Contacts of the helix formed by residues 299 - 313 (chain A) in PDB entry 5MCO
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 LYS 299 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297A LEU 3.4 0.4 + - - -
298A PRO* 1.3 70.1 - - - +
300A LYS* 1.3 83.1 + - + +
302A PHE* 3.1 6.5 + - - +
303A GLU* 3.0 46.8 + - - +
387A GLN* 3.3 29.6 + - + +
388A SER 3.4 11.3 + - - +
389A SER* 6.2 1.6 - - - -
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Residues in contact with LYS 300 (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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276A MET* 3.8 20.2 - - + +
280A GLU* 3.5 38.2 + - - +
298A PRO* 3.4 2.7 - - + +
299A LYS* 1.3 96.8 - - + +
301A VAL* 1.3 62.2 + - + +
303A GLU* 3.7 8.3 + - - +
304A ALA* 3.3 22.0 + - - +
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Residues in contact with VAL 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A VAL* 5.3 3.1 - - + -
274A LEU* 4.3 9.6 - - + +
276A MET* 3.9 15.3 - - - -
280A GLU* 3.3 36.1 - - + +
281A TYR* 3.9 28.5 - - + -
297A LEU* 4.2 24.5 - - + -
298A PRO* 2.9 17.8 + - + +
300A LYS* 1.3 76.6 - - + +
302A PHE* 1.3 66.0 + - - +
304A ALA* 3.5 0.9 + - - +
305A ALA* 3.0 23.0 + - - +
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Residues in contact with PHE 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A LEU* 3.9 19.6 - - + +
298A PRO 2.7 16.2 + - - +
299A LYS 3.4 7.2 - - - +
301A VAL* 1.3 74.9 - - - +
303A GLU* 1.3 74.7 + - + +
305A ALA* 3.7 1.4 - - - +
306A VAL* 3.0 46.0 + - + +
323A TRP* 3.7 21.3 - - + -
324A LEU* 4.6 17.3 - - + -
383A PHE* 4.3 1.1 - + - -
385A ILE* 3.5 36.3 - - + -
386A SER* 3.6 21.1 - - - -
387A GLN* 3.7 33.9 - - + -
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Residues in contact with GLU 303 (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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299A LYS* 3.0 51.1 + - - +
300A LYS* 4.0 8.0 - - - +
301A VAL 3.3 0.2 - - - -
302A PHE* 1.3 86.7 - - + +
304A ALA* 1.3 61.8 + - - +
306A VAL* 3.5 3.7 + - - +
307A ALA* 3.1 23.4 + - - +
387A GLN* 3.6 12.1 + - - +
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Residues in contact with ALA 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A LEU* 4.1 16.8 - - + +
276A MET* 4.1 20.2 - - + -
300A LYS 3.3 15.4 + - - +
301A VAL 4.0 3.6 - - - +
302A PHE 3.4 0.2 - - - -
303A GLU* 1.3 77.3 - - - +
305A ALA* 1.3 56.9 + - - +
307A ALA* 3.4 7.7 - - - +
308A SER* 2.9 30.5 + - - -
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Residues in contact with ALA 305 (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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267A VAL* 6.0 0.7 - - + -
269A ILE* 4.3 15.3 - - + -
274A LEU* 4.3 12.5 - - + +
297A LEU* 4.2 17.7 - - + -
301A VAL 3.0 18.5 + - - +
302A PHE* 3.8 3.4 - - - +
304A ALA* 1.3 77.4 - - - +
306A VAL* 1.4 51.6 + - + +
308A SER* 3.2 6.3 + - - -
309A ILE* 2.7 47.1 + - + +
344A ILE* 6.2 0.7 - - + -
385A ILE* 5.4 4.0 - - + -
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Residues in contact with VAL 306 (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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302A PHE* 3.0 53.9 + - + +
303A GLU* 3.9 4.5 - - - +
305A ALA* 1.4 71.2 - - + +
307A ALA* 1.3 68.7 + - - +
309A ILE* 3.1 9.2 + - - +
310A LYS* 2.7 51.8 + - - +
323A TRP* 4.1 21.7 - - + -
383A PHE* 4.2 16.4 - - + -
385A ILE* 5.8 0.7 - - + -
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Residues in contact with ALA 307 (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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303A GLU 3.1 11.7 + - - +
304A ALA* 3.4 12.1 - - - +
306A VAL* 1.3 83.1 - - - +
308A SER* 1.3 60.6 + - - +
310A LYS* 3.3 10.7 + - - +
311A ALA* 3.0 23.3 + - - +
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Residues in contact with SER 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A ILE* 3.3 27.2 + - - +
272A GLN* 5.3 4.3 + - - +
274A LEU* 4.0 16.8 - - - +
304A ALA 2.9 21.0 + - - -
305A ALA 3.5 4.0 - - - -
307A ALA* 1.3 70.9 - - - +
309A ILE* 1.3 58.6 + - - +
311A ALA* 3.4 6.4 + - - +
312A ALA* 3.0 29.6 + - - +
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Residues in contact with ILE 309 (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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269A ILE* 4.0 17.7 - - + -
305A ALA* 2.7 31.1 + - + +
306A VAL 3.7 3.4 - - - +
308A SER* 1.3 69.9 - - - +
310A LYS* 1.3 57.8 + - - +
312A ALA* 3.2 1.9 + - - +
313A SER* 2.6 36.5 + - - +
323A TRP* 4.0 21.1 - - + -
341A PHE* 4.5 5.8 - - + -
342A PRO* 3.9 26.5 - - + -
344A ILE* 4.0 12.1 - - + -
366A TYR* 4.3 9.9 - - + +
383A PHE* 4.1 14.1 - - + -
385A ILE* 4.0 27.6 - - + -
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Residues in contact with LYS 310 (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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306A VAL* 2.7 37.2 + - + +
307A ALA* 3.4 8.7 - - - +
309A ILE* 1.3 72.4 - - - +
311A ALA* 1.3 60.8 + - - +
314A SER 3.3 3.1 + - - -
315A THR* 3.0 32.5 + - - -
316A GLU* 3.5 32.5 + - + +
318A PHE 5.6 2.1 + - - -
320A ASP* 4.9 9.9 - - - +
323A TRP* 3.3 50.3 - - + +
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Residues in contact with ALA 311 (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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307A ALA 3.0 13.4 + - - +
308A SER* 3.7 6.5 - - - +
310A LYS* 1.3 78.1 - - - +
312A ALA* 1.3 64.9 + - - +
313A SER 3.1 1.2 + - - -
314A SER* 3.3 10.9 + - - -
316A GLU* 3.5 16.3 - - - +
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Residues in contact with ALA 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A ILE* 5.2 1.6 - - + -
270A ASN* 4.2 20.2 + - + +
308A SER 3.0 16.1 + - - +
309A ILE 3.2 4.0 + - - +
311A ALA* 1.3 77.4 - - - +
313A SER* 1.3 57.5 + - - +
314A SER* 3.5 0.9 + - - -
340A ILE 3.5 8.1 - - - +
342A PRO* 4.0 25.6 - - + -
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Residues in contact with SER 313 (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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309A ILE* 2.6 23.3 + - - +
310A LYS 3.6 0.3 + - - -
312A ALA* 1.3 77.0 - - - +
314A SER* 1.3 68.0 + - - +
315A THR* 2.8 30.9 + - - +
340A ILE* 3.1 41.3 - - - +
341A PHE* 4.0 20.8 - - - -
342A PRO* 4.4 0.9 - - - -
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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