Contacts of the helix formed by residues 324 - 337 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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306A ASN* 4.2 3.7 - - - +
322A ASP 3.8 3.4 + - - -
323A SER* 1.3 71.8 - - - +
325A VAL* 1.3 65.7 + - - +
326A LEU 3.3 2.4 + - - -
327A GLU* 3.4 20.4 + - - -
328A ASN* 2.8 30.1 + - - -
366A LEU* 4.2 7.9 + - - +
369A ASP* 2.7 31.0 + - - +
372A LYS* 3.6 19.4 + - - -
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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
----------------------------------------------------------
306A ASN* 3.4 13.3 + - + +
309A LEU* 4.1 13.5 - - + -
310A ILE* 4.3 9.2 - - + -
316A LEU* 3.5 42.8 - - + +
317A ALA* 3.7 17.3 - - + +
320A TYR* 3.7 13.8 - - + -
322A ASP* 3.7 33.9 - - - +
323A SER 3.1 3.8 - - - +
324A SER* 1.3 76.9 - - - +
326A LEU* 1.3 63.9 + - - +
329A HIS* 3.1 19.4 + - - +
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Residues in contact with LEU 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A ASP 5.3 0.2 - - - +
301A HIS* 3.5 17.3 - - - +
302A PRO* 3.4 30.1 - - + -
304A VAL 3.4 23.3 - - - +
305A SER* 4.2 1.3 - - - -
306A ASN* 2.8 34.0 + - - +
309A LEU* 3.6 17.3 - - + -
316A LEU* 4.7 7.6 - - + -
325A VAL* 1.3 70.1 - - - +
327A GLU* 1.3 70.1 + - - +
329A HIS* 3.0 8.3 + - + +
330A HIS* 2.8 51.9 + - + +
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Residues in contact with GLU 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A ASN* 2.9 28.6 + - - -
324A SER* 3.5 15.6 - - - +
326A LEU* 1.3 78.3 - - - +
328A ASN* 1.3 62.2 + - - +
330A HIS* 3.4 10.3 + - - +
331A LEU* 3.2 27.2 + - - +
365A VAL* 3.8 13.3 - - - +
366A LEU* 4.2 13.7 - - + -
368A THR* 3.6 22.4 - - - +
369A ASP* 3.6 30.7 - - + +
370A MET 4.7 0.7 + - - -
2002A MG 3.6 15.8 - - - -
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Residues in contact with ASN 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A TYR* 3.5 33.1 + - + +
323A SER 2.9 27.3 + - - -
324A SER* 2.8 24.9 + - - +
325A VAL 3.8 1.3 - - - +
327A GLU* 1.3 72.5 - - - +
329A HIS* 1.3 63.4 + - - +
331A LEU 3.3 2.1 + - - -
332A ALA* 3.0 20.6 + - - +
366A LEU* 3.9 13.7 - - - +
320B TYR* 4.5 4.5 - - - +
321B ASN* 2.7 36.6 + - - +
323B SER* 6.0 0.9 - - - -
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Residues in contact with HIS 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A VAL 4.6 2.0 - - - -
300A ASP* 2.7 40.5 + - + -
316A LEU* 3.7 36.2 - - + +
320A TYR* 4.0 17.5 + - + -
325A VAL 3.1 11.9 + - - +
326A LEU* 3.0 13.0 + - + +
328A ASN* 1.3 77.2 - - - +
330A HIS* 1.3 69.9 + + - +
332A ALA* 3.1 4.0 + - + +
333A VAL* 3.0 44.1 + - + +
319B MET* 5.4 4.1 - - + +
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Residues in contact with HIS 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A ILE* 3.6 18.7 - - - +
297A HIS 3.0 23.3 - - - +
298A ASP* 3.2 31.2 + - - -
299A VAL* 2.8 36.0 + - - +
300A ASP 4.7 0.7 - - - -
301A HIS* 3.8 22.6 - + + -
326A LEU* 2.8 49.3 + - + +
327A GLU* 3.5 13.2 - - + +
328A ASN 3.3 0.2 - - - -
329A HIS* 1.3 74.4 - + - +
331A LEU* 1.3 57.1 + - - +
334A GLY* 2.9 26.5 + - - -
365A VAL* 4.5 3.4 - - + -
2002A MG 4.0 4.3 - - - -
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Residues in contact with LEU 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A ILE* 4.2 7.4 - - + +
327A GLU 3.2 10.8 + - - +
328A ASN 3.5 3.8 - - - +
329A HIS 3.2 0.6 - - - -
330A HIS* 1.3 78.2 - - - +
332A ALA* 1.3 63.7 + - - +
334A GLY 3.8 0.2 - - - -
335A PHE* 3.0 54.0 + - + -
361A VAL* 3.7 5.6 - - + +
362A ILE* 3.7 23.1 - - + +
365A VAL* 3.5 36.1 - - + -
366A LEU* 3.7 32.3 - - + -
321B ASN* 3.1 24.5 - - - +
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Residues in contact with ALA 332 (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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320A TYR* 3.7 22.4 - - - +
328A ASN 3.0 8.4 + - - +
329A HIS* 3.5 8.7 - - - +
331A LEU* 1.3 77.4 - - - +
333A VAL* 1.3 58.8 + - + +
335A PHE* 4.9 0.2 - - - -
336A LYS* 2.9 32.4 + - - +
318B LEU* 3.3 21.3 - - + +
319B MET* 4.0 23.3 - - + +
321B ASN* 3.9 0.4 + - - -
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Residues in contact with VAL 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A HIS* 4.4 13.5 - - + -
299A VAL* 4.0 25.4 - - + -
300A ASP* 4.3 9.9 - - + +
329A HIS* 3.0 48.2 + - + +
330A HIS 3.8 2.9 - - - +
332A ALA* 1.3 76.5 - - + +
334A GLY* 1.3 63.9 + - - +
336A LYS* 3.2 6.3 + - - +
337A LEU* 3.0 37.5 + - + +
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Residues in contact with GLY 334 (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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242A TYR* 2.8 31.4 + - - -
246A LEU* 4.7 4.3 - - - -
292A PHE* 4.3 0.6 - - - -
296A ILE* 4.2 21.5 - - - -
299A VAL* 4.0 4.2 - - - +
330A HIS 2.9 17.3 + - - -
331A LEU 3.9 0.9 - - - -
333A VAL* 1.3 77.9 - - - +
335A PHE* 1.3 61.4 + - - +
337A LEU* 3.8 4.3 + - - -
338A LEU* 3.9 5.2 - - - +
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Residues in contact with PHE 335 (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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292A PHE* 4.2 15.5 - + - -
296A ILE* 5.0 0.9 - - + -
331A LEU* 3.0 51.8 + - + +
332A ALA* 5.1 0.2 - - - -
334A GLY* 1.3 74.9 - - - +
336A LYS* 1.3 67.1 + - - +
338A LEU* 3.1 37.9 + - + +
339A GLN* 4.0 5.7 + - - +
357A LEU* 5.3 4.5 - - + -
358A ARG* 3.2 51.6 - - + +
361A VAL* 3.5 26.9 - - + -
362A ILE* 3.7 9.2 - - + -
318B LEU* 3.9 17.8 - - + +
321B ASN* 4.4 2.0 - - - -
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Residues in contact with LYS 336 (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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332A ALA 2.9 20.0 + - - +
333A VAL* 3.5 7.4 - - + +
335A PHE* 1.3 77.3 - - - +
337A LEU* 1.3 66.5 + - + +
339A GLN* 3.0 40.9 + - - +
340A GLU* 4.2 3.5 + - - +
315B GLU* 2.7 36.2 + - - +
318B LEU* 3.9 19.2 - - + +
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Residues in contact with LEU 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A TYR* 3.7 14.8 - - + -
245A THR* 3.7 11.9 - - + -
246A LEU* 3.7 43.5 - - + +
249A HIS* 3.6 42.6 - - + +
333A VAL* 3.0 28.0 + - + +
334A GLY 4.0 1.1 - - - +
335A PHE 3.3 0.6 - - - -
336A LYS* 1.3 80.1 - - + +
338A LEU* 1.3 62.5 + - - +
339A GLN 3.2 0.8 + - - -
340A GLU* 3.4 23.9 + - - +
343A CYS* 3.2 19.6 - - - +
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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