Contacts of the helix formed by residues 343 - 357 (chain A) in PDB entry 3SN5
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 343 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314A GLU* 3.3 26.5 - - + +
315A VAL* 5.3 2.0 - - - +
318A THR* 3.3 35.7 - - + +
335A LEU* 6.0 0.2 - - + -
339A GLU 3.7 3.6 - - - +
340A LEU* 3.3 29.8 - - + +
341A ASN 3.4 4.2 + - - -
342A ASP* 1.3 81.2 - - - +
344A PRO* 1.4 59.8 - - - +
345A VAL 3.4 0.2 + - - -
346A LEU* 3.4 16.9 + - + -
347A ASP* 2.9 31.8 + - - +
455A LYS* 3.9 12.6 - - + -
459A ILE* 3.7 28.9 - - + -
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Residues in contact with PRO 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A GLU* 3.3 13.5 - - - +
342A ASP* 3.4 17.0 - - - +
343A LEU* 1.4 87.2 - - - +
345A VAL* 1.4 55.7 + - + +
347A ASP* 3.4 8.7 + - + +
348A SER* 2.9 30.5 + - - -
412A TYR 5.2 0.2 - - - +
413A LEU* 3.6 13.4 - - + +
417A GLY 3.5 26.7 - - - +
418A LYS* 4.7 1.3 - - - -
419A THR* 4.3 16.2 + - - +
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Residues in contact with VAL 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A ALA* 3.9 20.4 - - + +
311A ALA* 3.8 28.5 - - - +
314A GLU* 3.1 26.0 + - + +
344A PRO* 1.4 73.4 - - + +
346A LEU* 1.4 60.5 + - - +
348A SER* 3.1 5.4 + - - -
349A ILE* 3.0 40.9 + - + +
409A TYR* 4.3 8.9 - - + +
413A LEU* 4.2 20.0 - - + -
417A GLY* 5.8 1.1 - - - +
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Residues in contact with LEU 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A MET* 4.6 4.9 - - - -
311A ALA* 4.0 26.7 - - + +
314A GLU* 3.0 15.0 + - - +
315A VAL* 4.0 14.6 - - + -
343A LEU* 3.9 25.4 - - + +
345A VAL* 1.4 74.1 - - - +
347A ASP* 1.4 57.2 + - - +
349A ILE* 3.2 7.7 + - + +
350A ILE* 2.9 36.7 + - + +
455A LYS* 4.2 21.1 - - + +
458A LEU* 4.1 24.0 - - + -
459A ILE* 3.9 29.6 - - + -
462A LEU* 4.7 0.9 - - + -
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Residues in contact with ASP 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A ASN 4.0 12.5 - - - +
343A LEU 2.9 18.0 + - - +
344A PRO* 3.5 8.7 - - + +
346A LEU* 1.4 74.5 - - - +
348A SER* 1.4 56.6 + - - +
350A ILE* 3.4 5.3 + - - +
351A LYS* 2.9 59.7 + - - +
419A THR* 4.9 7.3 + - - +
451A ILE* 3.6 13.3 - - - +
455A LYS* 2.9 35.0 + - - +
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Residues in contact with SER 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A PRO 2.9 18.3 + - - -
345A VAL 3.1 4.2 + - - -
347A ASP* 1.4 76.0 - - - +
349A ILE* 1.4 51.2 + - - +
351A LYS* 3.4 1.7 + - - +
352A GLU* 2.9 37.1 + - - +
409A TYR 2.7 24.7 + - - -
410A ASP* 3.6 2.6 - - - -
411A ARG 3.6 1.4 + - - -
412A TYR* 3.0 40.6 + - - -
413A LEU* 3.8 14.1 - - - -
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Residues in contact with ILE 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A SER* 3.8 27.4 - - - +
301A MET* 4.1 16.8 - - + -
307A ALA* 3.8 28.3 - - + +
311A ALA* 3.9 11.7 - - + -
345A VAL* 3.0 30.7 + - + +
346A LEU* 3.2 11.0 + - + +
348A SER* 1.4 75.2 - - - +
350A ILE* 1.4 52.3 + - - +
353A SER* 2.7 38.6 + - - +
407A PHE* 3.7 18.6 - - + -
409A TYR* 4.2 21.3 - - + +
458A LEU* 4.9 7.2 - - + -
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Residues in contact with ILE 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A SER* 3.7 16.4 - - - +
346A LEU 2.9 23.4 + - - +
347A ASP* 3.9 3.8 - - - +
349A ILE* 1.4 73.4 - - - +
351A LYS* 1.3 51.5 + - + +
353A SER* 3.1 4.0 + - - -
354A LEU* 2.8 43.4 + - + +
451A ILE* 3.6 38.1 - - + +
454A ILE* 3.7 38.4 - - + -
455A LYS* 3.7 31.2 - - + +
458A LEU* 4.1 11.0 - - + -
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Residues in contact with LYS 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347A ASP* 2.9 48.4 + - - +
348A SER 3.7 1.1 - - - +
350A ILE* 1.3 75.9 - - + +
352A GLU* 1.3 51.6 + - - +
354A LEU 3.2 1.0 + - - -
355A ARG* 2.8 32.6 + - - +
412A TYR* 3.5 42.1 - - + +
419A THR* 4.7 17.2 - - - +
433A TYR* 6.2 1.6 - - + -
434A TYR* 3.3 50.8 - - + +
451A ILE* 6.3 1.1 - - + -
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Residues in contact with GLU 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A SER 2.9 20.9 + - - +
351A LYS* 1.3 69.8 - - - +
353A SER* 1.4 63.1 + - - +
355A ARG* 2.6 42.5 + - - +
356A LEU* 3.4 24.4 + - - +
406A THR 3.2 2.1 - - - +
407A PHE* 3.3 28.7 - - + -
408A LYS 2.9 34.7 + - - +
409A TYR* 5.0 0.2 - - - -
411A ARG* 2.8 35.0 + - - +
412A TYR* 3.8 6.2 - - + -
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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
----------------------------------------------------------
293A ALA 4.9 1.1 - - - -
296A TRP* 3.6 15.3 + - - +
297A SER* 3.3 38.4 - - - -
300A GLN* 4.0 3.8 - - - +
349A ILE 2.7 24.3 + - - -
350A ILE 3.4 4.9 - - - -
352A GLU* 1.4 76.3 - - - +
354A LEU* 1.3 57.6 + - - +
356A LEU* 3.5 4.2 + - - +
357A SER* 2.7 31.2 + - - -
407A PHE* 3.5 15.1 - - - -
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Residues in contact with LEU 354 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A ALA* 3.6 36.8 - - + +
296A TRP* 6.0 0.2 - - + -
350A ILE* 2.8 31.7 + - + +
351A LYS 3.8 3.6 - - - +
353A SER* 1.3 76.5 - - - +
355A ARG* 1.4 59.7 + - - +
357A SER* 3.7 5.8 - - - +
358A SER* 2.8 36.6 + - - -
395A HIS* 5.4 0.2 - - - -
434A TYR* 3.5 18.8 - - - +
436A PRO* 3.9 26.9 - - + -
437A PHE* 3.9 21.8 - - + -
488A ILE* 3.7 15.7 - - + -
601A HEM 4.4 7.2 - - + -
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Residues in contact with ARG 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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351A LYS 2.8 19.7 + - - +
352A GLU* 2.6 45.8 + - - +
353A SER 3.4 0.4 - - - -
354A LEU* 1.4 72.1 - - - +
356A LEU* 1.3 74.5 + - - +
358A SER 4.4 3.1 + - - +
392A GLN* 5.4 0.7 - - - +
395A HIS* 2.7 81.5 + - + +
396A LEU* 3.9 9.9 - - - +
401A TYR* 3.8 19.5 - - - +
404A PRO* 2.8 36.4 + - - +
406A THR 3.3 11.1 + - - -
411A ARG* 3.7 9.6 - - - +
412A TYR* 3.5 23.6 - - - +
434A TYR* 4.5 4.0 - - + -
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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
----------------------------------------------------------
300A GLN* 3.7 26.9 - - - +
352A GLU 3.4 15.9 + - - +
353A SER 3.9 3.8 - - - +
354A LEU 3.2 0.6 - - - -
355A ARG* 1.3 93.0 - - - +
357A SER* 1.3 57.9 + - - +
392A GLN* 4.1 8.1 + - - -
396A LEU* 4.1 14.5 - - + +
404A PRO 3.6 24.2 - - - +
405A LEU* 3.8 21.8 - - + +
407A PHE* 3.9 25.6 - - + +
479A LEU* 3.5 20.0 - - - +
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Residues in contact with SER 357 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A TRP* 3.7 31.5 - - - -
353A SER 2.7 24.3 + - - -
354A LEU* 3.2 5.1 + - - +
356A LEU* 1.3 78.4 - - - +
358A SER* 1.4 63.8 + - - +
359A ALA 3.5 0.3 + - - -
392A GLN* 4.8 1.3 - - - -
479A LEU* 4.3 10.1 - - - -
488A ILE* 3.5 17.3 - - - +
489A LEU* 2.8 36.0 + - - +
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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
------------------------------------------------------------
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