Contacts of the helix formed by residues 324 - 337 (chain G) in PDB entry 1MKD
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 SER 324 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306G ASN* 4.2 3.9 - - - +
322G ASP 3.9 3.2 + - - -
323G SER* 1.3 71.3 - - - +
325G VAL* 1.3 66.8 + - - +
326G LEU 3.4 2.2 - - - -
327G GLU* 3.3 19.9 + - - -
328G ASN* 2.8 30.1 + - - -
366G LEU* 4.3 7.9 + - - +
369G ASP* 2.7 31.6 + - - +
372G LYS* 3.7 18.9 + - - -
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Residues in contact with VAL 325 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306G ASN* 3.4 13.7 + - + +
309G LEU* 4.1 14.1 - - + -
310G ILE* 4.3 9.6 - - + -
316G LEU* 3.6 41.7 - - + +
317G ALA* 3.8 17.3 - - + +
320G TYR* 3.7 13.8 - - + -
322G ASP* 3.6 33.0 - - - +
323G SER 3.1 3.3 - - - +
324G SER* 1.3 77.2 - - - +
326G LEU* 1.3 64.2 + - - +
329G HIS* 3.2 19.6 + - - +
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Residues in contact with LEU 326 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300G ASP 5.3 0.4 - - - +
301G HIS* 3.6 16.8 - - - +
302G PRO* 3.3 31.0 - - + -
304G VAL 3.4 23.6 - - - +
305G SER* 4.2 1.3 - - - -
306G ASN* 2.8 34.7 + - - +
309G LEU* 3.6 16.8 - - + -
316G LEU* 4.7 8.1 - - + -
325G VAL* 1.3 69.9 - - - +
327G GLU* 1.3 68.5 + - - +
329G HIS* 3.0 8.9 + - + +
330G HIS* 2.8 51.0 + - + +
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Residues in contact with GLU 327 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306G ASN* 2.9 28.5 + - - -
324G SER* 3.5 20.0 - - - +
326G LEU* 1.3 77.3 - - - +
328G ASN* 1.3 62.4 + - - +
330G HIS* 3.4 12.0 + - + +
331G LEU* 3.2 27.4 + - - +
365G VAL* 3.8 12.8 - - - +
366G LEU* 4.2 9.0 - - + -
368G THR* 3.6 23.1 - - - +
369G ASP* 3.6 30.8 - - + +
370G MET 4.8 0.5 + - - -
2014G MG 3.7 16.3 - - - -
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Residues in contact with ASN 328 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320F TYR* 4.5 5.8 - - - +
321F ASN* 2.9 34.3 + - - +
323F SER* 5.9 1.6 - - - -
320G TYR* 3.5 34.2 + - + +
323G SER* 2.9 28.1 + - - -
324G SER* 2.8 26.0 + - - +
325G VAL 3.7 1.6 - - - +
327G GLU* 1.3 72.9 - - - +
329G HIS* 1.3 63.8 + - - +
331G LEU 3.3 2.1 + - - -
332G ALA* 3.0 21.0 + - - +
366G LEU* 3.9 15.3 - - - +
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Residues in contact with HIS 329 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319F MET* 5.8 2.2 - - - +
299G VAL 4.6 1.8 - - - -
300G ASP* 2.7 41.3 + - + -
316G LEU* 3.7 36.1 - - + +
320G TYR* 4.0 17.1 + - + -
325G VAL 3.2 11.0 + - - +
326G LEU* 3.0 15.0 + - + +
328G ASN* 1.3 77.4 - - - +
330G HIS* 1.3 67.9 + - - +
332G ALA* 3.2 4.2 + - + +
333G VAL* 3.0 44.9 + - + +
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Residues in contact with HIS 330 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296G ILE* 3.6 18.3 - - - +
297G HIS 2.9 23.6 - - - +
298G ASP* 3.2 31.8 + - - -
299G VAL* 2.8 35.7 + - - +
300G ASP 4.7 0.7 - - - -
301G HIS* 3.9 22.8 - + + -
326G LEU* 2.8 49.5 + - + +
327G GLU* 3.5 12.6 - - + +
329G HIS* 1.3 73.4 - + - +
331G LEU* 1.3 57.4 + - - +
333G VAL 3.3 0.3 + - - -
334G GLY* 2.9 26.7 + - - -
365G VAL* 4.5 3.6 - - + -
2014G MG 4.2 3.9 - - - -
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Residues in contact with LEU 331 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321F ASN* 3.2 23.3 - - - +
296G ILE* 4.2 6.5 - - + +
327G GLU 3.2 12.6 + - - +
328G ASN 3.6 4.7 - - - +
329G HIS 3.2 0.2 - - - -
330G HIS* 1.3 77.6 - - - +
332G ALA* 1.3 62.8 + - - +
334G GLY* 3.3 0.9 + - - -
335G PHE* 3.0 53.2 + - + -
361G VAL* 3.7 6.7 - - + +
362G ILE* 3.7 22.2 - - + +
365G VAL* 3.6 36.8 - - + -
366G LEU* 3.7 32.3 - - + -
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Residues in contact with ALA 332 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318F LEU* 3.7 21.7 - - + +
319F MET* 4.1 21.1 - - + +
321F ASN* 3.9 0.4 + - - -
320G TYR* 3.7 17.5 - - - +
328G ASN 3.0 14.1 + - - +
329G HIS* 3.5 10.1 - - - +
331G LEU* 1.3 77.7 - - - +
333G VAL* 1.3 59.0 + - + +
335G PHE* 3.4 0.4 + - - -
336G LYS* 2.9 31.8 + - - +
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Residues in contact with VAL 333 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249G HIS* 4.4 14.1 - - + -
299G VAL* 4.0 25.8 - - + -
300G ASP* 4.3 10.3 - - + +
329G HIS* 3.0 47.3 + - + +
330G HIS 3.8 2.5 - - - +
332G ALA* 1.3 73.2 - - + +
334G GLY* 1.3 67.0 + - - +
336G LYS* 3.3 5.4 + - - +
337G LEU* 3.0 37.4 + - + +
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Residues in contact with GLY 334 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242G TYR* 2.7 33.6 + - - -
246G LEU* 4.7 4.5 - - - -
292G PHE* 4.3 0.6 - - - -
296G ILE* 4.1 22.2 - - - -
299G VAL* 4.1 4.0 - - - +
330G HIS 2.9 16.8 + - - -
331G LEU 3.8 0.9 - - - -
333G VAL* 1.3 79.0 - - - +
335G PHE* 1.3 61.8 + - - +
337G LEU* 3.8 3.7 + - - -
338G LEU* 3.9 3.1 - - - +
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Residues in contact with PHE 335 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318F LEU* 4.1 10.1 - - + -
321F ASN* 4.3 3.1 - - - -
292G PHE* 4.2 15.9 - + - -
296G ILE* 5.0 1.3 - - + -
331G LEU* 3.0 49.6 + - + +
332G ALA* 3.9 2.5 - - - +
334G GLY* 1.3 75.0 - - - +
336G LYS* 1.3 66.2 + - - +
338G LEU* 3.1 38.5 + - + +
339G GLN* 4.0 5.7 + - - +
346G PHE* 5.6 0.2 - + - -
357G LEU* 5.3 4.7 - - + -
358G ARG* 3.2 54.7 - - + +
361G VAL* 3.6 26.7 - - + -
362G ILE* 3.7 9.4 - - + -
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Residues in contact with LYS 336 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315F GLU* 3.3 24.6 + - - +
318F LEU* 4.2 14.8 - - + +
332G ALA 2.9 20.0 + - - +
333G VAL* 3.6 7.2 - - - +
335G PHE* 1.3 77.3 - - - +
337G LEU* 1.3 67.1 + - + +
339G GLN* 3.0 51.2 + - - +
340G GLU* 4.2 3.5 + - - +
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Residues in contact with LEU 337 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242G TYR* 3.7 15.3 - - + -
245G THR* 3.8 12.3 - - + -
246G LEU* 3.7 44.9 - - + +
249G HIS* 3.6 41.7 - - + +
333G VAL* 3.0 27.6 + - + +
334G GLY 4.0 1.1 - - - +
335G PHE 3.3 0.2 - - - -
336G LYS* 1.3 80.2 - - + +
338G LEU* 1.3 61.0 + - - +
339G GLN 3.1 1.0 + - - -
340G GLU* 3.4 23.0 + - - +
343G CYS* 3.2 19.8 - - - +
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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