Contacts of the helix formed by residues 406 - 422 (chain G) in PDB entry 3SRF
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 ASP 406 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421C LYS* 4.0 2.0 - - - +
404G SER* 3.2 13.8 + - - +
405G THR* 1.3 77.6 - - - +
407G LEU* 1.3 67.0 + - - +
408G MET* 2.9 34.4 + - - +
409G GLU* 3.2 20.3 + - + +
410G ALA* 3.1 21.1 + - - +
439G GLN* 5.1 2.0 + - - -
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Residues in contact with LEU 407 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422C CYS* 4.8 4.5 - - + -
507C VAL* 4.0 27.1 - - + -
526C VAL* 3.8 29.1 - - + +
527C VAL 5.9 3.1 - - - -
528C PRO* 5.9 3.8 - - + -
405G THR 4.4 8.1 - - - +
406G ASP* 1.3 75.9 + - - +
408G MET* 1.3 57.5 + - - +
410G ALA* 3.3 9.2 - - - +
411G MET* 3.0 29.8 + - - +
520G PHE* 3.6 33.2 - - + -
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Residues in contact with MET 408 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406G ASP* 2.9 15.2 + - - +
407G LEU* 1.3 76.2 - - - +
409G GLU* 1.3 60.0 + - - +
411G MET* 3.2 6.4 + - + -
412G ALA* 2.8 46.4 + - + +
435G ARG* 4.7 2.7 - - + +
436G SER* 3.4 45.5 - - - +
439G GLN* 3.8 20.2 - - + -
440G VAL* 4.3 4.5 - - + -
511G LEU* 5.1 0.7 - - + -
520G PHE* 3.8 25.7 - - + -
521G THR* 3.6 21.1 - - + -
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Residues in contact with GLU 409 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421C LYS* 3.0 25.5 + - - -
401G SER* 3.6 4.9 + - - +
404G SER* 3.3 21.2 + - - -
406G ASP* 3.2 19.5 + - + +
408G MET* 1.3 76.9 - - - +
410G ALA* 1.3 53.9 + - - +
412G ALA* 3.3 1.0 + - - +
413G MET* 2.8 41.3 + - - +
439G GLN* 3.3 26.7 + - + +
442G ARG* 3.4 19.9 + - - -
443G TYR* 2.5 31.7 + - + +
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Residues in contact with ALA 410 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418C ALA* 3.7 30.9 - - + +
421C LYS* 3.7 26.4 - - + +
422C CYS* 3.9 15.3 - - + -
526C VAL* 5.4 2.9 - - + -
406G ASP 3.1 13.3 + - - +
407G LEU* 3.3 11.2 - - - +
408G MET 3.2 0.2 - - - -
409G GLU* 1.3 73.5 - - - +
411G MET* 1.3 64.4 + - - +
413G MET* 3.6 1.8 + - - +
414G GLY 3.2 17.7 + - - -
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Residues in contact with MET 411 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524C MET* 3.7 24.3 - - + +
526C VAL* 3.4 28.3 - - + -
407G LEU 3.0 17.1 + - - +
408G MET* 3.2 15.9 + - + +
410G ALA* 1.3 76.7 - - - +
412G ALA* 1.3 55.2 + - - +
414G GLY* 3.3 1.4 + - - -
415G SER* 2.6 37.9 + - - +
511G LEU* 3.4 28.0 - - + -
520G PHE* 4.0 13.2 - - + -
521G THR 3.5 20.2 - - - +
522G ASN 3.7 9.6 - - - +
523G THR 3.5 20.2 - - - +
524G MET* 3.6 4.5 - - + +
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Residues in contact with ALA 412 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408G MET* 2.8 27.9 + - + +
409G GLU* 3.6 5.4 - - - +
411G MET* 1.3 70.8 - - - +
413G MET* 1.3 59.8 + - - +
415G SER* 3.0 7.3 + - - -
416G VAL* 2.8 36.5 + - - +
439G GLN 3.3 33.9 - - - +
440G VAL* 3.8 11.4 - - - +
443G TYR* 4.0 5.6 - - + -
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Residues in contact with MET 413 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417C GLU* 3.2 31.6 - - - +
420C TYR* 5.7 1.3 - - + -
421C LYS* 3.6 46.0 - - + +
394G PHE* 3.4 13.8 - - - -
398G VAL* 3.7 29.6 - - + +
401G SER* 5.5 0.2 - - - -
409G GLU 2.8 22.1 + - - +
410G ALA* 3.8 4.3 - - - +
412G ALA* 1.3 71.1 - - - +
414G GLY* 1.3 57.7 + - - +
416G VAL 3.4 0.2 + - - -
417G GLU* 2.9 30.0 + - - +
443G TYR* 3.7 38.1 - - + -
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Residues in contact with GLY 414 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414C GLY* 3.4 35.3 - - - -
417C GLU* 4.5 3.3 - - - +
524C MET* 5.0 2.7 - - - -
410G ALA 3.2 10.4 + - - -
411G MET 3.6 3.6 - - - -
413G MET* 1.3 78.1 - - - +
415G SER* 1.3 57.9 + - - +
417G GLU* 4.2 1.8 - - - -
418G ALA* 3.0 29.1 + - - +
524G MET* 4.0 6.2 - - - +
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Residues in contact with SER 415 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411G MET 2.6 21.8 + - - -
412G ALA* 3.0 6.0 + - - -
414G GLY* 1.3 74.7 - - - +
416G VAL* 1.3 61.1 + - - +
418G ALA* 3.7 1.7 + - - +
419G SER* 3.2 26.5 + - - -
427G LEU* 3.5 15.2 - - - +
440G VAL* 5.4 0.7 - - - -
509G ILE* 4.1 4.7 - - - +
511G LEU* 3.4 38.9 - - - +
524G MET* 3.7 20.2 - - - +
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Residues in contact with VAL 416 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394G PHE* 3.9 6.3 - - + -
412G ALA 2.8 21.3 + - - +
413G MET 3.8 2.9 - - - +
415G SER* 1.3 76.7 - - - +
417G GLU* 1.3 64.9 + - - +
419G SER* 2.8 20.5 + - - -
420G TYR* 3.0 42.3 + - + +
427G LEU* 4.9 0.7 - - + -
440G VAL* 3.9 33.7 - - + +
443G TYR* 3.4 26.7 - - + +
445G PRO* 3.8 17.0 - - + -
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Residues in contact with GLU 417 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394C PHE* 4.5 8.6 - - - -
398C VAL* 4.5 11.3 - - - +
410C ALA 5.3 0.4 - - - -
413C MET* 2.9 38.2 - - - +
414C GLY* 4.4 9.2 - - - -
417C GLU* 3.7 20.1 - - + -
391G ARG* 6.1 1.6 - - - +
394G PHE* 3.4 34.5 - - + -
395G GLU* 5.6 2.6 - - - +
413G MET 2.9 14.9 + - - +
414G GLY* 3.9 7.6 - - - +
416G VAL* 1.3 76.3 - - - +
418G ALA* 1.3 61.2 + - - +
420G TYR* 3.3 14.1 + - - +
421G LYS* 3.2 20.6 + - - +
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Residues in contact with ALA 418 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410C ALA* 3.7 31.8 - - + +
414C GLY* 4.7 0.6 - - - -
414G GLY 3.0 19.8 + - - +
415G SER 3.9 4.7 - - - +
416G VAL 3.3 0.2 - - - -
417G GLU* 1.3 75.4 - - - +
419G SER* 1.3 59.4 + - - +
421G LYS 3.6 0.3 + - - -
422G CYS* 3.2 29.3 + - - -
509G ILE* 4.2 10.1 - - + -
524G MET* 4.1 20.6 - - + -
526G VAL* 5.1 2.5 - - + -
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Residues in contact with SER 419 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415G SER 3.2 15.3 + - - -
416G VAL* 2.8 23.0 + - - +
418G ALA* 1.3 74.3 - - - +
420G TYR* 1.3 66.0 + - - +
423G LEU* 3.4 4.7 + - - +
424G ALA* 3.1 35.5 + - - +
427G LEU* 3.8 20.4 - - - +
445G PRO* 4.3 6.2 - - - +
446G ARG* 5.2 1.9 + - - -
447G ALA* 5.1 3.8 - - - +
509G ILE* 3.8 15.7 - - - +
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Residues in contact with TYR 420 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413C MET* 6.1 1.1 - - + -
390G HIS* 3.6 37.4 + - + +
391G ARG* 5.3 6.1 - - + -
394G PHE* 3.6 27.3 - + + +
416G VAL* 3.0 39.7 + - + +
417G GLU* 3.3 17.0 + - - +
419G SER* 1.3 80.4 - - - +
421G LYS* 1.3 63.0 + - - +
423G LEU* 3.6 20.2 + - - +
443G TYR 3.8 3.3 + - - -
444G ARG 2.5 24.4 + - - -
445G PRO* 4.4 0.2 - - + -
446G ARG* 3.6 44.5 + - + +
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Residues in contact with LYS 421 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398C VAL* 4.1 3.4 + - + -
401C SER* 2.8 46.5 + - - -
402C SER* 3.9 8.4 - - - +
404C SER 3.1 23.1 - - - +
405C THR* 3.4 23.2 - - - +
406C ASP 4.4 2.5 - - - +
409C GLU* 3.3 21.9 + - - -
410C ALA* 3.7 30.3 - - + +
413C MET* 3.5 36.7 - - + -
443C TYR* 3.3 4.2 + - - -
417G GLU 3.2 6.7 + - - +
418G ALA 3.6 0.2 + - - -
419G SER 3.5 0.2 - - - -
420G TYR* 1.3 83.1 - - - +
422G CYS* 1.3 58.1 + - - +
423G LEU* 3.3 0.9 + - - +
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Residues in contact with CYS 422 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405C THR* 3.7 26.0 - - - +
407C LEU* 3.9 13.8 - - + +
410C ALA* 3.8 15.9 - - + -
418G ALA 3.2 19.9 + - - -
421G LYS* 1.3 76.4 - - - +
423G LEU* 1.3 72.4 + - - +
424G ALA* 4.0 8.0 - - - -
507G VAL* 3.6 33.5 - - - +
509G ILE* 4.1 12.6 - - - -
526G VAL* 5.0 2.7 - - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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