Contacts of the helix formed by residues 415 - 427 (chain A) in PDB entry 1U1H
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 ASN 415 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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413A ALA 3.0 5.8 + - - -
414A THR* 1.3 76.9 - - - +
416A VAL* 1.3 74.7 + - - +
417A SER* 2.7 41.8 + - - +
418A ALA* 3.2 8.2 + - + +
419A ARG* 3.0 15.8 + - - +
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Residues in contact with VAL 416 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414A THR 3.4 1.4 + - - -
415A ASN* 1.3 85.6 + - - +
417A SER* 1.3 58.0 + - - +
419A ARG* 3.2 33.4 + - - +
420A LEU* 2.8 35.1 + - + +
664A ASP* 3.7 10.4 + - - +
665A ALA 3.8 18.2 - - - +
666A ASP* 4.0 12.8 - - - +
689A TYR 4.9 3.6 - - - +
690A GLY 3.4 18.4 - - - +
691A ALA* 3.9 16.2 - - + -
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Residues in contact with SER 417 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415A ASN* 2.7 26.1 + - - +
416A VAL* 1.3 74.4 - - - +
418A ALA* 1.3 64.2 + - - +
420A LEU* 3.5 15.6 + - - +
421A ASP* 3.3 21.8 + - - +
690A GLY* 4.6 8.1 - - - -
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Residues in contact with ALA 418 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414A THR* 4.1 13.5 - - + -
415A ASN* 3.2 12.1 + - + +
417A SER* 1.3 80.1 + - - +
419A ARG* 1.3 61.1 + - - +
421A ASP* 2.9 34.6 + - - +
422A ALA* 3.4 6.2 + - - +
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Residues in contact with ARG 419 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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411A ARG* 2.9 60.3 + - - +
412A ARG 5.6 0.2 - - - -
414A THR* 3.7 22.8 + - + +
415A ASN 3.0 13.2 + - - +
416A VAL* 3.4 21.1 - - - +
418A ALA* 1.3 78.6 - - - +
420A LEU* 1.3 59.7 + - - +
422A ALA* 3.3 2.9 + - - +
423A GLN* 2.8 31.3 + - - +
640A ASP* 3.2 41.8 - - + +
664A ASP* 2.9 44.1 + - - -
666A ASP* 3.0 23.1 + - - +
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Residues in contact with LEU 420 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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416A VAL* 2.8 27.5 + - + +
417A SER* 3.5 13.9 - - - +
418A ALA 3.1 0.2 - - - -
419A ARG* 1.3 76.7 - - - +
421A ASP* 1.3 57.6 + - - +
423A GLN* 3.3 20.2 + - - +
424A GLN* 3.0 32.2 + - - +
643A GLN* 3.8 14.3 + - - +
666A ASP* 3.7 22.0 - - + +
667A VAL* 4.7 2.5 - - + -
690A GLY 4.4 1.8 - - - +
691A ALA* 4.0 26.0 - - - -
692A GLY* 4.3 4.3 - - - +
726A ILE* 4.6 12.1 - - + -
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Residues in contact with ASP 421 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417A SER 3.3 16.0 + - - +
418A ALA* 2.9 17.4 + - - +
420A LEU* 1.3 78.5 - - - +
422A ALA* 1.3 61.1 + - - +
424A GLN* 3.2 8.4 + - - +
425A LYS* 3.1 19.9 + - - +
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Residues in contact with ALA 422 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418A ALA 3.4 5.0 + - - +
419A ARG* 3.3 9.0 + - - +
421A ASP* 1.3 79.0 - - - +
423A GLN* 1.3 61.7 + - - +
425A LYS* 3.1 25.9 - - + +
426A LYS* 3.4 12.0 + - - +
640A ASP* 3.9 19.1 - - + +
641A SER* 4.2 12.7 - - - -
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Residues in contact with GLN 423 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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411A ARG* 4.0 3.0 - - - +
419A ARG* 2.8 23.0 + - - +
420A LEU* 3.3 21.8 - - - +
421A ASP 3.2 0.2 - - - -
422A ALA* 1.3 73.2 - - - +
424A GLN* 1.3 53.4 + - - +
425A LYS 3.0 0.2 - - - -
426A LYS* 3.0 4.0 + - - +
427A LEU* 2.8 41.9 + - + +
640A ASP 3.2 15.1 + - - +
641A SER 3.4 18.6 - - - +
642A THR 3.0 17.6 + - - -
643A GLN* 2.9 42.1 + - + +
666A ASP* 2.7 32.6 + - - +
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Residues in contact with GLN 424 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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420A LEU 3.0 18.3 + - - +
421A ASP* 3.2 8.3 + - - +
423A GLN* 1.3 74.4 - - - +
425A LYS* 1.3 66.7 + - - +
427A LEU* 2.6 43.8 + - - +
428A ASN* 3.7 9.7 + - - +
429A LEU* 3.0 42.3 + - - +
643A GLN* 5.3 2.0 - - - +
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Residues in contact with LYS 425 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421A ASP 3.1 11.1 + - - +
422A ALA* 3.1 17.9 - - + +
423A GLN 3.0 0.4 - - - -
424A GLN* 1.3 79.7 - - - +
426A LYS* 1.3 90.5 + - - +
428A ASN* 4.6 4.7 + - - +
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Residues in contact with LYS 426 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422A ALA 3.4 10.9 + - - +
423A GLN* 3.0 10.3 + - - +
425A LYS* 1.3 116.5 - - + +
427A LEU* 1.3 67.2 + - + +
428A ASN 3.8 1.8 + - - -
641A SER* 4.6 22.0 - - - +
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Residues in contact with LEU 427 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423A GLN* 2.8 23.8 + - + +
424A GLN* 2.6 24.7 + - - +
426A LYS* 1.3 82.4 - - + +
428A ASN* 1.3 50.4 + - - +
429A LEU* 2.4 46.1 + - + -
485A VAL* 6.1 1.1 - - + -
553A PRO* 4.2 18.8 - - + -
600A GLY* 5.2 5.8 - - - +
601A VAL* 3.9 28.7 - - + -
641A SER 5.6 1.6 - - - +
643A GLN* 3.6 37.9 - - + +
728A TRP* 5.7 0.2 - - + -
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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