Contacts of the helix formed by residues 544 - 553 (chain A) in PDB entry 6UJX
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 GLY 544 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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441A TYR* 3.8 27.9 - - - +
458A VAL* 4.3 1.7 - - - +
543A GLY* 1.3 70.2 + - - -
545A ASN* 1.3 65.7 + - - +
546A GLU 3.0 0.7 - - - -
547A GLN* 3.2 14.0 + - - +
548A VAL* 3.1 24.1 + - - +
285B GLY 3.3 6.7 + - - -
286B THR* 3.9 17.0 - - - +
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Residues in contact with ASN 545 (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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441A TYR* 3.9 10.6 - - + -
442A VAL 4.6 6.7 + - - -
443A ASP* 4.6 2.8 - - - -
496A VAL* 5.6 2.1 + - + +
497A THR 5.3 0.2 - - - -
498A ASP* 3.0 34.9 + - - +
536A VAL* 4.1 23.3 - - + +
537A PRO 4.1 3.6 - - - +
538A ALA* 4.0 13.5 - - - -
539A HIS 4.1 6.1 + - - -
540A LYS 5.1 1.7 + - - -
541A GLY 5.6 0.2 + - - -
542A ILE* 2.8 18.1 + - + +
543A GLY 3.2 0.2 - - - -
544A GLY* 1.3 79.7 - - - +
546A GLU* 1.3 62.3 + - - +
548A VAL* 3.2 14.6 - - - +
549A ASP* 3.0 26.5 + - - +
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Residues in contact with GLU 546 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541A GLY* 3.3 42.1 - - - +
542A ILE 3.0 7.4 + - - +
543A GLY* 4.1 1.6 + - - +
544A GLY 3.0 0.2 - - - -
545A ASN* 1.3 80.2 - - - +
547A GLN* 1.3 75.3 + - - +
549A ASP* 3.3 7.6 + - + +
550A LYS* 3.3 50.1 + - - +
284B ARG* 6.2 0.3 - - - +
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Residues in contact with GLN 547 (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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458A VAL* 4.5 17.0 - - + -
543A GLY* 3.8 2.6 - - - -
544A GLY* 3.2 20.7 + - - +
546A GLU* 1.3 94.8 + - - +
548A VAL* 1.3 60.7 + - - +
550A LYS* 3.4 20.2 + - + +
551A LEU* 3.4 17.6 + - - +
285B GLY* 3.9 26.9 - - - +
286B THR* 4.2 11.1 - - + +
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Residues in contact with VAL 548 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441A TYR 3.4 27.6 - - - +
442A VAL 4.0 4.5 - - - +
443A ASP* 3.7 23.8 - - + -
456A GLY 3.6 22.7 - - - +
457A TYR* 3.8 10.1 - - - -
458A VAL* 4.4 5.8 - - + +
544A GLY 3.1 12.5 + - - +
545A ASN* 3.2 19.1 - - - +
547A GLN* 1.3 74.8 - - - +
549A ASP* 1.3 68.2 + - - +
551A LEU* 3.3 10.2 + - + +
552A VAL* 3.2 26.7 + - + +
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Residues in contact with ASP 549 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443A ASP* 3.5 22.0 - - - +
498A ASP* 4.3 7.3 - - - +
539A HIS* 3.8 39.8 + - - -
545A ASN* 3.0 22.1 + - - +
546A GLU* 3.4 9.4 - - + +
547A GLN 3.2 0.4 - - - -
548A VAL* 1.3 77.0 - - - +
550A LYS* 1.3 63.1 + - + +
552A VAL* 3.8 1.8 - - - +
553A SER* 3.0 42.1 + - - -
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Residues in contact with LYS 550 (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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546A GLU* 3.3 45.1 + - - +
547A GLN* 3.6 12.3 - - + +
548A VAL 3.3 0.2 - - - -
549A ASP* 1.3 79.9 - - - +
551A LEU* 1.3 63.1 + - + +
553A SER* 3.3 24.0 + - - +
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Residues in contact with LEU 551 (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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454A LYS* 4.2 10.0 + - - +
457A TYR 4.2 8.1 - - - +
458A VAL* 3.9 21.3 - - + -
464A GLN* 3.6 40.8 - - - +
466A VAL* 3.7 28.9 - - + +
547A GLN 3.4 11.0 + - - +
548A VAL* 3.3 10.5 + - + +
550A LYS* 1.3 82.0 - - + +
552A VAL* 1.3 62.5 + - + +
553A SER 3.3 0.7 + - - -
554A ALA* 4.1 9.0 + - - +
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Residues in contact with VAL 552 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443A ASP* 3.6 33.7 - - - +
444A GLY* 3.9 18.8 - - - -
445A ALA* 3.5 17.7 - - + +
454A LYS* 3.7 33.4 + - + +
455A ALA 4.3 2.2 - - - -
456A GLY* 3.9 16.2 - - - +
466A VAL* 4.8 3.8 - - + -
548A VAL* 3.2 28.6 + - + +
549A ASP* 3.8 4.7 - - - +
551A LEU* 1.3 78.3 - - + +
553A SER* 1.3 60.2 + - - +
554A ALA 3.5 4.5 + - - -
555A GLY 4.7 1.4 + - - -
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Residues in contact with SER 553 (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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445A ALA* 4.4 11.2 - - - +
549A ASP* 3.0 32.4 + - - -
550A LYS* 3.4 15.1 - - - +
551A LEU 3.1 1.2 - - - -
552A VAL* 1.3 78.9 + - - +
554A ALA* 1.3 55.7 + - - +
555A GLY 3.3 9.4 + - - +
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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