Contacts of the helix formed by residues 505 - 515 (chain A) in PDB entry 5UBT
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 GLU 505 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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504A THR* 1.4 75.4 + - - +
506A GLU* 1.4 64.7 + - - +
507A GLU 3.4 1.3 - - - -
508A GLN* 3.1 40.8 + - - +
509A LEU* 3.6 9.5 + - - +
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Residues in contact with GLU 506 (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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504A THR* 3.4 6.0 + - - +
505A GLU* 1.4 78.2 - - - +
507A GLU* 1.4 63.6 + - + +
508A GLN 3.3 0.4 + - - -
509A LEU* 3.7 17.9 + - + +
510A GLN* 3.5 17.2 + - - +
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Residues in contact with GLU 507 (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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504A THR* 3.1 32.7 + - - +
506A GLU* 1.4 77.6 - - + +
508A GLN* 1.4 54.7 + - - +
509A LEU 3.2 0.9 - - - -
510A GLN* 3.0 16.0 + - - +
511A LEU 2.9 28.9 + - - -
530A LEU* 3.4 28.7 - - + +
533A LYS* 5.1 9.0 - - - +
534A LEU* 3.6 26.3 - - + +
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Residues in contact with GLN 508 (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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504A THR 3.4 20.1 + - - +
505A GLU* 3.1 43.0 + - - +
506A GLU 3.3 0.2 - - - -
507A GLU* 1.4 78.2 - - - +
509A LEU* 1.3 57.7 + - - +
511A LEU* 3.9 10.4 + - + +
512A ARG* 3.6 19.9 + - - +
534A LEU* 4.6 5.5 - - + +
537A GLU* 4.3 23.9 + - + +
541A HIS* 5.0 16.1 + - + -
542A PHE* 5.4 1.9 - - - -
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Residues in contact with LEU 509 (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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505A GLU* 3.6 8.7 + - - +
506A GLU* 3.7 22.0 - - + +
507A GLU 3.2 0.2 - - - -
508A GLN* 1.3 75.7 - - - +
510A GLN* 1.4 61.9 + - + +
511A LEU 3.2 0.4 - - - -
512A ARG* 3.1 23.3 + - + +
513A GLU* 3.2 20.4 + - + +
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Residues in contact with GLN 510 (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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506A GLU 3.5 5.7 + - - +
507A GLU* 3.0 25.3 + - - +
509A LEU* 1.4 80.8 - - + +
511A LEU* 1.4 56.3 + - - +
513A GLU* 4.1 6.5 - - + +
514A ILE* 3.3 35.8 + - + +
530A LEU* 3.4 27.7 - - + +
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Residues in contact with LEU 511 (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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507A GLU 2.9 13.8 + - - +
508A GLN* 3.9 9.2 - - + +
510A GLN* 1.4 73.7 - - - +
512A ARG* 1.4 57.6 + - - +
513A GLU 3.2 0.2 - - - -
514A ILE* 3.2 3.9 + - - +
515A LEU* 2.9 40.7 + - + +
530A LEU* 4.4 4.3 - - + -
531A VAL* 3.9 37.7 - - + +
534A LEU* 3.8 30.7 - - + -
537A GLU* 4.5 11.2 - - + -
538A VAL* 4.0 18.6 - - + -
541A HIS* 6.1 0.2 - - + -
542A PHE* 3.6 30.3 - - + -
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Residues in contact with ARG 512 (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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508A GLN 3.6 10.6 + - - +
509A LEU* 3.1 14.3 + - + +
511A LEU* 1.4 78.2 - - - +
513A GLU* 1.4 58.6 + - - +
515A LEU 3.5 4.3 - - - +
516A GLU* 2.9 52.0 + - - +
542A PHE* 3.7 33.3 - - + -
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Residues in contact with GLU 513 (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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509A LEU* 3.2 22.0 + - + +
510A GLN* 4.3 8.3 - - + +
511A LEU 3.2 0.2 - - - -
512A ARG* 1.4 74.0 - - - +
514A ILE* 1.4 63.8 + - + +
516A GLU* 3.4 22.7 - - + +
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Residues in contact with ILE 514 (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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510A GLN* 3.3 26.1 + - + +
511A LEU* 3.2 6.1 + - - +
513A GLU* 1.4 74.7 - - + +
515A LEU* 1.3 59.4 + - + +
516A GLU 2.9 15.1 + - - +
523A LEU* 3.8 32.7 - - + +
526A HIS* 5.8 1.3 - - + -
527A GLU* 3.7 46.4 - - + +
530A LEU* 3.8 20.6 - - + -
531A VAL* 3.9 22.7 - - + -
548A ARG* 5.2 1.9 + - - -
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Residues in contact with LEU 515 (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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511A LEU* 2.9 40.3 + - + +
512A ARG 3.5 2.1 - - - +
514A ILE* 1.3 73.7 - - + +
516A GLU* 1.4 73.4 + - - +
523A LEU* 5.2 0.7 - - + -
531A VAL* 4.6 19.5 - - + -
538A VAL* 4.2 7.4 - - + -
542A PHE* 3.6 46.7 - - + -
545A ALA* 3.9 16.8 - - + -
548A ARG* 3.8 38.6 - - + +
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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
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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