Contacts of the helix formed by residues 354 - 366 (chain C) in PDB entry 4K9N
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 HIS 354 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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346C VAL* 4.3 14.4 - - + +
347C ASP 3.4 25.7 + - - -
348C GLN* 3.1 32.4 + - - +
349C ASP* 5.4 4.8 + - - -
352C ARG 4.7 0.4 + - - -
353C LEU* 1.3 76.1 - - - +
355C PRO* 1.3 73.3 - - - +
356C GLU* 3.5 15.0 + - - +
357C THR* 3.0 18.3 + - - +
358C VAL* 3.3 10.2 + - - +
524C VAL* 3.8 28.0 - - + +
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Residues in contact with PRO 355 (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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353C LEU 4.1 3.8 - - - +
354C HIS* 1.3 83.8 - - + +
356C GLU* 1.3 73.0 + - - +
358C VAL* 3.1 4.7 + - + +
359C PHE* 3.0 32.5 + - + -
379C THR* 3.4 39.9 - - + -
382C GLN* 4.3 7.6 - - - +
453C MET* 3.9 19.5 - - + -
523C THR* 5.3 5.4 - - - -
524C VAL* 4.1 16.4 - - + +
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Residues in contact with GLU 356 (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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346C VAL* 3.7 27.1 - - + +
354C HIS* 3.5 18.8 + - + +
355C PRO* 1.3 80.3 - - - +
357C THR* 1.3 62.4 + - - +
359C PHE* 3.5 1.7 + - - -
360C ASP* 3.0 31.0 + - - +
382C GLN* 3.8 30.3 + - + +
386C ARG* 3.4 43.6 - - - +
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Residues in contact with THR 357 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346C VAL* 4.8 6.4 + - - +
348C GLN* 2.7 35.8 + - + +
353C LEU* 3.6 24.5 - - + -
354C HIS* 3.0 15.4 + - - +
356C GLU* 1.3 76.9 - - - +
358C VAL* 1.3 64.9 + - - +
360C ASP* 3.4 6.7 + - + +
361C THR* 2.8 30.4 + - - +
500C LEU* 3.8 22.9 - - + -
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Residues in contact with VAL 358 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353C LEU* 4.0 18.6 - - + -
354C HIS 3.7 11.9 - - - +
355C PRO* 3.1 6.4 + - + +
357C THR* 1.3 76.8 - - - +
359C PHE* 1.3 60.8 + - + +
361C THR* 3.3 2.6 + - - -
362C LEU* 2.9 43.8 + - + +
425C VAL* 5.5 0.4 - - + -
451C VAL* 4.5 11.9 - - + -
453C MET* 4.0 33.4 - - + -
503C LEU* 3.9 21.0 - - + +
521C VAL* 4.2 13.7 - - + -
523C THR* 4.6 1.3 - - + -
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Residues in contact with PHE 359 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355C PRO* 3.0 29.5 + - + +
356C GLU* 4.0 2.9 - - - +
358C VAL* 1.3 74.1 - - + +
360C ASP* 1.3 61.0 + - - +
362C LEU* 3.2 14.0 + - + -
363C ASN* 2.8 31.2 + - - +
379C THR* 3.5 43.3 - - - -
382C GLN* 4.1 7.2 - - + -
383C MET* 3.6 48.2 - - + -
386C ARG* 3.8 19.7 - - + -
387C LEU* 3.5 14.6 - - + +
425C VAL* 4.0 24.9 - - + -
453C MET* 4.4 7.0 - - + -
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Residues in contact with ASP 360 (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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343C PRO* 4.9 2.9 - - - +
345C LYS* 4.4 16.1 - - - +
346C VAL 5.0 1.4 + - - -
356C GLU 3.0 21.6 + - - +
357C THR* 3.8 6.4 - - - +
358C VAL 3.4 0.2 - - - -
359C PHE* 1.3 74.6 - - - +
361C THR* 1.3 59.2 + - - +
363C ASN* 3.3 6.7 + - - +
364C ASP* 3.0 37.9 + - - +
386C ARG* 3.0 44.1 + - - +
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Residues in contact with THR 361 (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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357C THR* 2.8 22.3 + - - +
358C VAL 3.6 3.6 - - - -
360C ASP* 1.3 75.8 - - - +
362C LEU* 1.3 65.5 + - - +
364C ASP* 3.2 7.8 + - + +
365C MET* 3.0 38.8 + - + +
500C LEU* 3.7 18.4 - - - +
503C LEU* 3.9 14.0 - - + +
504C LYS* 4.2 20.4 - - + -
507C LEU* 3.8 20.4 - - + -
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Residues in contact with LEU 362 (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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358C VAL* 2.9 29.9 + - + +
359C PHE* 3.6 18.6 - - + +
361C THR* 1.3 76.9 - - - +
363C ASN* 1.3 58.8 + - - +
366C ALA* 2.8 38.5 + - + +
372C TYR* 4.3 12.3 - - + -
387C LEU* 4.2 7.2 - - + -
423C ILE* 4.0 31.4 - - + -
425C VAL* 4.0 26.7 - - + -
451C VAL* 4.7 4.7 - - + -
507C LEU* 3.7 35.4 - - + -
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Residues in contact with ASN 363 (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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245C ARG* 4.9 5.1 - - - +
359C PHE 2.8 11.8 + - - +
360C ASP* 3.6 6.7 - - - +
362C LEU* 1.3 78.2 - - - +
364C ASP* 1.3 66.7 + - - +
366C ALA* 4.2 8.3 + - - +
372C TYR* 4.6 5.3 + - - -
386C ARG 3.3 26.1 + - - +
387C LEU* 3.7 6.9 - - + +
388C ASN* 2.9 39.8 + - - +
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Residues in contact with ASP 364 (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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360C ASP* 3.0 25.4 + - - +
361C THR* 3.6 8.6 - - + +
362C LEU 3.2 0.2 - - - -
363C ASN* 1.3 85.0 + - - +
365C MET* 1.3 64.9 + - + +
366C ALA 4.8 1.3 - - - +
504C LYS* 6.1 0.9 - - - -
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Residues in contact with MET 365 (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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361C THR* 3.0 34.5 + - + +
362C LEU* 4.4 0.4 - - - +
364C ASP* 1.3 84.3 - - + +
366C ALA* 1.3 66.4 + - - +
367C PRO* 3.7 0.9 - - - +
504C LYS* 3.5 36.1 - - + +
507C LEU* 3.9 14.1 - - + -
508C GLN* 3.6 28.5 - - + +
511C LEU* 3.6 22.2 - - + +
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Residues in contact with ALA 366 (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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362C LEU* 2.8 25.9 + - + +
363C ASN 4.3 7.9 - - - +
364C ASP 4.8 1.0 - - - +
365C MET* 1.3 75.8 - - - +
367C PRO* 1.3 77.4 - - + +
368C GLU* 3.7 2.4 + - - +
370C ALA* 4.1 1.6 - - + -
372C TYR* 3.3 21.8 - - - +
423C ILE* 3.8 19.7 - - + -
511C LEU* 4.7 4.7 - - - -
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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
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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