Contacts of the helix formed by residues 423 - 436 (chain C) in PDB entry 3UO9
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 THR 423 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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278C THR 3.4 13.2 + - - -
279C LYS* 3.7 27.9 - - + +
280C VAL 3.8 13.5 - - - +
281C PRO* 4.1 3.6 - - + -
282C PHE* 3.9 5.4 - - - -
370C TYR* 3.9 23.4 - - + +
422C VAL* 1.3 76.5 - - - +
424C CYS* 1.3 65.5 + - - +
425C GLU* 3.4 7.1 + - - +
426C SER* 3.1 25.2 + - - -
427C ALA* 3.0 23.6 + - - +
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Residues in contact with CYS 424 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262C GLY* 3.7 26.5 - - - -
264C SER* 3.4 24.5 - - - +
277C ASP 4.3 3.6 - - - -
278C THR* 3.5 18.8 + - + -
280C VAL 4.6 0.6 + - - -
282C PHE* 3.7 6.9 - - - -
423C THR* 1.3 72.9 - - - +
425C GLU* 1.3 58.1 + - - +
428C SER* 2.9 26.3 + - - -
499C MET* 3.5 19.9 - - - +
501C TRP* 3.7 32.1 - - - -
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Residues in contact with GLU 425 (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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169C ARG* 3.7 20.9 + - - +
264C SER* 3.5 7.0 - - - +
272C ARG* 3.2 20.4 + - - +
274C SER* 3.2 25.7 + - - +
278C THR* 3.0 29.4 + - - +
279C LYS* 3.1 35.2 + - - +
369C GLU* 4.2 4.2 - - - +
423C THR* 3.2 8.0 - - - +
424C CYS* 1.3 75.9 - - - +
426C SER* 1.3 61.8 + - - +
428C SER* 2.8 19.5 + - - -
429C VAL* 3.4 3.5 - - - +
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Residues in contact with SER 426 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366C ALA* 3.7 6.2 - - - +
369C GLU* 3.7 17.2 + - - -
370C TYR 2.7 46.3 + - - -
422C VAL* 3.7 3.3 - - - +
423C THR* 3.1 24.3 + - - -
425C GLU* 1.3 79.3 - - - +
427C ALA* 1.3 60.1 + - - +
429C VAL* 3.4 7.1 + - - +
430C MET* 3.3 24.2 + - - +
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Residues in contact with ALA 427 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284C LEU* 5.1 1.1 - - + -
422C VAL* 3.9 13.2 - - + -
423C THR 3.0 19.6 + - - +
426C SER* 1.3 75.4 + - - +
428C SER* 1.3 64.2 + - - +
430C MET* 3.2 13.9 + - - +
431C ALA 3.0 17.7 + - - -
489C LEU* 3.5 11.5 - - + +
499C MET* 3.5 39.3 - - + -
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Residues in contact with SER 428 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264C SER* 3.3 36.7 - - - -
265C VAL 3.8 3.5 + - - -
266C CYS* 3.8 13.6 - - - +
272C ARG* 4.2 2.8 + - - -
424C CYS 2.9 17.3 + - - -
425C GLU* 2.8 17.5 + - - -
427C ALA* 1.3 71.3 - - - +
429C VAL* 1.3 56.0 + - - +
431C ALA* 3.3 4.2 + - - +
432C ALA* 2.8 28.1 + - - +
497C GLY 3.8 10.1 - - - -
498C MET 4.0 3.1 - - - -
499C MET* 3.7 10.7 - - - +
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Residues in contact with VAL 429 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266C CYS* 4.1 9.2 - - - -
272C ARG* 3.4 41.1 - - - +
365C MET 3.5 4.0 - - - +
366C ALA 3.4 27.1 - - - +
367C GLY 3.9 1.6 - - - +
369C GLU* 3.8 10.5 - - - +
425C GLU 3.4 6.1 - - - +
426C SER 3.4 7.4 + - - +
427C ALA 3.2 0.6 - - - -
428C SER* 1.3 73.3 + - - +
430C MET* 1.3 59.9 + - - +
432C ALA* 3.2 7.9 + - - +
433C THR* 3.0 27.9 + - - -
440C CYS* 4.0 13.2 - - - -
441C PRO* 4.5 2.6 - - + +
442C ILE* 4.0 9.4 - - + -
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Residues in contact with MET 430 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284C LEU* 5.2 1.6 - - + -
291C LEU* 3.9 33.2 - - + +
362C LEU* 3.7 35.7 - - + +
365C MET* 3.5 18.2 + - + +
366C ALA* 3.8 16.2 - - + +
370C TYR 5.2 0.2 - - - +
371C VAL* 3.8 24.0 - - + -
422C VAL* 4.0 24.5 - - + -
426C SER 3.5 12.6 - - - +
427C ALA* 3.2 11.1 + - - +
429C VAL* 1.3 72.4 - - - +
431C ALA* 1.3 64.7 + - - +
433C THR* 3.4 4.7 + - - -
434C LEU* 3.3 26.7 + - - +
489C LEU* 4.9 4.5 - - + -
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Residues in contact with ALA 431 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427C ALA 3.0 10.3 + - - +
428C SER 3.4 8.5 - - - +
430C MET* 1.3 75.6 - - - +
432C ALA* 1.3 57.6 + - - +
434C LEU* 3.2 9.4 + - - +
435C ALA* 2.9 26.2 + - - +
489C LEU* 3.8 13.1 - - + +
490C LEU 3.6 13.5 - - - +
491C VAL* 3.7 12.6 - - + +
497C GLY* 3.5 16.2 - - - -
498C MET 3.7 13.5 - - - +
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Residues in contact with ALA 432 (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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266C CYS* 3.1 32.5 - - - +
267C THR 4.1 2.9 - - - +
268C VAL* 4.2 1.2 - - - +
428C SER 2.8 14.8 + - - +
429C VAL 3.2 5.8 + - - +
431C ALA* 1.3 73.0 - - - +
433C THR* 1.3 57.8 - - - +
435C ALA* 3.3 4.3 + - - +
436C ASN* 2.8 31.5 + - - +
441C PRO* 3.5 21.9 - - + +
497C GLY* 3.5 8.7 - - - +
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Residues in contact with THR 433 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365C MET* 3.0 27.6 + - + +
429C VAL 3.0 5.8 + - - -
430C MET* 3.6 10.3 - - - -
432C ALA* 1.3 75.4 - - - +
434C LEU* 1.3 60.1 + - + +
436C ASN* 3.1 8.1 + - - +
437C GLY 3.3 0.2 + - - -
438C GLY* 3.0 52.1 + - - +
439C PHE 3.6 12.6 - - - -
440C CYS* 3.4 16.3 - - - +
441C PRO* 3.7 1.5 - - - +
447C VAL* 4.1 16.8 - - + -
448C LEU* 4.8 8.7 - - + -
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Residues in contact with LEU 434 (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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290C PRO* 5.2 0.7 - - + -
291C LEU* 4.2 21.3 - - + -
294C ALA* 4.8 3.1 - - + -
365C MET* 5.8 1.1 - - + -
430C MET 3.3 14.6 + - - +
431C ALA* 3.2 10.0 + - - +
433C THR* 1.3 77.8 - - + +
435C ALA* 1.3 60.0 + - - +
436C ASN 3.4 0.3 + - - -
437C GLY 3.6 1.6 + - - -
448C LEU* 3.7 28.9 - - + -
453C VAL* 3.1 34.9 - - + +
456C THR* 4.6 18.4 - - + -
457C LEU* 3.7 15.7 - - + +
460C MET* 4.4 19.7 - - + -
489C LEU* 5.0 4.3 - - + -
491C VAL* 4.0 22.4 - - + -
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Residues in contact with ALA 435 (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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532A ASN* 3.0 10.4 - - - +
268C VAL* 3.8 9.6 - - + -
431C ALA 2.9 12.0 + - - +
432C ALA 3.3 8.5 + - - +
434C LEU* 1.3 75.7 - - - +
436C ASN* 1.3 57.3 + - - +
437C GLY 3.4 1.3 - - - -
491C VAL* 3.6 14.1 - - + +
492C VAL 3.8 8.1 - - - +
493C PRO* 4.2 2.7 - - - +
494C ASN* 3.0 26.6 + - - +
496C MET 3.4 31.4 - - - +
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Residues in contact with ASN 436 (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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532A ASN* 3.5 8.2 + - - -
534A ARG* 3.3 24.9 + - - +
535A HIS* 3.2 22.8 + - - -
268C VAL* 3.6 32.2 + - + +
432C ALA 2.8 17.5 + - - +
433C THR 3.1 1.0 + - - -
435C ALA* 1.3 75.9 - - - +
437C GLY* 1.3 61.0 + - - +
438C GLY 3.3 2.1 + - - -
439C PHE* 3.0 39.8 + - - +
440C CYS 4.4 0.4 - - - -
441C PRO* 4.0 10.3 - - + +
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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