Contacts of the helix formed by residues 279 - 290 (chain A) in PDB entry 1MD9
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 VAL 279 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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230A LEU* 3.9 13.8 - - + +
236A TYR* 4.4 10.1 - - + -
278A LEU* 1.3 79.0 - - - +
280A PRO* 1.3 74.8 - - + +
281A PRO* 4.0 4.9 - - + -
282A LEU* 3.5 20.1 + - + -
283A ALA* 3.0 18.9 + - - +
305A VAL* 4.0 1.6 - - - -
306A GLY 3.2 12.6 - - - +
307A GLY* 4.6 1.3 - - - -
517A VAL* 4.1 34.3 - - + +
518A GLY* 3.9 22.7 - - - +
519A LYS* 4.1 10.3 - - + -
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Residues in contact with PRO 280 (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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279A VAL* 1.3 78.4 - - + +
281A PRO* 1.4 74.1 - - + +
283A ALA* 2.9 23.8 + - + +
284A MSE 3.1 18.0 + - + +
305A VAL* 4.1 10.1 - - + -
306A GLY 2.9 20.9 - - - +
307A GLY 4.7 0.4 - - - -
308A ALA* 3.3 37.0 - - + +
309A LYS 3.5 16.8 - - - +
310A PHE* 4.5 9.0 - - + -
457A ASP* 5.9 0.4 - - - -
519A LYS* 5.7 0.9 - - + -
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Residues in contact with PRO 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A VAL* 3.6 10.8 - - + -
280A PRO* 1.4 101.5 - - + +
282A LEU* 1.3 59.4 + - - +
284A MSE 3.5 10.5 + - + +
285A VAL* 3.3 16.6 - - - +
308A ALA* 5.7 1.1 - - + -
456A HIS* 4.9 2.3 - - - -
457A ASP* 4.0 17.0 - - - +
514A GLN* 3.6 24.2 - - - +
518A GLY 3.9 5.8 - - - +
519A LYS* 4.7 2.5 - - - -
520A VAL* 3.3 39.9 - - + +
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Residues in contact with LEU 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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229A ALA 4.8 0.9 - - - +
230A LEU* 3.7 21.5 - - + -
259A PRO* 3.6 35.0 - - + +
260A SER* 5.3 1.8 - - - -
261A PRO* 5.4 0.9 - - + -
278A LEU* 3.5 26.7 - - + -
279A VAL* 3.5 15.8 + - + +
280A PRO 3.2 0.4 - - - -
281A PRO* 1.3 77.7 - - - +
283A ALA* 1.3 60.0 + - - +
285A VAL* 3.2 14.2 + - + +
286A TRP* 3.0 49.9 + - + +
514A GLN* 5.4 0.4 - - - +
518A GLY 5.3 0.9 + - - +
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Residues in contact with ALA 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A LEU* 4.0 18.4 - - + -
279A VAL 3.0 14.9 + - - +
280A PRO* 2.9 17.4 + - + +
282A LEU* 1.3 74.8 - - - +
284A MSE 1.3 64.7 + - - +
286A TRP* 3.4 2.4 + - - +
287A MSE 3.0 28.9 + - + +
303A LEU* 6.3 0.9 - - + -
305A VAL* 3.9 17.5 - - + -
310A PHE* 4.0 15.9 - - + -
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Residues in contact with MSE 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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280A PRO* 3.1 21.5 + - + +
281A PRO 3.7 7.6 - - - +
282A LEU 3.2 0.4 - - - -
283A ALA* 1.3 77.8 - - - +
285A VAL* 1.3 62.9 + - - +
287A MSE 3.0 14.1 + - - +
288A ASP* 3.0 24.1 + - - +
310A PHE* 3.2 39.7 - - + -
311A SER 5.8 0.9 - - - +
314A ALA* 3.5 20.2 - - + -
317A ARG* 5.7 3.1 - - - -
450A LEU* 4.6 17.9 - - + -
456A HIS* 3.4 37.9 - - + +
457A ASP* 4.2 17.0 - - - +
479A ARG* 6.0 1.8 - - - +
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Residues in contact with VAL 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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261A PRO* 4.5 13.5 - - + -
281A PRO 3.3 19.3 - - - +
282A LEU* 3.5 19.7 - - + +
284A MSE 1.3 73.5 - - - +
286A TRP* 1.3 65.1 + - + +
288A ASP* 3.3 8.3 + - + +
289A ALA* 2.9 25.2 + - + +
456A HIS* 3.9 16.8 + - + +
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Residues in contact with TRP 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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227A LEU* 4.3 0.9 - - + -
229A ALA* 4.2 6.1 - - + -
259A PRO 2.8 23.1 + - - -
261A PRO* 3.8 17.0 - - + +
264A ALA* 3.3 33.7 - - + -
265A PHE* 3.6 22.5 - + - -
268A ILE* 3.7 25.4 - - + -
276A THR* 3.7 30.7 - - + -
278A LEU* 3.2 35.4 - - + +
282A LEU* 3.0 35.5 + - + +
283A ALA 3.6 8.5 - - - +
285A VAL* 1.3 76.5 - - - +
287A MSE 1.3 58.2 + - - +
289A ALA 3.2 0.3 + - - -
290A ALA* 2.8 28.6 + - - +
300A LEU* 5.2 1.1 - - + -
303A LEU* 4.4 3.8 - - + -
322A PHE* 3.5 20.6 - + + -
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Residues in contact with MSE 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 ALA* 3.0 17.2 + - + +
284A MSE 3.0 13.2 + - - +
286A TRP* 1.3 74.1 - - - +
288A ASP* 1.3 57.5 + - - +
290A ALA* 2.6 32.2 + - - +
291A SER* 3.8 5.1 + - - -
310A PHE* 4.9 7.9 - - + -
314A ALA* 4.3 18.6 - - - +
317A ARG* 3.4 63.9 - - + +
318A VAL* 3.9 6.7 - - + +
321A VAL* 3.5 34.7 - - + +
322A PHE* 3.7 22.9 - - + -
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Residues in contact with ASP 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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284A MSE 3.0 6.9 + - - +
285A VAL* 3.6 11.6 - - + +
287A MSE 1.3 79.3 - - - +
289A ALA* 1.3 60.1 + - - +
291A SER* 3.9 3.9 + - - -
292A SER* 3.4 25.8 + - - -
317A ARG* 5.4 4.8 + - - +
456A HIS* 2.8 37.0 + - - -
479A ARG* 2.6 27.0 + - - -
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Residues in contact with ALA 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A PRO* 3.5 31.6 - - + -
265A PHE* 3.5 7.6 - - + -
285A VAL* 2.9 17.4 + - + +
286A TRP 3.6 0.9 - - - +
288A ASP* 1.3 72.8 - - - +
290A ALA* 1.3 53.8 + - - +
291A SER 2.5 20.0 + - - -
292A SER* 4.5 3.6 - - - +
293A ARG* 2.9 37.4 + - - +
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Residues in contact with ALA 290 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A PHE* 3.8 9.8 - - + -
286A TRP 2.8 13.1 + - - +
287A MSE 2.6 10.9 + - - +
289A ALA* 1.3 66.7 - - - +
291A SER* 1.3 64.1 + - - +
293A ARG 5.0 4.0 - - - -
294A ARG* 5.7 0.9 - - - -
297A LEU* 4.7 6.1 - - + -
321A VAL* 3.2 39.6 - - + +
322A PHE* 3.9 15.5 - - + -
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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