Contacts of the helix formed by residues 340 - 353 (chain A) in PDB entry 1MUK
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 LEU 340 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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255A GLN 5.5 0.2 - - - -
256A ILE* 4.0 28.5 - - + -
259A HIS* 3.4 33.7 - - + +
269A PHE* 4.0 20.9 - - + -
273A THR* 4.0 20.2 - - + -
276A ILE* 4.6 9.0 - - + -
335A GLY* 2.8 22.9 + - - +
338A TYR* 3.2 11.4 - - + +
339A GLY* 1.3 84.2 - - - +
341A SER* 1.3 62.7 + - - +
342A SER* 3.2 6.1 - - - -
343A VAL* 2.9 26.5 + - + +
344A VAL* 3.0 11.6 + - - +
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Residues in contact with SER 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A ARG* 5.2 2.6 + - - -
335A GLY* 3.5 9.1 + - - -
336A GLU* 3.7 42.6 + - - +
339A GLY* 3.8 2.0 - - - -
340A LEU* 1.3 77.7 + - - +
342A SER* 1.3 53.4 + - - +
344A VAL* 3.8 4.6 - - - +
345A GLY* 2.7 32.4 + - - -
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Residues in contact with SER 342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A GLN* 4.4 6.9 + - - -
339A GLY 5.3 1.2 + - - -
340A LEU* 4.3 3.6 + - - -
341A SER* 1.3 79.4 + - - +
343A VAL* 1.3 67.0 + - - +
345A GLY* 3.9 0.8 - - - -
346A GLU* 2.9 30.7 + - - +
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Residues in contact with VAL 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A LEU* 4.4 22.9 - - + +
255A GLN* 3.7 33.9 - - + +
256A ILE* 4.1 20.2 - - + -
276A ILE* 4.1 14.1 - - + -
277A PHE* 4.8 0.2 - - + -
340A LEU* 2.9 20.7 + - + +
342A SER* 1.3 81.8 + - - +
344A VAL* 1.3 67.2 + - - +
346A GLU* 3.4 4.6 + - - +
347A LEU* 3.0 40.9 + - + +
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Residues in contact with VAL 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A ILE* 3.6 32.8 - - + -
280A ASN* 3.4 31.0 - - - +
331A ALA 3.9 18.6 - - - +
332A ARG* 4.2 14.6 - - + +
335A GLY* 3.8 15.3 - - - -
340A LEU 3.0 14.8 + - - +
341A SER* 3.8 7.9 - - - +
343A VAL* 1.3 75.1 - - - +
345A GLY* 1.3 64.7 + - - +
347A LEU* 3.1 4.7 + - - +
348A ARG* 2.9 28.7 + - + +
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Residues in contact with GLY 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A ARG* 4.0 22.9 + - - +
341A SER 2.7 21.0 + - - -
342A SER* 3.9 1.3 - - - -
344A VAL* 1.3 74.0 - - - +
346A GLU* 1.3 60.3 + - - +
348A ARG* 3.4 3.1 + - - +
349A LYS* 3.0 24.7 + - - +
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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
----------------------------------------------------------
252A LEU* 4.6 20.2 - - + -
342A SER 2.9 19.0 + - - +
343A VAL* 3.8 5.4 - - - +
345A GLY* 1.3 74.4 - - - +
347A LEU* 1.3 58.2 + - - +
349A LYS* 3.3 22.4 + - - +
350A ARG* 2.9 57.7 + - - +
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Residues in contact with LEU 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A LEU* 3.9 28.3 - - + -
252A LEU* 3.9 11.4 - - + -
276A ILE* 3.8 20.4 - - + -
277A PHE* 3.4 39.0 - - + -
280A ASN* 3.8 18.6 - - + +
281A THR* 4.1 17.9 - - + -
343A VAL* 3.0 23.7 + - + +
344A VAL* 3.6 3.8 - - - +
346A GLU* 1.3 77.0 - - - +
348A ARG* 1.3 56.1 + - - +
350A ARG* 3.4 2.1 + - - -
351A THR* 2.9 33.6 + - - -
364A TYR* 3.4 7.0 + - - +
368A ALA* 4.8 0.4 - - + -
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Residues in contact with ARG 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A ASN* 2.9 31.8 + - + +
284A SER* 3.0 24.0 + - - -
287A GLU* 4.8 8.3 + - - -
326A SER* 5.1 1.6 + - - -
327A ASN* 2.9 40.8 + - - +
328A ASP* 3.4 46.9 + - - +
331A ALA* 3.8 8.3 - - - +
332A ARG* 3.8 20.2 - - - +
344A VAL* 2.9 21.6 + - + +
345A GLY 3.7 4.5 - - - +
347A LEU* 1.3 74.6 - - - +
349A LYS* 1.3 62.5 + - - +
351A THR* 3.3 4.2 + - - -
352A LYS* 3.2 45.6 + - - +
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Residues in contact with LYS 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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332A ARG* 5.6 0.2 - - - +
345A GLY 3.0 16.8 + - - +
346A GLU* 3.5 21.5 + - - +
348A ARG* 1.3 74.4 - - - +
350A ARG* 1.3 69.2 + - + +
352A LYS* 3.4 18.1 + - - +
353A THR* 3.6 14.2 + - + +
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Residues in contact with ARG 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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246A ASP* 2.7 24.5 + - - -
248A SER* 2.8 28.2 + - - -
249A LEU* 3.4 31.3 - - - +
252A LEU* 5.5 1.4 - - - +
346A GLU* 2.9 46.4 + - - +
347A LEU* 3.8 2.0 - - - +
349A LYS* 1.3 76.4 - - + +
351A THR* 1.3 63.4 + - - +
353A THR* 2.7 32.9 + - - +
354A TYR* 3.5 14.1 + - + -
364A TYR* 3.5 28.9 - - + +
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Residues in contact with THR 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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280A ASN 2.7 25.6 + - - +
281A THR* 3.5 6.3 - - - +
284A SER* 3.4 33.2 - - - +
285A MET* 3.7 19.0 - - - +
286A TYR 5.3 2.1 + - - -
347A LEU 2.9 13.7 + - - -
348A ARG* 3.6 6.3 - - - +
349A LYS 3.3 0.4 - - - -
350A ARG* 1.3 76.7 - - - +
352A LYS* 1.3 64.8 + - + +
353A THR 3.2 0.7 + - - -
354A TYR* 3.3 20.8 + - - +
364A TYR* 3.1 20.2 + - - -
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Residues in contact with LYS 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A SER 6.1 0.7 - - - +
287A GLU* 4.3 33.2 + - + +
288A SER* 5.9 1.4 - - - -
328A ASP* 4.7 4.4 + - - -
332A ARG* 4.7 4.4 - - - +
348A ARG* 3.2 49.5 + - - +
349A LYS* 3.8 10.8 - - - +
350A ARG 3.2 1.0 - - - -
351A THR* 1.3 78.6 - - + +
353A THR* 1.3 60.4 + - + +
354A TYR 3.3 3.1 + - - +
355A VAL* 3.9 13.3 - - - +
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Residues in contact with THR 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 LYS* 3.6 15.3 - - + +
350A ARG* 2.7 24.9 + - - +
352A LYS* 1.3 77.1 - - - +
354A TYR* 1.3 74.1 + - - +
355A VAL* 3.2 13.1 + - - +
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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