Contacts of the helix formed by residues 344 - 358 (chain A) in PDB entry 5MJU
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 344 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89A MET* 4.6 4.9 - - - -
93A LYS* 4.7 7.5 - - - -
342A THR* 3.2 10.3 + - - -
343A SER* 1.3 79.9 - - - +
345A SER* 1.4 53.4 + - - +
346A SER* 3.1 25.2 + - - -
347A ALA* 3.4 15.8 + - - +
348A THR* 2.8 30.3 + - - -
460A THR* 3.6 4.6 - - - +
602A 7O9 3.4 13.4 + - - -
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Residues in contact with SER 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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344A SER* 1.4 70.4 - - - +
346A SER* 1.4 54.9 + - - +
348A THR* 3.5 8.9 + - - -
349A LEU* 2.9 29.1 + - - +
375A ALA* 2.8 35.9 + - - +
460A THR* 3.5 7.5 - - - +
463A ASN* 4.5 7.9 - - - -
464A VAL* 4.0 19.3 - - - +
467A ASP* 5.5 0.2 - - - -
602A 7O9 2.7 37.7 + - - -
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Residues in contact with SER 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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93A LYS* 4.9 7.9 - - - +
96A ILE* 3.1 39.3 - - - +
223A ILE* 5.2 0.2 - - - +
344A SER* 3.3 12.1 - - - -
345A SER* 1.4 76.8 + - - +
347A ALA* 1.4 63.5 + - - +
349A LEU* 3.2 12.5 + - - +
350A PRO* 3.4 1.2 - - - +
602A 7O9 3.4 48.7 - - - -
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Residues in contact with ALA 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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89A MET* 3.7 33.2 - - + -
92A LEU* 3.4 36.9 - - + +
93A LYS* 4.5 13.6 - - - +
96A ILE* 4.8 1.8 - - - -
342A THR* 3.9 9.6 - - + -
344A SER* 3.4 15.7 + - - +
346A SER* 1.4 77.4 + - - +
348A THR* 1.3 57.9 + - - +
350A PRO* 3.4 10.6 - - - +
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Residues in contact with THR 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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335A ALA 4.1 8.7 - - - -
338A THR* 3.4 28.3 - - - +
339A ALA* 3.5 14.8 - - - +
342A THR* 3.2 26.7 - - + +
344A SER 2.8 14.5 + - - -
345A SER* 3.5 10.9 + - - -
346A SER 3.2 0.2 - - - -
347A ALA* 1.3 72.4 - - - +
349A LEU* 1.4 58.6 + - - +
350A PRO* 3.3 3.4 - - - -
351A ILE* 3.0 11.1 + - + +
352A THR* 2.8 33.4 + - - -
464A VAL* 3.9 10.1 - - - +
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Residues in contact with LEU 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A ILE* 5.2 0.9 - - + -
99A LEU* 3.9 12.3 - - + -
100A ILE* 3.9 13.9 - - + -
345A SER 2.9 18.5 + - - +
346A SER 3.2 8.9 + - - +
348A THR* 1.4 74.8 - - - +
350A PRO* 1.4 57.6 - - + +
352A THR* 3.6 7.9 - - + -
353A PHE* 2.8 48.9 + - + +
371A LEU* 3.3 45.3 - - + +
372A PRO* 3.9 6.7 - - + -
375A ALA* 3.6 11.2 - - + -
467A ASP* 5.4 1.1 - - - +
602A 7O9 3.2 22.7 - - - -
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Residues in contact with PRO 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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92A LEU* 4.1 25.1 - - + +
95A LEU* 4.6 12.3 - - + -
96A ILE* 4.0 8.3 - - + -
99A LEU* 3.9 21.7 - - + -
258A THR 5.9 0.2 - - - +
259A MET* 4.1 0.3 - - - +
262A VAL* 3.4 31.9 - - + +
346A SER 3.4 13.5 - - - +
347A ALA 3.4 14.1 - - - +
348A THR 3.4 3.1 - - - -
349A LEU* 1.4 89.7 - - + +
351A ILE* 1.4 54.9 + - - +
353A PHE* 3.4 5.7 - - + +
354A LYS 3.2 18.5 + - - -
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Residues in contact with ILE 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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92A LEU* 3.8 31.4 - - + -
262A VAL* 4.2 9.9 - - + -
266A MET* 3.8 25.8 - - + -
269A ALA* 6.0 2.7 - - + -
334A GLN* 3.9 32.1 - - + +
335A ALA* 4.2 2.2 - - - -
338A THR* 3.6 29.6 - - + +
347A ALA 4.0 0.2 - - - +
348A THR* 3.0 25.9 + - + +
350A PRO* 1.4 72.0 - - - +
352A THR* 1.4 56.5 + - - +
353A PHE 3.2 0.2 - - - -
354A LYS* 3.0 4.2 + - - +
355A CYS* 2.8 33.7 + - - +
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Residues in contact with THR 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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332A ILE* 5.6 2.0 - - + -
335A ALA* 3.5 22.4 - - + +
348A THR* 2.8 21.6 + - - -
349A LEU* 3.6 11.6 - - + -
351A ILE* 1.4 70.9 - - - +
353A PHE* 1.4 63.1 + - - +
355A CYS* 3.3 1.8 + - - +
356A LEU* 3.1 43.9 + - + +
371A LEU* 3.9 15.3 - - + -
464A VAL* 3.5 29.7 - - + +
467A ASP* 6.1 0.9 - - - +
468A ALA* 4.8 4.9 - - + -
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Residues in contact with PHE 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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99A LEU* 3.7 19.3 - - + -
100A ILE* 5.9 0.2 - - + -
103A SER* 3.3 26.7 - - - -
255A ASN* 4.7 1.6 - - - -
259A MET* 3.7 13.2 - - + -
349A LEU* 2.8 48.6 + - + +
350A PRO* 3.4 9.2 - - + +
352A THR* 1.4 75.6 - - - +
354A LYS* 1.4 56.4 + - - +
356A LEU* 4.2 1.0 - - - +
357A GLU* 3.1 62.5 + - - +
367A THR* 3.7 18.2 - - + -
368A ARG* 3.9 17.7 - - + -
371A LEU* 3.6 25.0 - - + +
372A PRO* 3.7 10.3 - - + -
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Residues in contact with LYS 354 (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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259A MET* 3.5 41.5 - - + +
262A VAL* 3.9 6.1 - - + -
263A ALA* 4.8 10.3 - - + +
266A MET* 3.8 28.7 - - + -
350A PRO 3.2 8.5 + - - +
351A ILE 3.0 8.7 + - - +
353A PHE* 1.4 77.0 - - - +
355A CYS* 1.3 57.1 + - - +
357A GLU* 4.6 5.2 - - - +
358A GLU* 2.8 74.7 + - + +
359A ASN* 5.5 0.2 - - - -
364A LYS* 5.6 3.1 - - - +
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Residues in contact with CYS 355 (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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266A MET* 6.2 1.3 - - - -
331A GLY 3.3 20.4 - - - -
332A ILE* 3.6 31.8 - - + +
334A GLN* 3.8 29.6 - - - -
335A ALA* 3.9 11.9 - - + -
351A ILE* 2.8 20.4 + - - +
352A THR 3.3 4.0 + - - +
354A LYS* 1.3 71.1 - - - +
356A LEU* 1.3 55.7 + - - +
359A ASN* 3.3 32.8 - - - +
360A ASN 3.3 6.1 + - - -
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Residues in contact with LEU 356 (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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328A PHE* 3.7 31.0 - - + -
332A ILE* 3.7 17.7 - - + -
352A THR* 3.1 29.5 + - + +
353A PHE 4.3 1.8 - - - +
355A CYS* 1.3 73.3 - - - +
357A GLU* 1.3 57.1 + - - +
358A GLU 3.4 1.6 - - - -
360A ASN* 3.9 2.9 - - - +
361A GLY 3.2 9.1 + - - -
362A VAL* 2.8 49.1 + - + +
367A THR* 4.4 9.9 - - + -
371A LEU* 3.6 33.2 - - + -
468A ALA* 3.7 18.4 - - + +
471A ALA* 4.6 5.6 - - + -
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Residues in contact with GLU 357 (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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255A ASN* 5.0 0.3 - - - +
259A MET* 3.4 21.4 - - + +
353A PHE* 3.1 42.5 + - - +
354A LYS* 4.4 5.6 - - - +
356A LEU* 1.3 76.5 - - - +
358A GLU* 1.4 59.3 + - + +
361A GLY* 4.2 9.1 - - - -
362A VAL 4.1 9.3 - - - +
364A LYS* 2.8 60.0 + - + +
367A THR* 3.5 23.7 - - + +
368A ARG* 4.4 2.9 + - - +
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Residues in contact with GLU 358 (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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266A MET* 5.8 2.6 - - - +
354A LYS* 2.8 51.3 + - + +
357A GLU* 1.4 79.1 - - - +
359A ASN* 1.3 87.8 + - - +
361A GLY* 4.2 4.7 + - - -
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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