Contacts of the helix formed by residues 318 - 330 (chain A) in PDB entry 4MCA
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 ALA 318 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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309A LEU* 5.1 5.2 - - + -
314A VAL* 3.7 30.5 - - + -
315A SER* 4.5 5.4 - - - +
316A GLY 3.0 11.3 + - - +
317A ASP* 1.3 71.5 - - - +
319A VAL* 1.3 55.9 + - - +
320A GLU 3.3 2.7 - - - -
321A LYS* 3.2 14.7 + - + -
322A ILE* 2.8 45.6 + - + +
353A LEU* 5.3 4.9 - - + -
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Residues in contact with VAL 319 (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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317A ASP* 3.0 22.1 + - - +
318A ALA* 1.3 76.9 - - - +
320A GLU* 1.3 58.6 + - + +
322A ILE* 3.6 1.9 + - - -
323A MET* 3.1 14.6 + - + +
349A GLN* 3.0 37.1 + - - +
353A LEU* 5.0 14.6 - - + +
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Residues in contact with GLU 320 (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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317A ASP* 4.7 3.9 + - - +
318A ALA 3.3 0.2 - - - -
319A VAL* 1.3 77.9 - - - +
321A LYS* 1.3 71.1 + - + +
323A MET* 3.4 8.0 + - - +
324A ALA* 3.1 21.1 + - + +
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Residues in contact with LYS 321 (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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263A LEU* 3.8 25.8 - - + +
265A GLU* 2.6 35.4 + - - +
314A VAL* 4.8 7.0 - - + -
315A SER 5.4 6.7 - - - +
317A ASP 5.3 4.2 + - - +
318A ALA* 3.2 25.1 + - + +
320A GLU* 1.3 84.9 - - + +
322A ILE* 1.3 61.4 + - + +
324A ALA* 3.3 7.5 + - - +
325A VAL* 2.9 29.6 + - - +
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Residues in contact with ILE 322 (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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260A PHE* 4.0 17.7 - - + -
263A LEU* 4.4 6.3 - - + -
309A LEU* 4.0 27.8 - - + -
314A VAL* 4.7 6.1 - - + -
318A ALA* 2.8 31.8 + - + +
319A VAL 4.2 2.5 - - - +
321A LYS* 1.3 74.7 - - + +
323A MET* 1.3 60.3 + - - +
325A VAL* 3.2 7.0 + - + +
326A ALA* 2.8 28.2 + - - +
349A GLN* 3.9 22.2 - - + +
352A ILE* 3.6 32.8 - - + -
353A LEU* 4.2 17.0 - - + -
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Residues in contact with MET 323 (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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319A VAL* 3.1 19.1 + - + +
320A GLU* 3.8 7.9 - - - +
321A LYS 3.3 0.2 - - - -
322A ILE* 1.3 77.8 - - - +
324A ALA* 1.3 54.6 + - - +
326A ALA* 3.3 2.1 + - - +
327A GLN* 2.9 46.4 + - + +
345A PRO* 4.3 27.8 - - - +
346A ALA* 4.5 13.7 - - + -
349A GLN* 3.5 33.8 - - + +
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Residues in contact with ALA 324 (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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262A VAL* 4.3 16.1 - - + +
263A LEU* 5.1 2.0 - - + -
320A GLU* 3.1 13.9 + - + +
321A LYS* 3.3 12.5 + - - +
323A MET* 1.3 72.6 - - - +
325A VAL* 1.3 66.1 + - - +
327A GLN* 3.5 6.4 + - - +
328A ALA* 3.1 24.4 + - - +
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Residues in contact with VAL 325 (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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256A ILE* 4.1 5.6 - - + +
259A GLY* 3.6 35.4 - - - +
260A PHE* 3.7 23.6 - - + +
262A VAL* 4.4 0.4 - - + -
263A LEU* 3.7 29.2 - - + -
321A LYS 2.9 18.8 + - - +
322A ILE* 3.2 11.2 + - + +
324A ALA* 1.3 75.7 - - - +
326A ALA* 1.3 58.4 + - - +
328A ALA 3.3 0.3 + - - -
329A SER* 2.9 27.0 + - - -
352A ILE* 3.8 24.0 - - + -
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Residues in contact with ALA 326 (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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322A ILE 2.8 19.6 + - - +
323A MET* 3.5 6.5 - - - +
325A VAL* 1.3 71.3 - - - +
327A GLN* 1.3 62.9 + - - +
329A SER* 2.8 22.9 + - - -
330A CYS* 3.2 14.6 + - - -
345A PRO* 3.4 30.1 - - + +
348A VAL* 3.9 9.0 - - + -
349A GLN* 3.7 17.0 - - + +
352A ILE* 5.4 0.4 - - + -
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Residues in contact with GLN 327 (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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323A MET* 2.9 35.2 + - + +
324A ALA* 3.9 7.0 - - - +
326A ALA* 1.3 71.3 - - - +
328A ALA* 1.3 65.5 - - - +
330A CYS* 3.2 12.0 + - - +
331A ALA* 3.3 11.3 + - - +
345A PRO* 3.6 31.7 - - + +
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Residues in contact with ALA 328 (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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258A ASN* 5.1 1.6 - - - +
259A GLY* 3.9 15.8 + - - -
262A VAL* 4.1 19.1 - - + -
324A ALA 3.1 15.7 + - - +
325A VAL 3.6 4.0 - - - +
327A GLN* 1.3 79.3 - - - +
329A SER* 1.3 61.6 + - - +
330A CYS 3.3 0.5 + - - -
331A ALA* 3.4 19.6 + - - +
334A GLU* 3.9 8.3 - - - +
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Residues in contact with SER 329 (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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255A ALA* 3.3 36.1 - - - +
256A ILE* 4.0 13.7 - - - -
259A GLY* 4.2 0.6 - - - -
325A VAL 2.9 14.2 + - - -
326A ALA 2.8 15.1 + - - -
327A GLN 3.2 0.2 - - - -
328A ALA* 1.3 76.9 - - - +
330A CYS* 1.3 60.4 + - - +
331A ALA 3.4 0.2 - - - -
334A GLU* 3.2 22.7 - - - +
336A ILE* 3.4 11.9 - - - +
348A VAL* 3.4 20.9 - - - +
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Residues in contact with CYS 330 (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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326A ALA 3.2 16.2 + - - +
327A GLN 3.7 5.2 - - - +
328A ALA 3.2 0.6 - - - -
329A SER* 1.3 79.3 + - - +
331A ALA* 1.3 66.6 + - - +
332A ALA* 3.6 0.3 + - - -
336A ILE* 4.0 9.6 - - - -
337A HIS* 3.0 16.9 + - + +
343A VAL* 4.0 11.4 - - - +
344A THR* 3.7 4.5 - - - -
345A PRO* 3.6 32.1 - - + -
348A VAL* 3.6 28.3 - - - -
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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