Contacts of the helix formed by residues 324 - 337 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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306D ASN* 4.2 4.4 - - - +
322D ASP 3.9 2.6 + - - -
323D SER* 1.3 71.5 - - - +
325D VAL* 1.3 65.9 + - - +
326D LEU 3.4 2.5 - - - -
327D GLU* 3.3 24.6 + - - -
328D ASN* 2.8 31.4 + - - -
366D LEU* 4.3 8.1 + - - +
369D ASP* 2.7 26.0 + - - +
372D LYS* 3.7 19.2 + - - -
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Residues in contact with VAL 325 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306D ASN* 3.4 12.3 + - + +
309D LEU* 4.1 13.2 - - + -
310D ILE* 4.3 9.4 - - + -
316D LEU* 3.5 42.2 - - + +
317D ALA* 3.7 17.0 - - + +
320D TYR* 3.7 13.2 - - + -
322D ASP* 3.6 34.5 - - - +
323D SER 3.1 3.5 - - - +
324D SER* 1.3 77.5 - - - +
326D LEU* 1.3 64.6 + - - +
329D HIS* 3.2 19.9 + - - +
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Residues in contact with LEU 326 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300D ASP 5.3 0.4 - - - +
301D HIS* 3.5 17.5 - - + +
302D PRO* 3.4 31.6 - - + -
304D VAL 3.4 23.1 - - - +
305D SER* 4.2 0.9 - - - -
306D ASN* 2.7 38.5 + - - +
309D LEU* 3.6 17.5 - - + -
316D LEU* 4.7 7.6 - - + -
325D VAL* 1.3 69.9 - - - +
327D GLU* 1.3 63.9 + - - +
329D HIS* 2.9 8.4 + - + +
330D HIS* 2.8 57.4 + - + +
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Residues in contact with GLU 327 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306D ASN* 2.9 27.5 + - - -
324D SER* 3.5 15.8 - - - +
326D LEU* 1.3 78.6 - - - +
328D ASN* 1.3 62.7 + - - +
330D HIS* 3.3 13.9 + - + +
331D LEU* 3.2 26.9 + - - +
365D VAL* 3.8 13.1 - - - +
366D LEU* 4.2 13.9 - - + -
368D THR* 3.6 22.5 - - - +
369D ASP* 3.6 31.2 - - + +
370D MET 4.7 1.0 + - - -
2008D MG 3.8 14.2 - - - -
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Residues in contact with ASN 328 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320C TYR* 4.4 7.0 - - - +
321C ASN* 2.9 34.7 + - - +
323C SER* 5.8 1.2 - - - -
320D TYR* 3.5 32.6 + - + +
323D SER 2.9 27.7 + - - -
324D SER* 2.8 25.2 + - - +
325D VAL 3.7 1.3 - - - +
327D GLU* 1.3 73.2 - - - +
329D HIS* 1.3 64.1 + - - +
331D LEU 3.3 2.1 + - - -
332D ALA* 3.0 21.0 + - - +
366D LEU* 3.9 14.4 - - - +
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Residues in contact with HIS 329 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319C MET* 6.0 0.8 - - - +
299D VAL 4.6 2.0 - - - -
300D ASP* 2.7 41.7 + - + -
316D LEU* 3.7 37.8 - - + +
320D TYR* 4.0 17.0 + - + -
325D VAL 3.2 11.2 + - - +
326D LEU* 2.9 14.1 + - + +
328D ASN* 1.3 77.4 - - - +
330D HIS* 1.3 69.2 + - - +
332D ALA* 3.1 4.5 + - + +
333D VAL* 3.0 43.9 + - + +
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Residues in contact with HIS 330 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296D ILE* 3.6 19.4 - - - +
297D HIS 3.0 22.2 - - - +
298D ASP* 3.2 32.3 + - - -
299D VAL* 2.8 34.9 + - - +
300D ASP 4.6 0.7 - - - -
301D HIS* 3.8 22.7 - + + -
326D LEU* 2.8 50.3 + - + +
327D GLU* 3.5 13.0 - - + +
329D HIS* 1.3 74.8 - + - +
331D LEU* 1.3 64.9 + - - +
334D GLY* 2.9 20.8 + - - -
365D VAL* 4.5 3.1 - - + -
2008D MG 4.4 3.4 - - - -
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Residues in contact with LEU 331 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321C ASN* 3.3 22.9 - - - +
296D ILE* 4.2 6.5 - - + +
327D GLU 3.2 11.3 + - - +
328D ASN 3.5 4.3 - - - +
329D HIS 3.2 0.2 - - - -
330D HIS* 1.3 79.7 - - - +
332D ALA* 1.3 63.1 + - - +
334D GLY* 3.3 0.9 + - - -
335D PHE* 2.9 54.0 + - + -
361D VAL* 3.7 14.1 - - + +
362D ILE* 3.7 14.4 - - + +
365D VAL* 3.5 36.8 - - + -
366D LEU* 3.7 32.1 - - + -
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Residues in contact with ALA 332 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318C LEU* 4.0 18.0 - - + +
319C MET* 4.3 18.6 - - + +
321C ASN* 3.8 5.5 + - - +
320D TYR* 3.7 17.7 - - - +
328D ASN 3.0 13.0 + - - +
329D HIS* 3.1 9.6 + - - +
331D LEU* 1.3 75.4 - - - +
333D VAL* 1.3 59.4 + - + +
335D PHE* 3.4 2.0 + - - +
336D LYS* 2.8 32.4 + - - +
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Residues in contact with VAL 333 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249D HIS* 4.4 14.1 - - + -
299D VAL* 4.0 25.6 - - + -
300D ASP* 4.3 9.9 - - + +
329D HIS* 3.0 47.9 + - + +
330D HIS 3.8 2.9 - - - +
332D ALA* 1.3 75.5 - - + +
334D GLY* 1.3 63.8 + - - +
336D LYS* 3.2 6.5 + - - +
337D LEU* 3.0 39.0 + - + +
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Residues in contact with GLY 334 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242D TYR* 2.8 31.1 + - - -
246D LEU* 4.7 4.0 - - - -
292D PHE* 4.3 1.4 - - - -
296D ILE* 4.1 22.2 - - - -
299D VAL* 4.1 3.8 - - - +
330D HIS 2.9 16.4 + - - -
331D LEU 3.8 0.9 - - - -
333D VAL* 1.3 77.4 - - - +
335D PHE* 1.3 61.4 + - - +
337D LEU* 3.8 4.1 + - - -
338D LEU* 3.9 4.7 - - - +
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Residues in contact with PHE 335 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318C LEU* 4.5 10.3 - - + -
321C ASN* 4.3 2.9 - - - -
292D PHE* 4.3 16.4 - + - -
296D ILE* 5.0 1.6 - - + -
331D LEU* 2.9 41.2 + - + +
332D ALA* 3.9 2.5 - - - +
334D GLY* 1.3 73.9 - - - +
336D LYS* 1.3 67.6 + - - +
338D LEU* 3.1 37.7 + - + +
339D GLN* 4.0 6.6 + - - +
357D LEU* 5.3 4.9 - - + -
358D ARG* 3.2 55.0 - - + +
361D VAL* 3.5 26.7 - - + -
362D ILE* 3.7 17.7 - - + -
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Residues in contact with LYS 336 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315C GLU* 3.8 22.4 + - - +
318C LEU* 4.5 14.9 - - + +
332D ALA 2.8 20.0 + - - +
333D VAL* 3.2 8.7 + - + +
335D PHE* 1.3 77.4 - - - +
337D LEU* 1.3 65.7 + - + +
339D GLN* 3.0 52.4 + - - +
340D GLU* 4.2 3.9 + - - +
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Residues in contact with LEU 337 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242D TYR* 3.7 15.5 - - + +
245D THR* 3.7 12.3 - - + -
246D LEU* 3.7 44.4 - - + +
249D HIS* 3.6 42.6 - - + +
333D VAL* 3.0 26.7 + - + +
334D GLY 4.0 1.1 - - - +
335D PHE 3.3 0.4 - - - -
336D LYS* 1.3 79.1 - - + +
338D LEU* 1.3 61.8 - - - +
339D GLN 3.3 0.3 + - - -
340D GLU* 3.4 23.0 + - - +
343D CYS* 3.2 19.9 - - - +
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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