Contacts of the helix formed by residues 421 - 443 (chain C) in PDB entry 1U3Q
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 421 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422C SER* 1.3 63.3 + - - +
423C SER* 3.7 6.4 - - - +
424C ARG* 3.8 46.4 + - - +
425C LYS* 3.1 29.6 + - - +
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Residues in contact with SER 422 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321C GLU 5.8 0.7 - - - -
322C LEU* 3.6 14.7 - - - +
323C SER* 3.2 25.4 + - - -
326C ASP* 3.1 26.1 + - - -
421C ASP* 1.3 79.2 - - - +
423C SER* 1.3 65.5 + - - +
424C ARG 3.1 1.6 - - - -
425C LYS* 3.2 8.0 + - - +
426C LEU* 3.0 19.6 + - - +
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Residues in contact with SER 423 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326C ASP* 5.4 0.2 + - - -
421C ASP 4.2 3.5 - - - +
422C SER* 1.3 78.8 - - - +
424C ARG* 1.3 58.1 + - - +
426C LEU* 3.3 12.3 + - - +
427C ALA* 2.9 27.8 + - - +
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Residues in contact with ARG 424 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421C ASP* 3.8 43.9 + - - +
422C SER 3.1 0.8 - - - +
423C SER* 1.3 76.0 - - - +
425C LYS* 1.3 68.2 + - + +
427C ALA* 3.0 9.1 + - + +
428C HIS* 2.9 21.0 + - - +
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Residues in contact with LYS 425 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318C GLY* 5.5 4.9 - - - +
321C GLU* 4.4 36.2 + - - +
322C LEU* 4.0 14.6 - - + -
421C ASP* 3.1 22.2 + - - +
422C SER* 3.2 7.8 + - - +
424C ARG* 1.3 77.5 - - + +
426C LEU* 1.3 52.4 + - - +
428C HIS* 3.0 18.3 + - + +
429C LEU* 2.7 36.8 + - + +
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Residues in contact with LEU 426 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322C LEU* 3.8 14.3 - - + +
330C LEU* 4.0 30.5 - - + -
406C LEU* 3.6 44.6 - - + +
409C SER 5.5 5.2 - - - +
411C TYR 5.7 4.7 - - - +
422C SER 3.0 12.3 + - - +
423C SER* 3.4 14.6 - - - +
425C LYS* 1.3 76.1 - - - +
427C ALA* 1.3 56.1 + - - +
429C LEU* 2.8 23.8 + - + +
430C LEU* 2.9 17.9 + - + +
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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
----------------------------------------------------------
423C SER 2.9 13.2 + - - +
424C ARG* 3.2 13.0 - - + +
426C LEU* 1.3 76.5 - - - +
428C HIS* 1.3 61.1 + - - +
430C LEU* 3.5 5.5 + - - +
431C ASN* 3.1 25.2 + - - +
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Residues in contact with HIS 428 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424C ARG 2.9 12.2 + - - +
425C LYS* 3.0 19.9 + - + +
427C ALA* 1.3 75.5 - - - +
429C LEU* 1.3 64.7 + - + +
431C ASN* 3.3 9.4 + - - +
432C ALA* 3.1 33.0 + - + +
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Residues in contact with LEU 429 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268C LEU* 5.9 2.9 - - + -
316C ILE* 4.1 11.2 - - + +
317C PRO* 3.1 20.9 - - + +
318C GLY* 3.3 37.0 - - - +
319C PHE* 3.5 8.1 - - + +
322C LEU* 4.7 9.0 - - + -
406C LEU* 3.7 29.8 - - + -
425C LYS* 2.7 16.8 + - + +
426C LEU* 2.8 11.1 + - - +
428C HIS* 1.3 78.2 - - + +
430C LEU* 1.3 62.8 + - - +
432C ALA* 3.4 7.3 + - + +
433C VAL* 3.0 34.0 + - + +
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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
----------------------------------------------------------
386A ARG* 5.8 3.4 - - - +
457A ASN* 5.5 3.4 - - - +
460A MET* 4.0 16.6 - - + -
403C MET* 4.1 30.7 - - + +
406C LEU* 3.5 36.0 - - + +
407C ASN* 3.4 35.7 - - + +
426C LEU* 2.9 19.3 + - + +
427C ALA* 4.0 6.1 - - - +
429C LEU* 1.3 72.7 - - - +
431C ASN* 1.3 54.9 + - - +
433C VAL* 3.4 2.5 + - + +
434C THR* 2.7 38.1 + - - -
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Residues in contact with ASN 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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453A MET* 3.6 36.0 - - - +
457A ASN* 5.7 0.8 - - - +
427C ALA 3.1 19.5 + - - +
428C HIS* 3.3 13.4 + - + +
430C LEU* 1.3 77.3 - - - +
432C ALA* 1.3 58.1 + - - +
434C THR 3.3 0.5 + - - -
435C ASP* 3.0 46.8 + - - +
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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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263C LEU* 6.0 3.6 - - + +
265C PRO* 5.4 2.1 - - - +
268C LEU* 3.5 24.6 - - + +
428C HIS* 3.1 23.0 + - + +
429C LEU* 3.8 8.7 - - + +
430C LEU 3.4 0.2 - - - -
431C ASN* 1.3 80.1 + - - +
433C VAL* 1.3 57.7 + - - +
435C ASP* 3.4 10.8 + - - +
436C ALA* 3.0 19.6 + - - +
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Residues in contact with VAL 433 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268C LEU* 4.1 18.2 - - + -
272C LEU* 5.3 2.9 - - + -
316C ILE* 5.5 2.2 - - + -
399C CYS* 3.7 20.3 - - + +
402C ALA* 4.1 15.0 - - + -
403C MET* 3.5 26.7 - - + +
406C LEU* 3.6 19.5 - - + -
429C LEU* 3.0 25.7 + - + +
430C LEU* 3.7 4.9 - - - +
432C ALA* 1.3 73.8 - - - +
434C THR* 1.3 66.7 + - - +
436C ALA* 3.0 14.2 + - + +
437C LEU* 3.0 13.3 + - - +
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Residues in contact with THR 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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452A SER 4.6 2.9 - - - +
453A MET* 3.8 21.5 - - + -
456A ALA* 3.5 30.3 - - + -
460A MET* 3.3 21.4 - - + +
403C MET* 4.6 13.0 - - - -
430C LEU 2.7 25.9 + - - -
431C ASN 3.6 5.2 - - - -
433C VAL* 1.3 75.6 - - - +
435C ASP* 1.3 57.0 + - - +
437C LEU* 3.1 4.5 + - - +
438C VAL* 3.0 41.6 + - + +
455C LEU* 5.3 4.0 - - + -
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Residues in contact with ASP 435 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449A GLN* 2.7 43.0 + - - +
453A MET* 3.5 3.8 - - - +
265C PRO* 3.9 16.0 - - + +
431C ASN* 3.0 31.2 + - - +
432C ALA* 3.5 13.6 - - - +
433C VAL 3.2 0.2 - - - -
434C THR* 1.3 78.6 - - - +
436C ALA* 1.3 55.8 + - - +
438C VAL* 3.7 6.7 - - - +
439C TRP* 3.1 27.5 + - - +
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Residues in contact with ALA 436 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265C PRO* 3.9 17.7 - - + +
268C LEU* 4.2 13.2 - - + -
269C VAL* 4.0 13.0 - - + -
399C CYS* 3.9 16.4 - - - -
432C ALA 3.0 13.3 + - - +
433C VAL* 3.0 13.6 + - + +
435C ASP* 1.3 76.0 - - - +
437C LEU* 1.3 59.3 + - - +
439C TRP* 3.6 2.3 + - - +
440C VAL* 3.0 33.4 + - - +
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Residues in contact with LEU 437 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396C GLU* 4.1 25.8 - - + +
399C CYS* 3.9 15.7 - - + -
400C VAL* 4.4 10.8 - - + -
403C MET* 4.1 22.0 - - - -
433C VAL 3.0 11.4 + - - +
434C THR* 3.5 10.3 - - + +
436C ALA* 1.3 74.5 - - - +
438C VAL* 1.3 67.2 + - - +
440C VAL* 3.1 4.2 + - + +
441C ILE* 2.8 33.6 + - + +
455C LEU* 3.5 28.0 - - + -
458C LEU* 3.9 22.9 - - + -
459C LEU* 4.2 11.0 - - + -
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Residues in contact with VAL 438 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449A GLN* 4.7 15.0 - - - +
452A SER* 4.1 31.2 - - - +
434C THR* 3.0 22.6 + - + +
435C ASP* 3.7 10.5 - - - +
437C LEU* 1.3 77.2 - - - +
439C TRP* 1.3 54.2 + - - +
441C ILE* 2.9 10.1 + - - +
442C ALA* 2.8 33.9 + - + +
451C GLN* 4.2 11.5 - - - +
455C LEU* 4.2 16.6 - - + -
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Residues in contact with TRP 439 (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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265C PRO* 3.8 31.1 - - + +
266C GLU* 3.7 53.3 - - + +
269C VAL* 4.3 8.3 - - + -
395C LYS* 5.3 12.1 - - + -
435C ASP 3.1 14.4 + - - +
436C ALA 3.6 2.9 - - - +
438C VAL* 1.3 80.0 - - - +
440C VAL* 1.3 92.3 + - + +
442C ALA* 3.1 9.5 + - + +
443C LYS* 2.8 61.1 + - + +
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Residues in contact with VAL 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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269C VAL* 3.7 24.2 - - + -
393C GLN* 5.6 2.9 - - + -
395C LYS* 3.6 36.3 - - + +
396C GLU* 3.9 21.1 - - + -
399C CYS* 4.3 4.9 - - - -
436C ALA 3.0 24.4 + - - +
437C LEU* 3.5 5.6 - - + +
439C TRP* 1.3 88.0 - - + +
441C ILE* 1.3 64.5 + - - +
443C LYS* 3.1 20.9 + - + +
444C SER* 3.6 4.7 + - - -
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Residues in contact with ILE 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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396C GLU* 3.7 21.5 - - - +
437C LEU* 2.8 27.1 + - + +
438C VAL* 3.2 9.9 - - - +
440C VAL* 1.3 72.0 - - - +
442C ALA* 1.3 60.6 + - - +
444C SER* 2.6 32.1 + - - -
446C ILE* 4.3 4.9 - - + +
451C GLN* 3.9 32.8 - - + +
454C ARG* 4.3 14.8 - - + +
455C LEU* 3.8 44.2 - - + +
458C LEU* 3.9 15.5 - - + -
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Residues in contact with ALA 442 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438C VAL* 2.8 14.7 + - + +
439C TRP* 3.4 13.2 - - + +
441C ILE* 1.3 73.8 - - - +
443C LYS* 1.3 60.8 + - + +
444C SER 2.8 6.2 + - - -
445C GLY* 2.9 15.4 + - - -
446C ILE* 4.5 1.9 + - - +
451C GLN* 3.2 32.3 + - - +
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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
----------------------------------------------------------
439C TRP* 2.8 64.1 + - + +
440C VAL* 3.1 13.6 + - - +
442C ALA* 1.3 75.7 - - + +
444C SER* 1.3 60.8 + - - +
445C GLY* 3.2 1.5 + - - -
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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