Contacts of the helix formed by residues 414 - 429 (chain B) in PDB entry 1U2X
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 ARG 414 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360B TYR* 3.9 53.8 - - + +
361B TYR* 5.8 3.2 - - - -
412B ASN* 2.8 10.6 + - - +
413B GLU* 1.3 85.8 - - + +
415B SER* 1.3 63.9 + - - +
416B GLU 3.1 3.1 - - - -
417B TYR* 2.8 56.0 + - + +
418B VAL* 2.9 24.1 + - + +
1002B SO4 4.7 10.1 + - - -
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Residues in contact with SER 415 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A ARG* 3.9 11.0 - - - +
411B PHE* 3.5 8.4 - - - +
412B ASN* 2.8 29.2 + - - -
413B GLU 3.3 2.0 - - - -
414B ARG* 1.3 77.2 - - - +
416B GLU* 1.3 60.8 + - - +
418B VAL* 3.4 4.3 + - - +
419B LYS* 3.3 39.0 + - - +
440B PRO* 3.2 37.9 - - - +
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Residues in contact with GLU 416 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A ASN* 6.4 3.4 - - + -
188A ARG* 3.2 43.0 + - + +
191A LEU* 6.2 3.8 - - + -
414B ARG 3.1 1.0 - - - -
415B SER* 1.3 73.6 - - - +
417B TYR* 1.3 67.2 + - - +
419B LYS* 2.8 37.5 + - - +
420B LEU* 3.1 30.6 + - + +
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Residues in contact with TYR 417 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414B ARG* 2.8 52.1 + - + +
416B GLU* 1.3 79.0 - - - +
418B VAL* 1.3 62.5 + - - +
420B LEU* 3.6 12.4 - - + +
421B ARG* 2.9 60.2 + - + +
1002B SO4 3.4 26.1 + - - -
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Residues in contact with VAL 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335B LEU* 4.5 4.1 - - + +
360B TYR* 3.9 28.7 - - + +
361B TYR* 4.0 17.0 - - + -
414B ARG* 2.9 31.3 + - + +
415B SER* 3.5 11.2 - - - +
417B TYR* 1.3 72.7 - - - +
419B LYS* 1.3 55.2 + - + +
421B ARG* 3.3 5.1 + - - +
422B PHE* 2.8 33.8 + - - +
438B VAL* 3.7 29.8 - - + +
439B ILE 4.6 0.2 - - - -
440B PRO* 4.5 15.0 - - + -
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Residues in contact with LYS 419 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A ARG* 5.1 0.4 - - - +
415B SER* 3.3 21.6 + - - +
416B GLU* 2.8 43.9 + - - +
418B VAL* 1.3 81.1 - - + +
420B LEU* 1.3 64.0 + - - +
422B PHE* 3.2 8.9 + - - +
423B GLU* 2.9 31.0 + - + +
438B VAL 6.0 1.8 - - - +
440B PRO* 4.4 20.2 - - + +
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Residues in contact with LEU 420 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416B GLU* 3.1 22.5 + - + +
417B TYR* 3.6 12.3 - - + +
419B LYS* 1.3 80.1 - - - +
421B ARG* 1.4 65.4 + - + +
423B GLU* 3.2 8.9 + - - +
424B GLU* 3.1 48.6 + - + +
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Residues in contact with ARG 421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334B ARG* 6.0 3.8 - - - +
335B LEU* 3.7 16.4 - - + +
417B TYR* 2.9 62.1 + - + +
418B VAL* 3.9 4.3 - - - +
420B LEU* 1.4 75.8 - - - +
422B PHE* 1.3 62.5 + - - +
424B GLU* 3.3 33.9 + - - +
425B ALA* 3.0 23.4 + - - +
428B ARG* 3.7 23.0 - - - +
1002B SO4 3.0 30.0 + - - +
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Residues in contact with PHE 422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335B LEU* 3.6 9.6 - - + +
339B ILE* 4.0 17.0 - - + -
418B VAL 2.8 22.4 + - - +
419B LYS* 3.2 8.0 + - - +
421B ARG* 1.3 73.2 - - - +
423B GLU* 1.3 66.0 + - - +
425B ALA* 3.1 1.8 + - - +
426B LYS* 3.0 60.6 + - + +
431B MSE 5.6 1.1 - - + -
436B VAL* 3.4 38.8 - - + -
437B VAL* 4.7 0.9 - - - -
438B VAL* 3.7 51.1 - - + -
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Residues in contact with GLU 423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419B LYS* 2.9 20.6 + - + +
420B LEU* 3.5 9.6 - - - +
422B PHE* 1.3 80.2 - - - +
424B GLU* 1.3 62.6 + - + +
426B LYS* 3.0 34.3 + - - +
427B SER* 3.3 19.6 + - - -
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Residues in contact with GLU 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420B LEU* 3.1 36.5 + - + +
421B ARG* 3.3 42.4 + - - +
423B GLU* 1.3 75.7 - - + +
425B ALA* 1.3 63.3 + - - +
427B SER* 3.2 10.8 + - - -
428B ARG* 3.1 57.3 + - - +
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Residues in contact with ALA 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335B LEU* 4.5 2.7 - - + -
336B GLU* 4.4 22.0 - - + +
339B ILE* 3.7 29.4 - - + -
421B ARG 3.0 17.6 + - - +
422B PHE* 3.1 5.8 + - - +
424B GLU* 1.3 77.5 - - - +
426B LYS* 1.3 57.6 + - - +
428B ARG* 3.1 8.3 + - - +
429B LEU* 2.9 37.6 + - + +
431B MSE 5.0 0.7 - - - -
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Residues in contact with LYS 426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422B PHE* 3.0 56.4 + - + +
423B GLU* 3.0 40.3 + - - +
424B GLU 3.3 0.2 - - - -
425B ALA* 1.3 76.2 - - - +
427B SER* 1.4 59.9 - - - +
429B LEU 3.0 20.3 - - - +
431B MSE 4.1 27.7 - - + +
436B VAL 5.9 0.4 - - - -
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Residues in contact with SER 427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423B GLU 3.3 10.1 + - - -
424B GLU* 3.2 14.1 + - - -
426B LYS* 1.4 81.9 - - - +
428B ARG* 1.3 61.0 + - - +
429B LEU 4.9 0.3 - - - +
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Residues in contact with ARG 428 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336B GLU* 3.4 35.4 + - - +
421B ARG* 3.7 26.3 - - - +
424B GLU* 3.1 52.1 + - - +
425B ALA* 3.1 6.2 + - - +
427B SER* 1.3 82.8 - - - +
429B LEU* 1.3 61.8 + - + +
430B ARG 4.4 0.2 + - - -
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Residues in contact with LEU 429 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336B GLU* 3.4 51.6 - - + +
339B ILE* 3.9 24.5 - - + -
340B LEU* 4.1 27.4 - - + +
343B MSE 4.4 4.9 - - + -
425B ALA* 2.9 19.7 + - + +
426B LYS 3.0 17.2 - - - +
427B SER 4.8 0.2 - - - -
428B ARG* 1.3 85.1 - - - +
430B ARG* 1.3 64.5 + - - +
431B MSE 3.1 16.5 + - + +
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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
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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