Contacts of the helix formed by residues 324 - 337 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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306C ASN* 4.2 3.9 - - - +
322C ASP 3.9 3.0 + - - -
323C SER* 1.3 72.0 - - - +
325C VAL* 1.3 64.8 + - - +
326C LEU 3.3 2.9 + - - -
327C GLU* 3.4 22.8 + - - -
328C ASN* 2.8 31.2 + - - -
366C LEU* 4.3 8.2 + - - +
369C ASP* 2.7 28.0 + - - +
372C LYS* 3.7 18.5 + - - -
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Residues in contact with VAL 325 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306C ASN* 3.4 14.1 + - + +
309C LEU* 4.1 13.7 - - + -
310C ILE* 4.3 9.6 - - + -
316C LEU* 3.5 42.2 - - + +
317C ALA* 3.7 16.6 - - + +
320C TYR* 3.7 14.0 - - + -
322C ASP* 3.6 33.4 - - - +
323C SER 3.1 3.3 - - - +
324C SER* 1.3 77.0 - - - +
326C LEU* 1.3 63.0 + - - +
329C HIS* 3.2 20.3 + - - +
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Residues in contact with LEU 326 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301C HIS* 3.5 17.9 - - + +
302C PRO* 3.4 29.8 - - + -
304C VAL 3.4 24.0 - - - +
305C SER* 4.5 1.1 - - - -
306C ASN* 2.7 34.9 + - - +
309C LEU* 3.6 16.6 - - + -
316C LEU* 4.7 8.3 - - + -
325C VAL* 1.3 70.3 - - - +
327C GLU* 1.3 64.7 + - - +
329C HIS* 2.9 10.5 + - + +
330C HIS* 2.8 55.4 + - + +
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Residues in contact with GLU 327 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306C ASN* 2.9 28.4 + - - -
324C SER* 3.5 15.2 - - - +
326C LEU* 1.3 77.9 - - - +
328C ASN* 1.3 62.4 + - - +
330C HIS* 3.4 10.9 + - + +
331C LEU* 3.2 26.3 + - - +
365C VAL* 3.8 13.4 - - - +
366C LEU* 4.1 13.9 - - + -
368C THR* 3.6 21.8 - - - +
369C ASP* 3.5 32.0 - - + +
370C MET 4.7 0.9 + - - -
2006C MG 3.6 16.6 - - - -
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Residues in contact with ASN 328 (chain C).
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* 3.6 33.6 + - + -
323C SER* 2.9 27.5 + - - -
324C SER* 2.8 25.8 + - - +
325C VAL 3.8 1.8 - - - +
327C GLU* 1.3 72.5 - - - +
329C HIS* 1.3 63.8 + - - +
331C LEU 3.3 1.9 + - - -
332C ALA* 3.0 20.3 + - - +
366C LEU* 3.9 15.9 - - - +
320D TYR* 4.4 7.4 - - - +
321D ASN* 3.1 28.9 + - - +
323D SER* 5.6 2.6 - - - -
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Residues in contact with HIS 329 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299C VAL 4.6 2.0 - - - -
300C ASP* 2.7 41.9 + - + -
316C LEU* 3.7 36.7 - - + +
320C TYR* 4.0 17.2 + - + -
325C VAL 3.2 11.4 + - - +
326C LEU* 2.9 16.0 + - + +
328C ASN* 1.3 77.6 - - - +
330C HIS* 1.3 67.8 + - - +
332C ALA* 3.2 4.1 + - + +
333C VAL* 3.0 43.2 + - + +
319D MET* 6.0 2.0 - - - +
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Residues in contact with HIS 330 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296C ILE* 3.6 18.5 - - - +
297C HIS 3.0 22.0 - - - +
298C ASP* 3.2 31.4 + - - -
299C VAL* 2.7 35.2 + - - +
300C ASP 4.7 1.1 - - - -
301C HIS* 3.9 21.5 - + + -
326C LEU* 2.8 50.5 + - + +
327C GLU* 3.5 13.0 - - + +
328C ASN 3.3 0.2 - - - -
329C HIS* 1.3 73.8 - + - +
331C LEU* 1.3 64.7 + - - +
333C VAL 3.3 0.2 + - - -
334C GLY* 2.9 21.7 + - - -
365C VAL* 4.5 3.1 - - + -
2006C MG 4.0 4.1 - - - -
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Residues in contact with LEU 331 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296C ILE* 4.2 6.2 - - + +
327C GLU 3.2 9.4 + - - +
328C ASN 3.5 4.7 - - - +
330C HIS* 1.3 80.6 - - - +
332C ALA* 1.3 64.2 + - - +
334C GLY* 3.8 0.3 - - - -
335C PHE* 2.9 51.8 + - + -
361C VAL* 3.7 6.5 - - + +
362C ILE* 3.7 28.7 - - + +
365C VAL* 3.5 35.7 - - + -
366C LEU* 3.7 31.9 - - + -
321D ASN* 3.3 20.2 - - - +
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Residues in contact with ALA 332 (chain C).
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* 3.7 22.7 - - - +
328C ASN 3.0 8.6 + - - +
329C HIS* 3.2 10.1 + - + +
331C LEU* 1.3 73.7 - - - +
333C VAL* 1.3 59.1 + - + +
335C PHE* 3.8 0.8 - - - -
336C LYS* 2.8 32.4 + - - +
318D LEU* 3.8 16.5 - - + +
319D MET* 4.0 20.0 - - + +
321D ASN* 3.5 7.1 + - - -
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Residues in contact with VAL 333 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249C HIS* 4.5 13.7 - - + -
299C VAL* 4.0 24.7 - - + -
300C ASP* 4.3 10.5 - - + +
329C HIS* 3.0 47.0 + - + +
330C HIS 3.8 3.4 - - - +
332C ALA* 1.3 74.9 - - + +
334C GLY* 1.3 64.4 + - - +
336C LYS* 3.3 6.1 + - + +
337C LEU* 3.1 37.0 + - + +
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Residues in contact with GLY 334 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242C TYR* 2.8 31.5 + - - -
246C LEU* 4.7 4.0 - - - -
292C PHE* 4.2 0.6 - - - -
296C ILE* 4.1 21.5 - - - -
299C VAL* 4.1 3.8 - - - +
330C HIS 2.9 16.7 + - - -
331C LEU 3.8 0.7 - - - -
333C VAL* 1.3 79.4 - - - +
335C PHE* 1.3 62.0 + - - +
337C LEU* 3.8 4.0 + - - -
338C LEU* 3.9 5.0 - - - +
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Residues in contact with PHE 335 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292C PHE* 4.2 15.9 - + - -
296C ILE* 4.9 0.9 - - + -
331C LEU* 2.9 50.0 + - + +
332C ALA 3.9 2.0 - - - +
334C GLY* 1.3 74.2 - - - +
336C LYS* 1.3 67.7 + - - +
338C LEU* 3.0 38.0 + - + +
339C GLN* 4.0 5.9 + - - +
346C PHE* 6.1 0.2 - + - -
357C LEU* 5.3 5.2 - - + -
358C ARG* 3.2 57.2 - - + +
361C VAL* 3.5 27.1 - - + -
362C ILE* 3.7 9.0 - - + -
318D LEU* 4.6 9.9 - - + -
321D ASN* 4.2 3.6 - - - -
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Residues in contact with LYS 336 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332C ALA 2.8 20.1 + - - +
333C VAL* 3.3 7.6 + - - +
335C PHE* 1.3 78.6 - - - +
337C LEU* 1.3 67.1 + - + +
339C GLN* 3.0 50.5 + - - +
340C GLU* 4.2 3.8 + - - +
315D GLU* 3.5 25.2 + - - +
318D LEU* 4.0 17.4 - - + +
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Residues in contact with LEU 337 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242C TYR* 3.7 14.4 - - + -
245C THR* 3.7 12.8 - - + +
246C LEU* 3.7 43.7 - - + +
249C HIS* 3.6 43.1 - - + +
333C VAL* 3.1 27.1 + - + +
334C GLY* 4.0 1.6 - - - +
335C PHE 3.2 0.2 - - - -
336C LYS* 1.3 80.3 - - + +
338C LEU* 1.3 60.7 + - - +
339C GLN 3.2 1.0 + - - -
340C GLU* 3.4 23.7 + - - +
343C CYS* 3.2 20.1 - - - +
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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