Contacts of the helix formed by residues 510 - 519 (chain B) in PDB entry 1U5T
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 510 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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508B GLY 3.8 2.2 + - - +
509B SER* 1.3 76.0 - - - +
511B LEU* 1.3 91.1 + - - +
512B LEU* 2.9 26.1 + - - +
513B ARG* 3.3 12.4 + - + +
514B LEU* 2.8 21.9 + - - +
554B ILE 4.1 8.6 - - - +
555B TYR* 4.8 17.1 - - + -
556B TYR* 5.1 1.6 - - - -
20C SER* 3.4 22.6 + - - -
21C LEU* 4.0 8.5 - - - +
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Residues in contact with LEU 511 (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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107A LYS* 4.4 4.9 - - - +
510B ASP* 1.3 83.2 + - - +
512B LEU* 1.3 53.9 + - - +
514B LEU* 2.9 9.6 + - + +
515B THR* 2.6 35.1 + - - +
529B LEU* 4.3 12.3 - - + -
532B LEU* 3.5 29.2 - - + -
533B MET* 3.9 28.5 - - - -
536B LEU* 3.8 22.0 - - + -
554B ILE 4.5 5.5 + - - -
556B TYR* 5.2 5.8 - - + -
21C LEU* 4.3 28.7 - - + -
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Residues in contact with LEU 512 (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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510B ASP* 2.9 18.6 + - - +
511B LEU* 1.3 81.6 - - - +
513B ARG* 1.3 59.4 + - - +
515B THR* 2.7 36.6 - - + +
516B GLN* 2.9 41.6 + - + +
20C SER* 5.0 6.7 - - - +
21C LEU* 4.9 12.5 - - + +
24C ARG* 4.0 36.1 - - + +
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Residues in contact with ARG 513 (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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506B ASN* 3.3 31.5 + - - +
507B PRO 5.4 3.0 + - - -
509B SER* 3.8 12.1 + - - +
510B ASP* 3.3 24.2 + - + +
511B LEU 3.1 1.0 - - - -
512B LEU* 1.3 72.9 - - - +
514B LEU* 1.3 55.3 + - - +
515B THR 2.3 19.5 + - - -
516B GLN* 2.5 35.2 + - - +
517B ILE* 3.0 29.6 - - + +
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Residues in contact with LEU 514 (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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499B LEU* 3.7 22.2 - - + -
502B LEU* 5.2 6.7 - - + -
503B ILE* 3.2 35.2 - - + +
506B ASN* 5.4 1.1 - - + +
509B SER* 3.7 20.6 - - - +
510B ASP 2.8 11.6 + - - +
511B LEU* 3.0 19.1 - - + +
513B ARG* 1.3 78.4 - - - +
515B THR* 1.3 58.5 + - - +
517B ILE* 4.0 6.7 - - + +
518B LEU* 3.1 30.5 + - + +
532B LEU* 3.3 33.4 - - + +
536B LEU* 4.1 13.2 - - + -
556B TYR* 5.3 3.4 - - + -
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Residues in contact with THR 515 (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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511B LEU* 2.6 9.1 + - - +
512B LEU* 2.7 24.2 - - + +
513B ARG 2.3 11.1 + - - -
514B LEU* 1.3 65.2 - - - +
516B GLN* 1.3 85.1 + - + +
518B LEU* 2.5 30.6 + - - -
519B SER* 2.6 25.9 + - - +
520B SER* 5.6 1.1 - - - +
529B LEU* 4.5 12.0 + - - +
532B LEU* 4.1 16.9 - - - +
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Residues in contact with GLN 516 (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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512B LEU* 2.9 34.3 + - + +
513B ARG* 2.5 30.2 + - - +
515B THR* 1.3 84.3 - - + +
517B ILE* 1.3 69.4 + - + +
519B SER 2.9 8.3 + - - -
520B SER* 3.1 28.4 + - - +
521B ASN* 3.7 6.5 + - - +
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Residues in contact with ILE 517 (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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502B LEU* 3.4 29.4 - - + -
506B ASN* 3.6 21.5 - - + +
509B SER* 5.1 2.2 - - - +
513B ARG* 3.0 59.4 + - + +
514B LEU* 3.8 6.3 - - + +
516B GLN* 1.3 74.4 - - - +
518B LEU* 1.3 73.1 + - + +
519B SER 3.3 0.3 + - - -
521B ASN* 3.9 20.9 - - - +
525B SER* 5.6 0.2 - - - -
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Residues in contact with LEU 518 (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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432B TYR* 5.5 0.2 - - - +
499B LEU* 5.1 3.4 - - + -
502B LEU* 3.1 35.4 - - + -
514B LEU* 3.1 21.7 + - + +
515B THR* 2.5 13.1 + - - +
517B ILE* 1.3 82.0 - - + +
519B SER* 1.3 60.2 + - - +
521B ASN 6.1 0.4 - - - -
525B SER* 2.6 36.0 + - - +
527B TRP* 3.0 56.8 - - + +
532B LEU* 4.7 12.8 - - + -
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Residues in contact with SER 519 (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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515B THR* 2.6 29.4 + - - -
516B GLN 2.9 3.6 + - - -
518B LEU* 1.3 83.6 + - - +
520B SER* 1.3 57.4 + - - -
521B ASN 3.1 10.2 + - - -
522B ASN* 3.4 19.6 + - - +
525B SER* 5.0 1.6 - - - -
527B TRP* 3.9 14.4 + - - +
528B THR* 5.5 0.9 - - - -
529B LEU 5.7 1.0 + - - -
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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