Contacts of the helix formed by residues 284 - 295 (chain A) in PDB entry 4MFU
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 284 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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281A GLY 3.1 7.0 + - - -
282A GLU 3.7 1.4 - - - -
283A LEU* 1.3 75.9 - - - +
285A GLY* 1.3 62.0 + - - +
286A ILE* 3.5 13.9 - - - +
287A ASP* 2.7 41.7 - - - +
288A VAL* 3.4 15.1 - - - +
329A ARG* 5.7 1.9 - - - +
332A LYS* 5.1 8.0 + - - -
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Residues in contact with GLY 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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246A LEU* 4.0 11.7 - - - -
280A LEU* 3.3 28.1 + - - -
283A LEU 3.1 5.4 - - - -
284A ASP* 1.3 72.9 - - - +
286A ILE* 1.3 60.0 + - - +
287A ASP 3.1 1.3 - - - -
288A VAL* 2.6 33.8 + - - +
289A LEU* 2.8 15.6 + - - +
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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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280A LEU* 3.5 11.7 - - + +
281A GLY* 4.7 1.6 - - - -
284A ASP* 3.5 12.1 - - - +
285A GLY* 1.3 82.8 - - - +
287A ASP* 1.3 73.6 + - - +
289A LEU* 3.6 6.9 - - + +
290A LEU* 2.8 44.9 + - + +
317A LEU* 3.9 23.8 - - + -
320A CYS* 4.6 6.5 - - + -
321A LEU* 5.4 1.1 - - + -
326A ASN* 4.2 24.2 - - + +
329A ARG* 3.8 42.8 - - + +
330A PHE* 4.9 6.7 - - - +
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Residues in contact with ASP 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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284A ASP* 2.7 41.0 - - - +
285A GLY 3.1 0.2 - - - -
286A ILE* 1.3 87.8 - - - +
288A VAL* 1.3 54.8 + - + +
290A LEU* 3.2 6.6 + - - +
291A GLN* 2.7 38.3 + - - +
329A ARG 5.1 1.0 - - - +
332A LYS* 5.2 2.9 + - - +
333A GLY* 4.0 22.2 + - - -
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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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246A LEU* 4.5 24.7 - - + +
249A LEU* 4.8 5.6 - - + -
250A LYS* 4.5 28.7 - - + +
283A LEU 5.3 2.0 - - - +
284A ASP 3.4 16.8 - - - +
285A GLY* 2.6 20.5 + - - +
287A ASP* 1.3 68.3 - - + +
289A LEU* 1.3 73.0 + - + +
291A GLN* 3.0 10.0 + - - +
292A GLN* 2.9 35.9 + - + +
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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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246A LEU* 5.4 4.0 - - + -
249A LEU* 5.4 2.5 - - + -
266A LEU* 4.1 24.0 - - + -
280A LEU* 4.6 7.0 - - + -
285A GLY 2.8 17.8 + - - +
286A ILE* 3.6 12.3 - - - +
288A VAL* 1.3 79.8 - - + +
290A LEU* 1.3 65.7 + - - +
292A GLN* 2.7 14.9 + - + +
293A LEU* 2.7 23.5 + - + +
313A LEU* 4.4 17.9 - - + +
316A SER* 4.0 9.0 - - - -
317A LEU* 3.4 47.6 - - + +
320A CYS* 4.3 12.3 - - - -
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Residues in contact with LEU 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 ILE* 2.8 37.1 + - + +
287A ASP* 3.5 5.2 - - - +
289A LEU* 1.3 74.0 - - - +
291A GLN* 1.3 51.8 + - - +
293A LEU* 3.1 6.8 + - + +
294A SER* 2.5 36.3 + - - -
317A LEU* 3.9 25.8 - - + -
330A PHE* 4.2 14.4 - - + +
333A GLY* 4.1 26.7 - - - -
334A GLU 4.7 1.3 - - - +
335A GLY* 4.0 25.6 - - - -
338A LEU* 3.9 13.5 - - + +
339A MET* 4.3 14.4 - - + -
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Residues in contact with GLN 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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250A LYS* 4.3 27.0 + - - +
287A ASP 2.7 21.0 + - - +
288A VAL* 3.5 7.5 - - - +
290A LEU* 1.3 72.0 - - - +
292A GLN* 1.3 74.2 + - - +
294A SER* 2.7 34.7 + - - +
295A VAL* 3.2 15.4 + - + +
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Residues in contact with GLN 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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249A LEU* 3.6 21.3 + - + +
250A LYS* 4.3 10.7 + - - +
259A LYS* 3.0 30.9 + - - +
288A VAL* 2.9 26.3 + - + +
289A LEU* 2.7 12.6 + - - +
291A GLN* 1.3 88.7 + - - +
293A LEU* 1.3 60.2 + - - +
295A VAL* 3.2 25.5 - - - +
296A PHE* 3.3 9.4 - - - -
309A MET* 5.4 1.3 - - + +
313A LEU* 3.4 31.6 - - + +
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Residues in contact with LEU 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* 2.7 42.4 - - + +
290A LEU* 3.1 10.7 + - + +
292A GLN* 1.3 75.3 - - - +
294A SER* 1.3 67.3 + - - +
296A PHE* 3.1 18.5 + - - +
310A MET* 4.3 4.5 - - + +
313A LEU* 3.6 33.7 - - + +
314A PHE* 3.7 46.4 - - + +
317A LEU* 4.4 13.0 - - + -
338A LEU* 5.3 0.4 - - + -
339A MET* 5.2 5.2 - - + -
342A MET* 3.1 30.6 - - + +
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Residues in contact with SER 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 LEU 2.5 18.1 + - - -
291A GLN* 2.7 28.8 + - - +
293A LEU* 1.3 72.7 - - - +
295A VAL* 1.3 55.5 + - - -
297A LYS* 2.8 53.0 + - - +
338A LEU* 3.8 19.4 - - - +
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Residues in contact with VAL 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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291A GLN* 3.8 18.4 - - + +
292A GLN* 3.2 20.9 - - - +
294A SER* 1.3 76.7 - - - +
296A PHE* 1.3 82.8 + - + +
297A LYS* 3.2 6.8 + - - +
299A HIS* 3.2 27.2 + - - -
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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