Contacts of the helix formed by residues 343 - 356 (chain A) in PDB entry 1MK2
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 ASN 343 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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301A GLU* 3.4 9.8 + - - -
318A ASN* 3.3 12.4 + - - +
322A ARG* 3.1 26.8 - - - +
340A LYS* 3.6 23.3 - - + +
342A PHE* 1.3 70.8 - - - +
344A ASN* 1.3 64.9 + - - +
345A GLN* 2.9 24.4 + - - +
346A GLU* 2.8 40.0 + - + +
347A PHE* 2.9 16.8 + - - +
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Residues in contact with ASN 344 (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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225A TYR* 3.3 47.8 - - - -
299A GLY 4.1 5.2 + - - +
300A GLY* 3.0 33.8 + - - +
301A GLU* 2.7 11.2 + - - +
342A PHE* 3.6 19.8 - - - -
343A ASN* 1.3 71.9 - - - +
345A GLN* 1.3 56.4 + - + +
347A PHE* 3.0 14.9 - - - +
348A ALA* 2.8 27.0 + - - +
402A PRO* 4.4 0.3 - - - +
405A TRP* 4.2 2.1 - - - -
701B PRO* 3.8 17.4 - - - +
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Residues in contact with GLN 345 (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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299A GLY 5.7 1.6 - - - +
301A GLU* 3.8 20.1 - - - +
340A LYS* 5.1 1.7 + - - -
343A ASN* 3.1 15.2 + - - +
344A ASN* 1.3 73.7 - - + +
346A GLU* 1.3 61.0 + - - +
347A PHE 2.8 0.9 - - - -
348A ALA* 2.6 31.0 + - - +
349A ALA* 2.8 12.6 + - - +
693B SER* 5.0 8.0 + - - +
694B GLY 5.6 0.3 - - - +
695B ALA* 4.8 10.4 - - - +
698B SER* 6.1 1.3 - - - +
701B PRO* 5.6 4.0 - - + -
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Residues in contact with GLU 346 (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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318A ASN* 3.1 43.6 + - - +
321A GLN* 3.5 18.2 - - + +
322A ARG* 3.5 21.3 + - + +
343A ASN* 2.8 30.8 + - + +
345A GLN* 1.3 73.4 - - - +
347A PHE* 1.3 61.4 + - - +
349A ALA* 3.4 10.2 + - + +
350A LEU* 3.2 43.8 + - + +
368A MET* 4.0 1.4 - - - +
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Residues in contact with PHE 347 (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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318A ASN* 4.5 0.4 - - - +
342A PHE* 3.4 24.9 - + + -
343A ASN 2.9 13.7 + - - +
344A ASN* 3.0 18.8 - - - +
345A GLN 2.7 1.0 + - - -
346A GLU* 1.3 79.8 + - - +
348A ALA* 1.3 51.9 + - - -
350A LEU* 3.1 6.1 + - + +
351A LEU* 2.7 37.2 + - + +
365A LEU* 3.9 32.8 - - + -
368A MET* 3.9 19.3 - - + -
369A CYS* 4.5 1.6 - - - -
402A PRO* 3.8 19.1 - - + -
405A TRP* 3.7 31.6 - + - -
406A LEU* 3.3 39.5 - - + -
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Residues in contact with ALA 348 (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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344A ASN 2.8 9.2 + - - +
345A GLN* 2.6 15.6 + - - +
347A PHE* 1.3 71.7 - - - +
349A ALA* 1.3 52.2 + - - +
351A LEU* 3.3 1.9 - - - +
352A ALA* 2.5 39.3 + - - +
405A TRP* 3.2 35.2 - - + -
701B PRO* 4.0 17.0 - - + -
702B THR 5.6 0.9 - - - +
703B VAL* 3.7 5.4 - - + +
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Residues in contact with ALA 349 (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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345A GLN 2.8 9.9 + - - +
346A GLU* 3.4 14.6 - - + +
348A ALA* 1.3 78.3 - - - +
350A LEU* 1.3 60.7 + - + +
352A ALA* 3.3 7.3 - - - +
353A GLN* 2.9 29.5 + - - +
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Residues in contact with LEU 350 (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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321A GLN* 3.2 40.2 - - + +
346A GLU* 3.2 35.7 - - + +
347A PHE* 3.1 6.2 + - - +
349A ALA* 1.3 75.0 - - + +
351A LEU* 1.3 57.0 + - - +
353A GLN* 3.1 20.6 + - - +
354A SER* 2.5 44.7 + - - +
365A LEU* 3.9 11.0 - - + -
368A MET* 3.8 20.9 - - + -
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Residues in contact with LEU 351 (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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347A PHE* 2.7 19.3 + - + +
348A ALA* 3.3 8.7 - - - +
350A LEU* 1.3 73.4 - - - +
352A ALA* 1.3 63.0 + - - +
354A SER* 3.5 0.6 - - - -
355A VAL* 2.9 32.1 + - + +
362A VAL* 4.4 8.5 - - + -
365A LEU* 3.5 12.7 - - + +
405A TRP* 3.3 50.7 - - + +
406A LEU* 3.5 30.3 - - + -
409A VAL* 3.9 26.0 - - + -
703B VAL* 3.9 13.2 - - + -
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Residues in contact with ALA 352 (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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348A ALA 2.5 20.7 + - - +
349A ALA* 3.3 9.4 - - - +
351A LEU* 1.3 75.6 - - - +
353A GLN* 1.3 65.0 + - - +
355A VAL* 3.2 18.8 + - - +
356A ASN* 3.7 9.7 + - - -
703B VAL* 3.7 20.5 - - + +
704B MET 5.4 0.8 - - - +
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Residues in contact with GLN 353 (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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349A ALA 2.9 13.6 + - - +
350A LEU* 3.5 26.1 - - - +
352A ALA* 1.3 76.2 - - - +
354A SER* 1.3 67.5 + - - +
356A ASN* 3.1 26.7 + - - +
357A GLN* 3.6 24.8 + - - +
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Residues in contact with SER 354 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A LEU* 2.5 32.8 + - - +
351A LEU* 3.5 5.6 - - - -
353A GLN* 1.3 75.1 + - - +
355A VAL* 1.3 69.1 + - - +
357A GLN* 2.6 30.1 + - - +
358A GLY 3.7 5.7 + - - +
361A ALA* 3.9 4.3 + - - +
362A VAL* 3.6 26.5 - - - -
365A LEU* 3.4 18.1 - - - +
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Residues in contact with VAL 355 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A LEU* 2.9 46.1 + - + +
352A ALA* 3.3 11.9 - - - +
354A SER* 1.3 70.7 - - - +
356A ASN* 1.3 59.1 + - - +
357A GLN 3.0 6.2 + - - -
358A GLY 3.2 4.3 + - - -
362A VAL* 3.5 9.2 - - - +
409A VAL* 4.2 4.9 - - + -
413A MET* 3.1 27.4 - - + +
703B VAL* 4.8 1.3 - - + -
704B MET 3.7 6.5 - - - +
705B VAL* 3.3 34.1 - - + -
706B PRO* 3.2 35.0 - - + +
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Residues in contact with ASN 356 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220A LEU* 5.3 3.1 - - - +
352A ALA 3.9 13.4 + - - -
353A GLN* 3.1 11.5 + - - +
354A SER 2.8 3.8 + - - -
355A VAL* 1.3 79.4 - - - +
357A GLN* 1.3 64.8 + - + +
358A GLY 3.6 0.9 - - - -
704B MET 5.2 2.4 + - - +
706B PRO* 4.4 11.9 - - - +
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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