Contacts of the strand formed by residues 326 - 332 (chain D) in PDB entry 1MK9
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 VAL 326 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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316D LYS* 4.7 0.4 - - - -
317D GLU* 3.0 21.9 + - - +
319D MET* 3.1 35.9 - - + -
322D LYS* 4.4 9.6 - - - +
324D LYS* 3.9 11.7 - - - +
325D LEU* 1.3 76.3 - - - +
327D PRO* 1.3 72.9 - - - +
328D ARG* 3.3 21.7 + - - +
374H GLN* 5.8 2.9 - - + +
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Residues in contact with PRO 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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314D LEU* 5.3 9.0 - - + -
315D VAL 3.6 7.4 - - - +
316D LYS* 3.3 29.6 - - + +
324D LYS* 4.7 6.5 - - - +
325D LEU 3.5 10.8 - - - +
326D VAL* 1.3 89.2 - - - +
328D ARG* 1.3 66.4 + - - +
342D GLU* 3.4 32.9 - - + +
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Residues in contact with ARG 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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314D LEU* 3.5 7.6 - - - +
315D VAL* 2.6 48.3 + - + +
317D GLU* 2.1 62.6 + - - +
319D MET* 3.2 32.8 - - - +
326D VAL* 3.8 10.5 - - - +
327D PRO* 1.3 81.9 - - - +
329D LEU* 1.3 67.3 + - - +
339D ARG* 2.6 38.3 - - + +
340D VAL 3.6 14.6 - - - +
341D ASP* 4.6 2.2 + - - +
342D GLU* 4.3 8.9 - - - +
348D ILE* 3.5 23.6 - - - +
378D TYR* 5.1 0.4 - - - +
374H GLN* 4.7 6.5 - - - +
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Residues in contact with LEU 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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229D PRO* 4.2 34.1 - - + -
312D PHE* 3.9 16.2 - - + -
313D PHE 3.6 4.0 - - - +
314D LEU* 3.6 23.3 - - + -
315D VAL* 5.0 0.2 - - - -
328D ARG* 1.3 75.0 - - - +
330D LEU* 1.3 59.5 + - - +
331D GLY 4.0 0.2 - - - -
339D ARG* 3.8 2.4 - - - +
340D VAL* 2.7 62.3 + - + +
341D ASP 3.6 14.6 - - - +
342D GLU* 3.5 29.4 - - - +
345D LYS* 4.2 5.4 - - + +
378D TYR* 5.6 0.6 + - - -
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Residues in contact with LEU 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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311D SER 3.6 2.3 - - - +
312D PHE* 2.8 28.4 - - - -
313D PHE* 2.8 18.3 + - + +
315D VAL* 3.6 31.0 - - + -
328D ARG 3.9 0.6 + - - -
329D LEU* 1.3 72.8 - - - +
331D GLY* 1.3 67.2 + - - +
332D ILE* 3.9 9.0 - - + -
337D VAL* 3.8 22.4 - - + -
338D MET 3.4 11.9 - - - +
339D ARG* 5.2 1.6 - - + -
351D TRP* 5.6 0.2 - - + -
366D PHE* 4.1 31.4 - - + -
368D LEU* 5.9 0.2 - - + -
378D TYR* 4.6 23.3 - - + +
380D VAL* 5.1 0.2 - - + -
388D ILE* 4.2 17.3 - - + -
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Residues in contact with GLY 331 (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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310D VAL* 3.5 17.9 - - - -
311D SER 4.1 0.9 - - - -
312D PHE* 3.6 15.1 - - - -
330D LEU* 1.3 72.3 - - - +
332D ILE* 1.3 76.3 + - - +
333D THR* 5.4 0.2 - - - -
337D VAL* 3.3 0.7 - - - -
338D MET* 2.9 38.3 + - - -
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Residues in contact with ILE 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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309D GLY 5.0 0.2 - - - +
310D VAL* 3.2 4.3 - - - +
311D SER* 3.2 35.1 + - - +
313D PHE* 4.8 2.0 - - + -
330D LEU* 3.9 17.9 - - + -
331D GLY* 1.3 93.6 - - - +
333D THR* 1.3 75.8 + - - +
336D CYS 3.6 5.4 - - - +
337D VAL* 3.3 32.5 - - + -
353D LEU* 4.4 2.0 - - + -
368D LEU* 5.2 0.7 - - + -
388D ILE* 4.6 12.8 - - + -
391D LEU* 3.8 25.8 - - + -
392D ILE* 4.0 25.6 - - + -
395D TYR* 4.3 9.7 + - + -
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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