Contacts of the helix formed by residues 355 - 365 (chain A) in PDB entry 1GM5
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 GLY 355 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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353A ILE 3.5 6.3 + - - -
354A GLU* 1.3 69.1 - - - +
356A LYS* 1.3 67.7 + - - +
357A LEU 3.4 0.2 + - - -
358A ALA* 3.6 5.7 + - - +
359A GLU* 3.0 26.9 + - - +
381A ARG* 5.5 5.1 - - - +
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Residues in contact with LYS 356 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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354A GLU* 2.4 47.6 + - + +
355A GLY* 1.3 69.0 - - - +
357A LEU* 1.3 75.6 + - + +
359A GLU* 3.3 4.4 + - - +
360A GLU* 3.1 21.7 + - - +
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Residues in contact with LEU 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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354A GLU* 3.0 6.3 + - - +
356A LYS* 1.3 81.8 - - + +
358A ALA* 1.3 49.8 + - - +
360A GLU* 2.7 17.1 + - + +
361A PHE* 2.6 31.2 + - - +
411A LEU* 3.6 35.9 - - + +
412A ASP* 5.9 0.2 - - - +
414A TYR* 4.4 10.5 - - + -
415A GLU* 2.5 58.3 - - + +
444A PHE* 5.0 19.9 - - + -
445A ASN* 5.7 5.4 - - - +
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Residues in contact with ALA 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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354A GLU 4.5 0.4 + - - +
355A GLY* 3.6 7.0 + - - +
356A LYS 3.5 0.6 - - - -
357A LEU* 1.3 76.9 - - - +
359A GLU* 1.3 55.5 + - - +
360A GLU 2.8 0.3 + - - -
361A PHE* 2.8 8.4 + - - -
362A ILE* 2.3 59.5 + - + +
377A HIS* 3.9 15.7 - - - +
381A ARG* 4.1 15.9 - - - +
408A LEU* 4.4 3.6 - - + -
411A LEU* 4.2 4.4 - - + +
412A ASP* 4.8 1.5 + - - +
415A GLU* 4.4 0.8 + - - -
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Residues in contact with GLU 359 (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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355A GLY 3.0 21.3 + - - +
356A LYS* 3.6 4.7 - - - +
358A ALA* 1.3 74.7 - - - +
360A GLU* 1.3 72.0 + - + +
362A ILE* 3.9 6.3 - - - +
363A LYS* 2.8 57.6 + - - +
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Residues in contact with GLU 360 (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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356A LYS* 3.1 14.8 + - - +
357A LEU* 2.7 17.4 + - + +
359A GLU* 1.3 79.1 - - + +
361A PHE* 1.3 68.1 + - - +
362A ILE 2.7 2.1 + - - -
363A LYS* 2.9 6.9 + - - +
364A SER* 2.9 22.6 + - - -
444A PHE* 4.8 12.6 - - + -
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Residues in contact with PHE 361 (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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357A LEU 2.6 9.7 + - - -
358A ALA* 2.8 8.0 + - - +
360A GLU* 1.3 73.5 - - - +
362A ILE* 1.3 67.1 + - + +
364A SER* 3.0 17.2 + - - -
365A LEU* 3.0 31.5 - - + +
404A VAL* 5.7 3.8 - - + -
407A GLN* 3.7 42.8 - - + -
408A LEU* 4.5 14.8 - - + -
411A LEU* 3.2 36.6 - - + -
440A SER* 4.6 18.8 - - - -
441A PHE* 4.3 13.7 - + - -
444A PHE* 4.5 12.8 - + + -
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Residues in contact with ILE 362 (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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358A ALA* 2.3 66.2 + - + +
359A GLU* 3.9 5.8 - - - +
360A GLU 2.7 1.6 + - - -
361A PHE* 1.3 70.4 - - - +
363A LYS* 1.3 66.3 + - + +
365A LEU* 3.1 28.2 + - + +
367A PHE 5.4 1.0 - - - +
368A LYS 5.1 4.7 - - - +
369A LEU* 3.7 32.3 - - + -
374A LYS* 5.8 2.2 - - - +
377A HIS* 4.3 7.6 - - + +
408A LEU* 3.6 22.0 - - + -
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Residues in contact with LYS 363 (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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359A GLU* 2.8 53.7 + - - +
360A GLU* 2.9 6.0 + - - +
362A ILE* 1.3 81.1 - - + +
364A SER* 1.3 62.6 + - - +
365A LEU 3.3 7.1 + - - +
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Residues in contact with SER 364 (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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360A GLU* 2.9 11.7 + - - -
361A PHE* 3.0 21.3 + - - -
363A LYS* 1.3 77.7 - - - +
365A LEU* 1.3 65.7 + - - +
366A PRO* 4.4 0.9 - - - +
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Residues in contact with LEU 365 (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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361A PHE* 3.0 45.3 - - + +
362A ILE* 3.1 33.5 + - + +
363A LYS 3.4 7.6 - - - +
364A SER* 1.3 82.2 - - - +
366A PRO* 1.3 77.9 - - + +
367A PHE* 4.1 38.7 - - + +
368A LYS 5.6 0.4 - - - +
369A LEU* 5.1 3.8 - - + -
404A VAL* 5.0 10.3 - - + -
408A LEU* 6.3 0.7 - - + -
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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