Contacts of the helix formed by residues 324 - 337 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306I ASN* 4.2 3.9 - - - +
322I ASP 3.9 3.2 + - - -
323I SER* 1.3 72.4 - - - +
325I VAL* 1.3 66.2 + - - +
326I LEU 3.3 2.4 + - - -
327I GLU* 3.3 24.5 + - - -
328I ASN* 2.9 30.3 + - - -
366I LEU* 4.2 7.9 + - - +
369I ASP* 2.7 27.1 + - - +
372I LYS* 3.7 18.5 + - - -
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Residues in contact with VAL 325 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306I ASN* 3.4 13.2 + - + +
309I LEU* 4.1 14.8 - - + -
310I ILE* 4.3 9.9 - - + -
316I LEU* 3.6 41.7 - - + +
317I ALA* 3.8 16.6 - - + +
320I TYR* 3.7 14.3 - - + -
322I ASP* 3.6 33.9 - - - +
323I SER 3.1 3.6 - - - +
324I SER* 1.3 77.8 - - - +
326I LEU* 1.3 62.9 + - - +
328I ASN 3.6 0.2 + - - -
329I HIS* 3.2 19.8 + - - +
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Residues in contact with LEU 326 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300I ASP 5.3 0.4 - - - +
301I HIS* 3.5 17.9 - - + +
302I PRO* 3.4 30.1 - - + -
304I VAL 3.4 23.6 - - - +
305I SER* 4.5 1.3 - - - -
306I ASN* 2.8 35.6 + - - +
309I LEU* 3.6 16.2 - - + -
316I LEU* 4.7 8.1 - - + -
325I VAL* 1.3 70.7 - - - +
327I GLU* 1.3 68.2 + - - +
329I HIS* 2.9 8.4 + - + +
330I HIS* 2.8 51.3 + - + +
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Residues in contact with GLU 327 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306I ASN* 2.9 28.6 + - - -
324I SER* 3.5 16.9 - - - +
326I LEU* 1.3 77.1 - - - +
328I ASN* 1.3 62.3 + - - +
330I HIS* 3.4 11.4 + - + +
331I LEU* 3.2 27.0 + - - +
365I VAL* 3.8 12.2 - - - +
366I LEU* 4.2 14.4 - - + -
368I THR* 3.6 23.1 - - - +
369I ASP* 3.6 30.3 - - + +
370I MET 4.7 1.0 + - - -
2018I MG 3.6 18.0 - - - -
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Residues in contact with ASN 328 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320I TYR* 3.5 32.6 - - + +
323I SER* 3.0 27.3 + - - -
324I SER* 2.9 22.2 + - - +
325I VAL 3.8 1.8 - - - +
327I GLU* 1.3 75.6 - - - +
329I HIS* 1.3 63.4 + - - +
331I LEU 3.3 1.6 + - - -
332I ALA* 3.1 13.9 + - - +
366I LEU* 3.9 16.2 - - - +
320J TYR* 4.2 6.8 - - - +
321J ASN* 2.9 41.2 + - - +
323J SER* 5.5 1.9 - - - -
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Residues in contact with HIS 329 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299I VAL 4.6 1.8 - - - -
300I ASP* 2.8 42.6 + - + -
302I PRO* 5.8 0.2 - - + -
316I LEU* 3.7 37.5 - - + +
320I TYR* 4.0 17.0 + - + -
325I VAL 3.2 11.0 + - - +
326I LEU* 2.9 14.5 + - + +
328I ASN* 1.3 77.4 - - - +
330I HIS* 1.3 68.3 + - - +
332I ALA* 3.1 4.7 + - + +
333I VAL* 3.0 45.0 + - + +
319J MET* 5.6 2.6 - - + +
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Residues in contact with HIS 330 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296I ILE* 3.6 13.9 - - - +
297I HIS 2.9 28.3 - - - +
298I ASP* 3.2 32.9 + - - -
299I VAL* 2.8 34.4 + - - +
300I ASP 4.7 0.7 - - - -
301I HIS* 3.9 23.0 - + + -
326I LEU* 2.8 49.3 + - + +
327I GLU* 3.5 12.3 - - + +
329I HIS* 1.3 74.5 - + - +
331I LEU* 1.3 64.6 + - - +
333I VAL 3.3 0.2 + - - -
334I GLY* 2.9 21.1 + - - -
365I VAL* 4.5 2.9 - - + -
2018I MG 4.1 4.5 - - - -
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Residues in contact with LEU 331 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296I ILE* 4.2 6.5 - - + +
327I GLU 3.2 10.6 + - - +
328I ASN 3.5 2.2 - - - +
330I HIS* 1.3 78.6 - - - +
332I ALA* 1.3 62.6 + - - +
334I GLY* 3.3 0.5 + - - -
335I PHE* 2.9 52.1 + - + -
361I VAL* 3.8 6.7 - - + +
362I ILE* 3.7 22.9 - - + +
365I VAL* 3.5 35.4 - - + -
366I LEU* 3.7 31.4 - - + -
321J ASN* 3.1 27.6 - - - +
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Residues in contact with ALA 332 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320I TYR* 3.7 22.9 - - - +
328I ASN 3.1 7.2 + - - +
329I HIS* 3.5 9.4 - - - +
331I LEU* 1.3 75.5 - - - +
333I VAL* 1.3 60.0 + - + +
335I PHE* 3.4 0.6 + - - -
336I LYS* 2.8 32.4 + - - +
318J LEU* 3.6 26.8 - - + +
319J MET* 4.0 9.6 - - + +
321J ASN* 3.4 6.6 + - - -
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Residues in contact with VAL 333 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249I HIS* 4.4 13.9 - - + -
299I VAL* 4.0 26.0 - - + -
300I ASP* 4.3 10.1 - - + +
329I HIS* 3.0 47.5 + - + +
330I HIS 3.7 2.7 - - - +
332I ALA* 1.3 76.9 - - + +
334I GLY* 1.3 63.0 + - - +
336I LYS* 3.3 6.6 + - - +
337I LEU* 3.0 38.2 + - + +
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Residues in contact with GLY 334 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242I TYR* 2.7 31.3 + - - -
246I LEU* 4.7 4.0 - - - -
292I PHE* 4.2 1.5 - - - -
296I ILE* 4.1 22.2 - - - -
299I VAL* 4.0 4.2 - - - +
330I HIS 2.9 15.2 + - - -
331I LEU 3.8 1.1 - - - -
333I VAL* 1.3 78.9 - - - +
335I PHE* 1.3 61.7 + - - +
337I LEU* 3.8 4.1 + - - +
338I LEU* 3.9 4.2 - - - +
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Residues in contact with PHE 335 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292I PHE* 4.2 15.5 - + - -
296I ILE* 5.0 0.9 - - + -
331I LEU* 2.9 49.6 + - + +
332I ALA 3.9 2.2 - - - +
334I GLY* 1.3 74.6 - - - +
336I LYS* 1.3 67.1 + - - +
338I LEU* 3.1 38.4 + - + +
339I GLN* 4.0 6.0 + - - +
357I LEU* 5.3 4.9 - - + -
358I ARG* 3.2 52.9 - - + +
361I VAL* 3.5 27.4 - - + -
362I ILE* 3.7 9.6 - - + -
318J LEU* 4.7 9.6 - - + -
321J ASN* 4.3 3.4 - - - -
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Residues in contact with LYS 336 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332I ALA 2.8 20.8 + - - +
333I VAL* 3.6 8.3 - - - +
335I PHE* 1.3 76.8 - - - +
337I LEU* 1.3 65.3 + - + +
339I GLN* 3.0 53.6 + - - +
340I GLU* 4.2 3.5 + - - +
315J GLU* 3.6 26.6 + - - +
318J LEU* 3.8 19.5 - - + +
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Residues in contact with LEU 337 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242I TYR* 3.7 15.3 - - + -
245I THR* 3.7 11.9 - - + -
246I LEU* 3.7 44.6 - - + +
249I HIS* 3.6 42.8 - - + +
333I VAL* 3.0 26.6 + - + +
334I GLY* 4.0 1.6 - - - +
335I PHE 3.3 0.4 - - - -
336I LYS* 1.3 80.0 - - + +
338I LEU* 1.3 61.4 + - - +
339I GLN 3.2 0.5 + - - -
340I GLU* 3.4 24.5 + - - +
343I CYS* 3.3 19.1 - - - +
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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