Contacts of the helix formed by residues 349 - 360 (chain A) in PDB entry 1SR0
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 PHE 349 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A ALA* 3.4 25.6 - - + -
25A ILE* 4.1 11.0 - - + -
26A ASP* 3.9 18.2 - - + -
29A LEU* 3.6 30.5 - - + -
333A LEU* 4.0 31.6 - - + -
336A ASP* 3.4 23.0 - - + +
337A ASP 3.1 8.8 + - - -
338A PHE* 3.5 30.5 - - + -
348A THR* 1.3 99.0 + - + +
350A PRO* 1.3 73.5 - - - +
351A LEU 3.3 0.2 + - - -
352A THR* 4.4 1.3 - - - -
353A SER* 2.6 28.4 + - - +
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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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275A TYR* 4.1 15.7 - - + -
310A GLN* 4.5 13.4 - - - +
336A ASP* 3.2 18.4 - - - +
337A ASP* 3.5 25.8 - - + +
343A CYS* 4.8 3.8 - - + -
345A GLN* 4.2 19.7 - - + +
347A LEU* 3.8 28.6 - - + +
348A THR 3.1 3.7 - - - -
349A PHE* 1.3 91.5 - - - +
351A LEU* 1.3 63.2 + - - +
353A SER* 3.0 10.2 + - - -
354A ALA* 3.0 13.0 + - - +
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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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238A PRO 4.7 3.6 - - - +
239A THR* 3.2 32.5 - - - +
275A TYR* 3.4 59.7 - - + +
308A ASP 3.9 10.3 - - - +
310A GLN* 3.9 22.7 - - + +
313A VAL* 4.1 18.8 - - + +
336A ASP* 3.3 9.8 + - - +
350A PRO* 1.3 78.5 - - - +
352A THR* 1.3 66.4 + - - +
354A ALA* 2.8 21.2 + - - +
355A VAL* 3.2 9.5 + - - +
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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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3A LEU* 4.2 6.5 - - + +
5A CYS* 4.1 17.9 - - - -
29A LEU* 4.2 16.8 - - + +
30A CYS* 4.2 5.6 - - - -
239A THR* 4.8 0.4 + - - -
330A VAL* 3.9 28.4 - - + +
333A LEU* 3.8 28.5 - - + +
336A ASP* 2.7 26.3 + - - +
349A PHE* 4.2 3.5 - - - +
351A LEU* 1.3 72.3 - - - +
353A SER* 1.3 60.2 + - - +
355A VAL* 3.6 4.8 + - - +
356A LYS* 3.3 19.2 + - - +
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Residues in contact with SER 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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29A LEU* 4.3 9.8 - - - +
347A LEU* 3.9 14.8 - - - +
348A THR 3.5 10.0 + - - -
349A PHE* 2.6 21.8 + - - +
350A PRO 3.0 10.3 + - - -
351A LEU 2.8 1.6 + - - -
352A THR* 1.3 74.1 - - - +
354A ALA* 1.3 55.7 - - - -
355A VAL 3.1 1.8 - - - -
356A LYS* 2.9 8.0 + - - +
357A ASP* 2.7 48.6 + - - +
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Residues in contact with ALA 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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310A GLN* 4.1 18.8 - - + +
313A VAL* 3.8 9.2 - - + -
314A LYS* 3.4 39.7 - - + +
350A PRO 3.0 10.6 + - - +
351A LEU 2.8 13.8 + - - +
353A SER* 1.3 71.9 - - - +
355A VAL* 1.3 61.4 + - - +
357A ASP* 3.5 3.7 + - - +
358A VAL* 3.2 26.3 + - - +
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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
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3A LEU* 4.7 8.1 - - + -
237A ILE* 3.9 18.8 - - + -
313A VAL* 3.0 41.3 - - + +
317A ALA* 4.3 12.8 - - + -
328A ALA* 3.7 29.4 - - + -
330A VAL* 5.1 8.3 - - + -
351A LEU 3.2 5.4 + - - +
352A THR* 4.0 7.9 - - - +
353A SER 3.1 0.6 - - - -
354A ALA* 1.3 76.7 - - - +
356A LYS* 1.3 59.6 + - - +
358A VAL* 3.3 2.4 + - - +
359A LEU* 2.9 35.0 + - + +
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Residues in contact with LYS 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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3A LEU* 3.9 16.4 - - + +
28A PHE* 3.2 23.5 + - - +
29A LEU* 3.5 34.5 - - + +
352A THR 3.3 12.2 + - - +
353A SER* 2.9 10.7 + - - +
355A VAL* 1.3 79.2 - - - +
357A ASP* 1.3 59.2 + - - +
359A LEU* 3.2 5.6 + - + +
360A ALA* 2.7 43.8 + - + +
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Residues in contact with ASP 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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314A LYS* 4.7 13.0 + - - +
353A SER* 2.7 33.2 + - - +
354A ALA* 3.9 7.4 + - - +
356A LYS* 1.3 81.9 - - - +
358A VAL* 1.3 60.8 + - - +
360A ALA* 3.5 7.5 + - - +
361A GLU* 3.5 22.8 + - - +
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Residues in contact with VAL 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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314A LYS* 3.7 31.6 - - + +
317A ALA* 3.6 26.0 - - + +
318A ARG* 3.9 24.2 - - + +
321A LYS* 3.3 14.8 + - - +
354A ALA 3.2 15.6 + - - +
355A VAL 3.6 5.6 - - - +
356A LYS 3.2 0.4 - - - -
357A ASP* 1.3 75.7 - - - +
359A LEU* 1.3 62.8 + - - +
361A GLU* 2.8 42.1 + - - +
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Residues in contact with LEU 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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1A TYR* 3.4 37.8 - - + +
2A LYS 3.6 24.0 - - - +
3A LEU* 4.6 7.6 - - + -
317A ALA* 4.0 11.7 - - + +
320A LEU* 3.6 27.4 - - + -
321A LYS* 4.0 14.6 - - + -
327A GLY 4.8 0.9 - - - -
328A ALA* 3.7 23.1 - - + +
355A VAL* 2.9 23.5 + - + +
356A LYS* 3.8 4.9 - - - +
358A VAL* 1.3 77.6 - - - +
360A ALA* 1.3 58.1 + - - +
361A GLU 3.0 14.0 - - - +
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Residues in contact with ALA 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* 2.7 28.8 + - + +
357A ASP* 3.8 9.6 - - - +
358A VAL 3.0 0.2 - - - -
359A LEU* 1.3 76.6 - - - +
361A GLU* 1.3 59.9 + - - +
362A VAL* 5.8 0.2 - - - +
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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