Contacts of the helix formed by residues 406 - 422 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404C SER* 3.5 10.3 + - - +
405C THR* 1.3 78.3 - - - +
407C LEU* 1.3 65.3 + - - +
408C MET* 3.5 14.7 + - - +
409C GLU* 3.2 38.1 + - + +
410C ALA* 3.0 26.7 + - - +
439C GLN* 4.6 4.9 + - - +
421G LYS* 4.4 0.5 - - - +
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Residues in contact with LEU 407 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405C THR 3.3 13.9 + - - +
406C ASP* 1.3 77.1 + - - +
408C MET* 1.3 57.9 + - - +
410C ALA* 3.5 5.6 + - - +
411C MET* 3.0 31.2 + - - +
520C PHE* 3.5 32.1 - - + -
422G CYS* 3.9 12.3 - - + +
507G VAL* 3.9 28.0 - - + -
526G VAL* 3.8 21.1 - - + +
528G PRO* 6.0 6.7 - - + -
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Residues in contact with MET 408 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406C ASP* 3.3 14.2 + - - +
407C LEU* 1.3 75.6 - - - +
409C GLU* 1.3 60.4 + - - +
410C ALA 3.1 0.9 - - - -
411C MET* 4.2 3.6 - - + -
412C ALA* 2.8 46.8 + - + +
435C ARG* 4.5 3.8 - - + +
436C SER* 3.3 34.8 - - - +
439C GLN* 4.0 15.7 - - + -
440C VAL* 4.4 4.9 - - + -
511C LEU* 5.0 1.1 - - + -
520C PHE* 3.7 35.5 - - + -
521C THR* 3.5 32.8 - - + +
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Residues in contact with GLU 409 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401C SER* 3.6 9.2 - - - -
404C SER* 3.0 24.4 + - - -
406C ASP* 3.2 26.1 + - + +
408C MET* 1.3 74.7 - - - +
410C ALA* 1.3 56.9 + - - +
412C ALA* 3.7 2.1 - - - +
413C MET* 3.1 34.1 + - - +
439C GLN* 3.3 27.5 + - + +
442C ARG* 3.3 20.4 + - - +
443C TYR* 2.9 25.9 + - + +
421G LYS* 3.3 20.9 + - - -
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Residues in contact with ALA 410 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406C ASP 3.0 13.7 + - - +
407C LEU* 3.5 9.6 - - - +
409C GLU* 1.3 74.3 - - - +
411C MET* 1.3 65.9 + - - +
412C ALA 3.3 0.2 + - - -
413C MET* 3.4 3.0 + - - +
414C GLY 3.2 18.0 + - - -
418G ALA* 3.7 35.8 - - + +
421G LYS* 3.7 17.4 - - + +
422G CYS* 3.8 17.5 - - + -
526G VAL* 5.5 2.5 - - + -
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Residues in contact with MET 411 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407C LEU 3.0 20.7 + - - +
408C MET* 3.7 12.3 - - + +
410C ALA* 1.3 76.3 - - - +
412C ALA* 1.3 61.9 + - - +
414C GLY* 3.6 1.0 + - - -
415C SER* 3.0 29.2 + - - -
511C LEU* 3.6 21.3 - - + -
520C PHE* 3.7 13.5 - - + -
521C THR 3.7 14.6 - - - +
522C ASN* 3.5 12.6 - - - +
523C THR 3.6 5.2 - - - -
524C MET* 3.6 36.3 - - + +
524G MET* 3.7 17.6 - - + +
526G VAL* 3.3 28.0 - - + +
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Residues in contact with ALA 412 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408C MET* 2.8 24.6 + - + +
409C GLU 3.7 4.7 - - - +
411C MET* 1.3 70.4 - - - +
413C MET* 1.3 67.0 + - - +
415C SER* 3.1 5.2 + - - -
416C VAL* 2.9 28.9 + - - +
439C GLN* 3.4 37.0 - - + +
440C VAL* 3.9 16.8 - - + +
443C TYR* 4.1 4.5 - - + -
511C LEU* 5.6 0.4 - - - -
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Residues in contact with MET 413 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394C PHE* 3.3 17.8 - - + -
398C VAL* 3.7 28.5 - - + -
409C GLU 3.1 17.3 + - - +
410C ALA 3.8 4.5 - - - +
412C ALA* 1.3 78.9 - - - +
414C GLY* 1.3 57.4 + - - +
416C VAL* 3.4 0.7 + - - +
417C GLU* 2.9 25.5 + - - +
443C TYR* 3.4 46.4 - - + -
417G GLU* 2.9 32.5 - - + +
420G TYR* 6.1 0.7 - - + -
421G LYS* 3.5 40.8 - - + +
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Residues in contact with GLY 414 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410C ALA 3.2 10.8 + - - -
411C MET 4.0 2.5 - - - -
413C MET* 1.3 78.4 - - - +
415C SER* 1.3 58.0 + - - +
417C GLU* 3.4 2.8 + - - -
418C ALA* 2.8 25.6 + - - +
524C MET* 4.2 4.2 - - - +
414G GLY* 3.4 38.9 - - - -
417G GLU* 4.4 5.3 - - - +
418G ALA* 4.7 1.3 - - - -
524G MET* 5.1 1.8 - - - -
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Residues in contact with SER 415 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411C MET 3.0 17.3 + - - -
412C ALA 3.1 4.8 + - - -
414C GLY* 1.3 73.6 - - - +
416C VAL* 1.3 59.9 + - - +
418C ALA* 3.3 3.3 + - - +
419C SER* 3.0 26.9 + - - -
427C LEU* 3.9 9.3 - - - +
440C VAL* 5.7 0.2 - - - -
509C ILE* 4.0 11.1 - - - +
511C LEU* 3.3 37.4 - - - +
524C MET* 3.4 24.5 - - - +
524G MET* 4.8 0.2 - - - +
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Residues in contact with VAL 416 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394C PHE* 3.7 7.6 - - + -
412C ALA 2.9 19.4 + - - +
413C MET 3.7 4.3 - - - +
415C SER* 1.3 74.0 - - - +
417C GLU* 1.3 64.1 + - - +
419C SER* 2.8 23.2 + - - -
420C TYR* 3.2 33.6 + - + +
427C LEU* 4.5 1.6 - - + -
440C VAL* 3.8 37.7 - - + +
443C TYR* 3.5 28.3 - - + +
445C PRO* 3.8 15.5 - - + -
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Residues in contact with GLU 417 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394C PHE* 3.4 33.6 - - + -
413C MET 2.9 13.5 + - - +
414C GLY* 3.5 9.2 - - - +
416C VAL* 1.3 73.7 - - - +
418C ALA* 1.3 65.1 + - - +
420C TYR* 3.2 23.2 + - - +
421C LYS* 3.3 13.7 + - - +
394G PHE* 3.7 15.1 - - - -
398G VAL* 4.3 9.7 - - - +
410G ALA 5.1 0.7 - - - -
413G MET* 3.2 41.1 - - - +
414G GLY* 4.5 4.5 - - - -
417G GLU* 3.7 19.2 - - + +
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Residues in contact with ALA 418 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414C GLY 2.8 17.4 + - - +
415C SER 3.5 7.4 - - - +
417C GLU* 1.3 77.2 - - - +
419C SER* 1.3 60.0 + - - +
420C TYR 3.2 1.0 + - - -
421C LYS 3.3 1.4 + - - -
422C CYS* 3.0 31.3 + - - -
509C ILE* 3.8 16.6 - - + -
524C MET* 4.1 14.8 - - + -
526C VAL* 5.0 1.6 - - + -
410G ALA* 3.7 30.6 + - + +
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Residues in contact with SER 419 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415C SER 3.0 13.6 + - - -
416C VAL* 2.8 22.5 + - - +
418C ALA* 1.3 75.4 - - - +
420C TYR* 1.3 63.8 + - - +
423C LEU* 3.4 5.4 - - - +
424C ALA* 3.2 36.8 + - - +
427C LEU* 4.0 24.6 - - - +
445C PRO* 4.2 8.0 - - - +
446C ARG* 4.9 4.3 + - - +
447C ALA* 4.9 5.1 + - - +
509C ILE* 4.1 8.5 - - - +
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Residues in contact with TYR 420 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390C HIS* 3.7 34.1 + + + +
391C ARG* 5.2 6.1 - - + -
394C PHE* 3.7 23.7 - + + +
416C VAL* 3.2 33.0 + - + +
417C GLU* 3.5 23.6 - - - +
418C ALA 3.1 0.4 - - - -
419C SER* 1.3 79.2 - - - +
421C LYS* 1.3 65.5 + - - +
423C LEU* 3.6 19.1 + - - +
443C TYR 3.8 2.3 + - - -
444C ARG 2.7 27.9 + - - -
445C PRO* 4.4 0.9 - - + -
446C ARG* 3.5 43.8 + - + +
413G MET* 5.7 1.8 - - + -
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Residues in contact with LYS 421 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417C GLU 3.3 2.9 + - - +
418C ALA 3.3 2.5 + - - +
420C TYR* 1.3 82.9 - - - +
422C CYS* 1.3 59.7 + - - +
423C LEU* 3.2 4.7 + - - +
398G VAL 5.3 0.4 + - - -
401G SER* 2.4 36.0 + - - -
402G SER* 3.9 7.0 + - - +
404G SER* 2.7 34.1 + - - +
405G THR* 3.4 25.4 - - - +
406G ASP 4.0 3.6 - - - +
409G GLU* 3.0 31.2 + - - -
410G ALA* 3.7 27.1 - - + +
413G MET* 3.6 36.0 - - + +
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Residues in contact with CYS 422 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418C ALA 3.0 26.2 - - - -
421C LYS* 1.3 75.4 - - - +
423C LEU* 1.3 71.5 + - - +
424C ALA* 3.2 8.6 + - - -
507C VAL* 3.8 35.7 - - + +
509C ILE* 4.1 12.1 - - - -
526C VAL* 4.7 3.4 - - - -
405G THR* 3.7 24.7 - - - +
407G LEU* 4.8 9.6 - - + -
410G ALA* 3.9 16.4 - - + -
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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
------------------------------------------------------------
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