Contacts of the strand formed by residues 365 - 372 (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 SER 365 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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361D ALA* 3.5 4.3 - - - +
362D SER* 2.3 51.9 + - - +
364D LYS* 1.3 81.0 - - - +
366D PHE* 1.3 63.7 + - - +
367D THR* 4.9 5.3 + - - -
379D SER* 5.9 2.0 - - - -
380D VAL 3.2 14.8 - - - -
382D THR* 3.1 10.5 + - - -
385D GLY* 4.1 2.3 - - - -
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Residues in contact with PHE 366 (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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330D LEU* 4.1 16.6 - - + -
332D ILE* 6.0 0.2 - - + -
359D TRP* 4.6 6.3 - - + -
360D ALA 3.5 17.5 - - - -
361D ALA* 4.6 0.2 - - + -
365D SER* 1.3 76.1 - - - +
367D THR* 1.3 68.7 + - - +
368D LEU* 4.0 28.5 - - + -
378D TYR* 3.7 4.8 - + - +
379D SER* 3.2 2.8 - - - -
380D VAL* 2.9 45.3 + - + +
382D THR* 3.4 21.5 - - + -
385D GLY* 4.0 16.4 - - - -
388D ILE* 3.6 29.6 - - + -
389D ALA* 4.2 7.4 - - + -
392D ILE* 3.4 30.1 - - + -
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Residues in contact with THR 367 (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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739A TRP* 4.1 12.1 - - + -
359D TRP* 3.3 6.4 - - - +
360D ALA* 3.0 39.5 + - - +
365D SER* 4.9 4.9 + - - -
366D PHE* 1.3 81.6 + - - +
368D LEU* 1.3 64.2 + - - +
369D ASP 4.2 0.2 - - - -
377D TYR* 3.7 36.6 - - + -
378D TYR 3.4 4.7 - - - +
379D SER* 2.6 27.7 + - - +
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Residues in contact with LEU 368 (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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330D LEU* 5.9 0.2 - - + -
332D ILE* 5.2 0.4 - - + -
337D VAL* 4.0 34.3 - - + -
351D TRP* 5.6 0.4 - - + -
356D ILE* 3.4 47.8 - - + -
358D ARG 4.0 2.9 - - - +
359D TRP* 4.7 5.4 - - + -
366D PHE* 4.0 28.5 - - + -
367D THR* 1.3 73.4 - - - +
369D ASP* 1.3 59.9 + - - +
370D PHE* 4.0 22.1 + - + -
376D GLY 4.6 0.3 - - - +
377D TYR* 3.8 5.5 - - - -
378D TYR* 3.1 43.7 + - + +
392D ILE* 4.4 5.4 - - + -
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Residues in contact with ASP 369 (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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739A TRP* 3.9 2.9 - - + -
356D ILE* 4.1 0.3 - - - -
357D LYS* 3.0 53.1 + - - +
358D ARG* 2.9 40.5 + - + +
367D THR 4.2 0.6 + - - -
368D LEU* 1.3 72.2 - - - +
370D PHE* 1.3 60.7 + - - +
371D GLY* 3.0 18.6 + - - -
372D ASP 4.6 0.2 + - - -
376D GLY 4.2 6.4 - - - +
377D TYR* 3.2 34.5 - - + -
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Residues in contact with PHE 370 (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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747A TYR* 3.1 16.8 + - - -
300B LYS* 3.2 11.4 + - - +
337D VAL* 4.8 1.3 - - + -
351D TRP* 3.2 71.8 - + + -
352D SER 4.0 4.7 - - - -
355D ASN* 2.9 41.8 - - + +
356D ILE* 3.2 27.1 - - + -
357D LYS* 4.0 1.6 - - - -
368D LEU* 4.0 29.8 + - + -
369D ASP* 1.3 76.9 + - - +
371D GLY* 1.3 60.1 + - - +
372D ASP* 4.2 18.6 - - + +
376D GLY 4.7 5.1 + - - +
378D TYR* 5.4 2.7 - - + -
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Residues in contact with GLY 371 (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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747A TYR* 4.7 5.2 - - - -
297B ARG* 3.4 15.4 + - - -
300B LYS* 4.0 8.6 + - - -
357D LYS* 4.4 15.3 - - - -
369D ASP* 3.0 15.4 + - - -
370D PHE* 1.3 81.2 - - - +
372D ASP* 1.3 60.4 + - - +
373D TYR 3.8 0.8 + - - -
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Residues in contact with ASP 372 (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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297B ARG* 3.4 21.7 + - - +
300B LYS* 5.3 2.9 - - - +
351D TRP* 5.8 0.9 + - - -
369D ASP* 4.6 1.0 + - - -
370D PHE* 4.2 16.6 - - + +
371D GLY* 1.3 76.7 - - - +
373D TYR* 1.3 70.3 + - - +
374D GLN* 4.9 2.5 + - - +
375D ASP* 2.4 44.8 + - + +
376D GLY* 3.0 21.5 + - - +
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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