Contacts of the helix formed by residues 336 - 351 (chain C) in PDB entry 6DWN
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 336 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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332C TYR* 2.8 31.3 + - - +
333C LEU 3.1 9.1 - - - +
335C MET* 1.3 90.7 + - - +
337C PRO* 1.3 66.3 - - - +
338C ARG* 3.1 7.4 + - + +
339C VAL* 3.2 36.1 + - + +
340C GLN 3.4 1.2 + - - -
427C PHE* 3.8 35.1 - - + +
490C MET* 5.7 0.2 - - - +
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Residues in contact with PRO 337 (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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333C LEU 3.4 7.6 - - - +
334C VAL* 3.6 12.6 - - - +
335C MET 3.5 8.3 - - - +
336C ASN* 1.3 88.8 - - - +
338C ARG* 1.3 62.1 + - - +
340C GLN* 3.3 12.0 + - + +
341C ARG* 3.1 42.0 + - - +
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Residues in contact with ARG 338 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336C ASN* 3.1 5.4 + - + +
337C PRO* 1.3 80.2 - - - +
339C VAL* 1.3 84.9 + - + +
341C ARG* 3.2 24.4 + - - +
342C LYS* 3.0 40.1 + - + +
367C TYR* 4.0 1.4 + - - -
427C PHE 4.6 5.1 + - - -
428C LEU* 4.1 12.0 - - - +
429C PRO* 4.6 2.4 - - - +
430C GLU* 2.7 38.8 + - - -
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Residues in contact with VAL 339 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332C TYR 4.6 1.6 - - - +
333C LEU* 4.1 15.9 - - + -
336C ASN* 3.2 31.9 + - + +
338C ARG* 1.3 105.2 - - - +
340C GLN* 1.3 61.3 + - - +
342C LYS* 3.8 0.8 - - - -
343C ILE* 2.9 34.5 + - - +
367C TYR* 3.8 23.7 - - + +
371C PHE* 4.2 7.9 - - + -
427C PHE* 4.2 14.6 - - + -
429C PRO* 4.2 15.9 - - + -
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Residues in contact with GLN 340 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333C LEU* 3.5 50.1 + - + +
334C VAL* 4.8 0.4 - - - +
336C ASN 3.4 0.4 + - - -
337C PRO* 3.3 15.3 + - - +
338C ARG 3.2 0.6 - - - -
339C VAL* 1.3 82.0 - - - +
341C ARG* 1.3 57.6 + - + +
343C ILE* 3.2 4.9 + - - +
344C GLN* 2.8 45.7 + - - +
475C LEU* 3.8 18.4 - - + +
479C GLU* 3.9 10.4 - - - +
480C PHE* 3.1 44.8 + - - +
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Residues in contact with ARG 341 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337C PRO* 3.1 35.8 + - - +
338C ARG* 3.7 27.4 + - - +
340C GLN* 1.3 74.4 - - + +
342C LYS* 1.3 61.0 + - + +
344C GLN* 3.0 16.5 + - - +
345C GLU* 2.7 43.9 + - + +
479C GLU* 6.0 2.9 - - - +
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Residues in contact with LYS 342 (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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338C ARG* 3.0 34.9 + - + +
339C VAL 3.9 0.7 - - - +
341C ARG* 1.3 75.0 - - + +
343C ILE* 1.3 63.0 + - - +
345C GLU* 3.7 16.6 + - - +
346C GLU* 3.4 17.2 + - - +
367C TYR* 3.6 36.4 - - + +
430C GLU* 3.3 34.4 + - - +
433C LEU* 5.3 2.0 - - - +
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Residues in contact with ILE 343 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333C LEU* 3.7 20.4 - - + -
339C VAL 2.9 24.1 + - - +
340C GLN* 3.3 6.5 - - - +
341C ARG 3.1 0.2 - - - -
342C LYS* 1.3 73.3 - - - +
344C GLN* 1.3 62.1 + - - +
346C GLU* 2.8 26.1 + - + +
347C LEU* 3.1 23.2 + - + +
367C TYR* 3.5 24.5 - - + +
368C MET* 4.2 20.2 - - + +
371C PHE* 3.7 36.8 - - + -
475C LEU* 3.6 20.6 - - + -
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Residues in contact with GLN 344 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340C GLN* 2.8 45.0 + - + +
341C ARG* 3.0 16.3 + - - +
343C ILE* 1.3 74.2 - - - +
345C GLU* 1.3 62.0 + - + +
347C LEU* 3.4 6.4 + - - +
348C ASP* 3.1 29.5 + - - +
475C LEU* 3.5 23.2 + - + +
478C VAL 3.4 23.6 + - - -
479C GLU* 4.0 17.8 - - - +
511C ARG* 3.8 29.4 + - - +
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Residues in contact with GLU 345 (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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341C ARG* 2.7 31.2 + - + +
342C LYS* 3.8 16.7 - - - +
343C ILE 3.0 0.2 + - - -
344C GLN* 1.3 75.5 - - + +
346C GLU* 1.3 56.3 + - - +
348C ASP* 3.5 5.9 + - - +
349C THR* 3.0 34.9 + - - +
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Residues in contact with GLU 346 (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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342C LYS 3.4 9.7 + - - +
343C ILE* 2.8 16.5 + - + +
345C GLU* 1.3 75.7 - - - +
347C LEU* 1.3 56.2 + - - +
349C THR* 4.3 4.7 - - - -
350C VAL* 2.8 45.3 + - + +
365C LEU* 2.9 45.1 - - + +
366C PRO* 3.7 16.0 - - - +
367C TYR* 3.1 31.4 + - + +
368C MET* 3.5 5.0 + - - +
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Residues in contact with LEU 347 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343C ILE* 3.1 23.5 + - + +
344C GLN* 3.8 8.3 - - - +
345C GLU 3.3 0.4 - - - -
346C GLU* 1.3 74.2 - - - +
348C ASP* 1.3 69.2 + - - +
351C ILE* 2.9 32.0 + - + +
352C GLY 3.0 8.3 + - - +
357C PRO* 4.6 12.1 - - + -
365C LEU* 4.3 21.8 - - + -
368C MET* 5.5 3.8 - - - -
472C ALA* 3.8 30.5 - - + +
475C LEU* 3.9 16.2 - - + +
476C GLN* 3.6 37.0 - - + +
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Residues in contact with ASP 348 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344C GLN 3.1 12.3 + - - +
345C GLU* 3.9 5.1 - - - +
347C LEU* 1.3 77.0 - - - +
349C THR* 1.3 63.6 + - - +
352C GLY* 3.1 25.9 + - - +
353C ARG* 4.0 20.6 + - + -
476C GLN* 4.9 1.2 - - - +
511C ARG* 2.7 39.5 + - - -
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Residues in contact with THR 349 (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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345C GLU* 3.0 21.2 + - - +
346C GLU* 3.8 6.3 - - - -
348C ASP* 1.3 80.2 - - - +
350C VAL* 1.3 70.1 + - + +
351C ILE 3.6 0.7 + - - -
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Residues in contact with VAL 350 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346C GLU* 2.8 36.1 + - + +
347C LEU 4.5 0.2 - - - +
349C THR* 1.3 82.3 - - + +
351C ILE* 1.3 69.5 + - + +
355C ARG* 5.0 2.4 + - - -
361C ASP* 5.8 1.1 - - + -
364C HIS* 3.7 42.0 - - + +
365C LEU* 4.1 11.2 - - + -
366C PRO* 5.8 0.2 - - + -
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Residues in contact with ILE 351 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347C LEU* 2.9 15.5 + - + +
348C ASP 4.1 0.4 - - - -
349C THR 4.9 0.9 - - - -
350C VAL* 1.3 93.1 - - + +
352C GLY* 1.3 63.2 + - - +
354C SER* 3.9 13.5 + - - -
355C ARG* 3.7 56.3 + - + +
356C ARG 4.9 1.6 - - - +
357C PRO* 4.0 22.7 - - + -
361C ASP* 3.3 34.3 - - + +
365C LEU* 4.8 9.9 - - + -
476C GLN* 4.4 3.1 - - - +
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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