Contacts of the helix formed by residues 384 - 396 (chain A) in PDB entry 3RSG
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 384 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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380A ASP 2.9 24.6 + - - +
381A VAL* 3.0 19.2 + - - +
382A LYS 3.1 1.7 - - - +
383A TYR* 1.3 75.4 - - - +
385A TYR* 1.3 61.9 + - - +
386A GLU* 3.6 9.2 + - - +
387A LEU* 3.0 33.1 + - + +
388A ALA* 3.0 20.1 + - - +
401A LEU* 4.6 2.1 - - - +
407A ILE* 4.5 2.3 - - - +
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Residues in contact with TYR 385 (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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155A ASN* 2.7 34.6 + - - +
156A THR* 5.0 4.9 - - + +
177A ILE* 3.2 25.9 - - + +
181A LEU* 3.8 13.0 - - + -
208A ARG* 3.6 38.7 + - - -
383A TYR 3.1 15.5 + - - -
384A ASN* 1.3 74.1 + - - +
386A GLU* 1.3 91.5 + - + +
388A ALA* 3.2 5.6 + - - +
389A GLU* 2.9 36.5 + - - +
407A ILE* 3.7 28.9 - - + -
414A THR* 4.6 0.9 - - + -
416A PHE* 4.3 10.1 - + + -
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Residues in contact with GLU 386 (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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208A ARG* 4.3 6.9 + - - +
384A ASN* 3.3 7.9 + - - +
385A TYR* 1.3 107.0 + - + +
387A LEU* 1.3 61.8 + - - +
389A GLU* 3.3 14.7 + - - +
390A GLU* 3.0 29.9 + - + +
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Residues in contact with LEU 387 (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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370A MET* 4.6 11.2 - - + -
374A VAL* 4.4 11.4 - - + -
376A LYS* 3.9 33.7 - - + +
380A ASP 4.4 0.9 - - - +
381A VAL* 3.9 31.6 - - + -
384A ASN* 3.0 37.2 + - + +
386A GLU* 1.3 72.5 - - - +
388A ALA* 1.3 66.2 + - - +
390A GLU* 3.3 18.6 + - + +
391A PHE* 3.0 24.7 + - + +
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Residues in contact with ALA 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370A MET* 4.6 3.5 - - + +
384A ASN 3.0 13.5 + - - +
385A TYR* 3.2 11.6 + - - +
387A LEU* 1.3 76.5 - - - +
389A GLU* 1.3 56.3 + - - +
391A PHE* 3.3 3.6 + - - +
392A ALA* 3.0 29.5 + - - +
399A LEU* 3.6 27.4 - - + +
401A LEU* 4.9 12.8 - - + -
407A ILE* 4.5 10.1 - - + +
409A THR* 3.7 14.1 - - + +
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Residues in contact with GLU 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A ARG* 2.7 43.2 + - - -
385A TYR* 2.9 20.1 + - - +
386A GLU* 3.6 15.7 - - - +
387A LEU 3.3 0.2 - - - -
388A ALA* 1.3 75.0 - - - +
390A GLU* 1.3 59.0 + - + +
392A ALA 3.3 0.5 + - - -
393A LYS* 3.0 30.8 + - - +
409A THR* 3.3 17.2 - - - +
411A GLY* 3.4 17.4 - - - +
412A GLU 5.7 1.1 - - - +
414A THR* 2.6 33.1 + - + +
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Residues in contact with GLU 390 (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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386A GLU* 3.0 21.5 + - + +
387A LEU* 3.3 21.2 + - + +
389A GLU* 1.3 71.9 - - + +
391A PHE* 1.3 62.5 + - - +
393A LYS* 3.4 5.0 + - - +
394A GLU* 2.9 49.8 + - - +
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Residues in contact with PHE 391 (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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351A THR* 4.2 18.2 - - + -
354A LEU* 4.3 2.0 - - + -
363A LEU* 4.1 15.3 - - + -
370A MET* 4.1 12.1 - - + -
373A LEU* 3.7 22.0 - - + -
374A VAL* 3.7 28.9 - - + -
387A LEU* 3.0 20.1 + - + +
388A ALA 3.6 3.6 - - - +
390A GLU* 1.3 77.4 - - - +
392A ALA* 1.3 64.5 + - - +
394A GLU* 4.7 2.5 - - - -
395A ASN* 2.9 56.8 + - + +
397A CYS* 3.9 21.8 - - - -
399A LEU* 4.2 17.7 - - + -
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Residues in contact with ALA 392 (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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388A ALA 3.0 15.9 + - - +
389A GLU 3.7 0.9 - - - +
390A GLU 3.2 0.4 - - - -
391A PHE* 1.3 77.1 - - - +
393A LYS* 1.3 58.0 + - - +
396A ASP* 2.9 26.2 + - - -
397A CYS* 3.1 36.8 + - - +
399A LEU* 4.4 4.9 - - + -
409A THR* 3.8 13.7 - - + +
410A ASP 3.5 3.7 - - - +
411A GLY* 3.5 22.0 - - - +
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Residues in contact with LYS 393 (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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389A GLU 3.0 18.2 + - - +
390A GLU* 3.8 4.9 - - - +
392A ALA* 1.3 79.8 - - - +
394A GLU* 1.3 65.8 + - + +
395A ASN 3.2 0.5 + - - -
396A ASP* 3.4 16.3 - - - +
410A ASP 4.4 2.9 - - - +
411A GLY* 4.0 17.4 - - - +
412A GLU* 4.1 22.0 - - - +
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Residues in contact with GLU 394 (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 LYS* 3.7 25.7 + - - +
390A GLU* 2.9 39.8 + - - +
391A PHE* 5.4 1.0 - - - -
393A LYS* 1.3 76.3 - - + +
395A ASN* 1.3 70.2 + - - +
396A ASP* 3.5 3.3 - - - +
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Residues in contact with ASN 395 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A THR* 3.6 18.4 - - - +
354A LEU* 3.8 34.5 - - + +
355A LYS* 2.5 37.0 + - - +
391A PHE* 2.9 57.6 + - + +
394A GLU* 1.3 83.5 + - - +
396A ASP* 1.3 73.6 + - - +
397A CYS* 3.3 11.7 + - - +
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Residues in contact with ASP 396 (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 LEU 5.2 3.7 - - - +
355A LYS* 4.6 12.2 - - - +
357A ARG 5.7 2.6 - - - +
359A SER 5.6 0.7 - - - +
360A PRO* 5.3 4.0 - - - +
361A ALA* 4.9 5.9 + - - +
392A ALA 2.9 7.5 + - - -
393A LYS* 3.4 13.0 + - - +
394A GLU 5.0 2.6 - - - +
395A ASN* 1.3 80.3 - - - +
397A CYS* 1.3 57.5 - - - +
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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