Contacts of the helix formed by residues 424 - 445 (chain C) in PDB entry 1U2Z
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 MET 424 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201B SER* 3.7 42.8 - - - +
202B HIS* 4.3 1.8 - - - -
363C HIS* 6.3 1.3 - - + -
365C LYS* 3.7 30.3 - - + +
370C TYR* 3.8 18.2 - - + +
422C GLU* 2.9 24.2 + - - +
423C ILE* 1.3 72.4 - - + +
425C ASP* 1.3 58.4 + - - +
426C ASP* 4.7 5.6 - - + +
427C ALA* 3.9 17.0 - - + +
428C SER* 2.7 37.1 + - - -
803C SAH 3.4 11.9 - - - +
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Residues in contact with ASP 425 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B TYR* 4.5 6.5 + - - -
202B HIS* 3.0 34.0 + - + +
204B ILE 5.4 2.1 - - - +
206B SER* 4.1 15.6 + - - -
443B LYS* 4.8 4.9 + - - -
423C ILE 3.5 1.0 + - - -
424C MET* 1.3 71.7 - - - +
426C ASP* 1.3 68.9 + - - +
428C SER* 3.2 3.5 + - - -
429C ASP* 3.0 30.5 + - - +
457C LYS* 3.1 37.4 + - - +
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Residues in contact with ASP 426 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360C LYS* 3.3 45.8 - - + +
361C LEU* 4.3 3.4 - - + -
363C HIS* 3.2 26.2 + - - -
424C MET* 4.7 5.1 - - + +
425C ASP* 1.3 75.3 - - - +
427C ALA* 1.3 66.9 + - - +
429C ASP* 3.1 12.6 + - - +
430C LEU* 3.0 27.3 + - - +
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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
----------------------------------------------------------
361C LEU* 3.5 24.4 - - + +
372C TYR* 5.4 3.6 - - + -
401C GLY* 3.5 23.1 - - - +
402C VAL* 3.8 2.7 - - - +
422C GLU* 3.9 15.7 - - + -
424C MET* 3.7 15.9 + - + +
425C ASP 3.4 0.4 - - - -
426C ASP* 1.3 78.7 - - - +
428C SER* 1.3 57.1 + - - +
430C LEU* 3.4 2.8 + - - +
431C THR* 2.9 30.9 + - - -
803C SAH 5.7 0.7 - - - +
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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
----------------------------------------------------------
422C GLU* 3.5 9.8 + - - +
424C MET 2.7 22.4 + - - -
425C ASP 3.5 5.6 - - - -
426C ASP 3.1 0.2 - - - -
427C ALA* 1.3 76.0 - - - +
429C ASP* 1.3 64.9 + - - +
431C THR* 3.3 16.8 + - - -
432C ILE* 3.3 18.5 + - - +
456C LEU* 3.5 17.0 - - - +
457C LYS* 3.1 39.0 + - - -
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Residues in contact with ASP 429 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425C ASP* 3.0 23.2 + - - +
426C ASP* 3.6 14.3 - - - +
428C SER* 1.3 75.9 - - - +
430C LEU* 1.3 66.1 + - + +
432C ILE* 3.2 16.9 + - - +
433C LEU* 3.2 22.0 + - + +
457C LYS* 3.1 26.3 + - - -
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Residues in contact with LEU 430 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353C SER 3.6 23.1 - - - +
354C ILE* 3.6 21.0 - - + +
357C GLN* 3.9 46.4 - - + +
360C LYS* 5.1 4.9 - - + -
361C LEU* 3.7 39.3 - - + -
402C VAL* 3.8 4.0 - - + -
426C ASP* 3.0 16.1 + - + +
427C ALA 3.8 4.3 - - - +
429C ASP* 1.3 77.9 - - + +
431C THR* 1.3 58.9 + - - +
433C LEU* 3.7 7.9 - - + +
434C GLN* 2.9 32.9 + - - +
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Residues in contact with THR 431 (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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400C SER* 5.6 0.3 + - - -
401C GLY 3.1 15.9 + - - -
402C VAL* 3.2 20.0 + - - +
427C ALA 2.9 20.8 + - - -
428C SER* 3.4 10.2 - - - -
429C ASP 3.2 0.4 - - - -
430C LEU* 1.3 74.9 - - - +
432C ILE* 1.3 58.7 + - + +
434C GLN* 3.8 1.0 - - - +
435C TYR* 2.8 29.3 + - + +
454C PHE* 3.6 50.7 - - + -
456C LEU* 4.1 12.4 - - + +
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Residues in contact with ILE 432 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428C SER 3.4 13.7 - - - +
429C ASP* 3.2 10.2 + - - +
431C THR* 1.3 77.4 - - + +
433C LEU* 1.3 65.8 + - + +
435C TYR* 3.3 11.2 + - + +
436C GLU* 2.9 42.9 + - + +
454C PHE* 5.7 3.4 - - + -
456C LEU* 3.4 24.2 - - + -
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Residues in contact with LEU 433 (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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210C ILE* 5.7 4.1 - - + +
353C SER* 3.9 18.5 - - - +
357C GLN* 3.6 27.1 - - - +
429C ASP* 3.2 16.6 + - + +
430C LEU* 3.7 20.4 - - + +
432C ILE* 1.3 86.6 - - + +
434C GLN* 1.3 64.3 + - - +
436C GLU* 3.4 5.7 + - + +
437C GLU* 3.2 23.9 + - - +
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Residues in contact with GLN 434 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346C LEU* 4.4 4.0 - - + +
349C VAL* 3.6 11.7 - - + +
350C TYR* 3.7 33.6 + - - +
353C SER* 3.2 17.4 + - - +
354C ILE* 3.8 7.6 - - + +
402C VAL* 3.0 28.5 + - - +
403C GLY 4.3 1.8 - - - -
404C ASN* 2.9 29.9 + - - +
407C VAL* 5.0 14.5 - - + +
430C LEU 2.9 17.3 + - - +
431C THR 3.9 2.9 - - - +
433C LEU* 1.3 76.0 - - - +
435C TYR* 1.3 65.1 + - - +
437C GLU 3.4 0.3 + - - -
438C LEU* 2.9 24.9 + - + +
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Residues in contact with TYR 435 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407C VAL* 4.9 3.8 - - + -
431C THR 2.8 20.7 + - - +
432C ILE* 3.6 11.0 - - + +
434C GLN* 1.3 79.0 - - - +
436C GLU* 1.3 81.7 + - - +
438C LEU* 3.2 12.9 + - + +
439C LYS* 3.0 49.7 + - + +
449C LEU* 3.9 16.0 - - + +
452C VAL* 3.6 49.3 + - + +
454C PHE* 4.5 16.6 - + + -
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Residues in contact with GLU 436 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432C ILE* 2.9 30.6 + - + +
433C LEU* 3.6 7.2 - - - +
435C TYR* 1.3 97.8 - - - +
437C GLU* 1.3 61.1 + - - +
439C LYS* 2.8 33.7 + - - +
440C LYS* 3.3 37.7 + - - +
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Residues in contact with GLU 437 (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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209C PRO* 3.6 8.2 - - - +
210C ILE* 3.0 40.4 + - + +
349C VAL* 4.1 13.2 - - + -
352C ARG* 3.6 23.3 - - + +
353C SER* 4.8 2.7 - - - -
433C LEU 3.2 12.9 + - - +
434C GLN* 3.9 2.9 - - - +
436C GLU* 1.3 76.2 - - - +
438C LEU* 1.3 69.9 + - - +
440C LYS* 3.0 10.5 + - - +
441C ARG* 2.6 65.0 + - + +
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Residues in contact with LEU 438 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345C PHE* 3.7 26.7 - - + -
346C LEU* 3.8 18.2 - - + -
349C VAL* 3.9 17.2 - - + +
407C VAL* 3.5 41.1 - - + -
411C LEU* 4.3 4.7 - - + -
434C GLN* 2.9 20.0 + - + +
435C TYR* 3.4 7.0 - - + +
437C GLU* 1.3 77.8 - - - +
439C LYS* 1.3 57.0 + - - +
441C ARG* 3.3 0.9 + - - +
442C CYS* 2.8 34.0 + - - +
449C LEU* 3.9 27.1 - - + -
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Residues in contact with LYS 439 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435C TYR* 3.0 55.6 + - + +
436C GLU* 2.8 35.1 + - - +
437C GLU 3.1 0.2 - - - -
438C LEU* 1.3 75.1 - - - +
440C LYS* 1.3 66.5 + - + +
442C CYS* 3.3 6.9 + - - +
443C LYS* 3.2 42.4 + - - +
449C LEU* 4.2 13.0 - - + -
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Residues in contact with LYS 440 (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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205C TYR* 3.0 27.1 + - - +
207C GLY* 5.3 2.5 - - - -
208C THR* 2.8 53.4 + - - +
209C PRO* 3.6 12.3 - - + +
210C ILE* 5.3 4.2 - - - +
436C GLU* 3.3 26.3 + - - +
437C GLU* 3.0 13.9 + - - +
439C LYS* 1.3 75.4 - - + +
441C ARG* 1.3 65.4 + - - +
443C LYS* 3.1 10.1 + - - +
444C LEU 3.1 12.5 + - - -
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Residues in contact with ARG 441 (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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209C PRO* 3.9 9.8 - - - +
210C ILE 2.8 30.9 + - - -
247C TYR* 4.2 3.2 + - - -
249C GLU* 2.8 35.5 + - - -
251C TYR* 4.9 2.2 + - - -
267C GLU* 4.9 0.6 + - - -
271C LEU* 5.9 1.6 - - - +
345C PHE* 3.7 19.6 - - + -
348C ILE* 4.7 14.8 - - - +
349C VAL* 4.1 10.7 - - + +
352C ARG* 3.0 20.7 - - - +
437C GLU* 2.6 41.1 + - + +
438C LEU 3.7 2.9 - - - +
440C LYS* 1.3 76.9 - - - +
442C CYS* 1.3 63.0 + - - +
444C LEU* 3.2 22.0 + - - +
445C TYR* 3.2 36.9 + - - -
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Residues in contact with CYS 442 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345C PHE* 3.9 23.1 - - - -
411C LEU* 4.0 23.6 - - - -
438C LEU* 2.8 26.7 + - - +
439C LYS* 3.6 7.9 - - - +
440C LYS 3.1 0.2 - - - -
441C ARG* 1.3 77.2 - - - +
443C LYS* 1.3 59.3 + - + +
445C TYR 3.3 2.1 + - - -
446C GLY 3.1 3.3 + - - -
447C MET* 2.7 51.2 + - - +
449C LEU* 4.1 19.5 - - + -
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Residues in contact with LYS 443 (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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457A LYS* 6.4 4.3 - - - -
198C TYR* 4.1 31.5 - - + +
205C TYR* 3.9 13.4 - - + -
207C GLY* 6.3 2.2 - - - -
244C PHE* 3.3 17.3 - - - -
439C LYS* 3.2 29.9 + - - +
440C LYS* 3.1 11.1 + - - +
442C CYS* 1.3 78.9 - - + +
444C LEU* 1.3 63.3 + - - +
446C GLY* 3.1 13.2 + - - +
447C MET 4.7 2.9 - - - +
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Residues in contact with LEU 444 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205C TYR* 3.5 26.0 - - + -
209C PRO* 4.6 6.1 - - + -
241C SER* 4.3 10.5 + - - +
243C LEU* 4.0 5.7 - - - +
244C PHE* 3.2 23.8 - - + -
247C TYR* 3.6 59.5 - - + +
440C LYS 3.1 12.2 + - - +
441C ARG* 3.3 31.6 - - - +
442C CYS 3.2 0.2 - - - -
443C LYS* 1.3 77.9 - - - +
445C TYR* 1.3 76.5 + - + +
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Residues in contact with TYR 445 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194C PHE* 4.1 3.8 - - - -
239C LEU* 5.2 2.4 - - - +
242C ILE* 5.6 8.3 - - + -
243C LEU* 3.3 19.0 - - + +
271C LEU* 3.3 42.2 - - + +
279C PHE* 3.7 33.7 - + + -
341C PHE* 5.3 3.8 - + - -
345C PHE* 3.5 21.1 - + - -
348C ILE* 6.2 1.1 - - + -
441C ARG* 3.2 26.5 + - - +
443C LYS 3.3 0.2 - - - -
444C LEU* 1.3 97.2 - - + +
446C GLY* 1.3 64.0 + - - +
447C MET* 3.1 32.6 + - + +
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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