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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