Contacts of the helix formed by residues 509 - 518 (chain B) in PDB entry 5UFL
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 LEU 509 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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453B PHE* 3.8 9.4 - - + -
479B ILE* 4.0 10.5 - - + -
480B LEU* 3.7 20.2 - - + -
483B LEU* 3.3 33.9 - - + -
503B ILE* 3.9 8.5 - - + +
504B LEU* 3.7 40.2 - - + +
506B ASP* 3.1 14.5 + - + +
508B ARG* 1.3 79.0 - - - +
510B ILE* 1.3 64.6 + - + +
511B THR 3.3 0.6 + - - -
512B PRO* 3.3 6.3 - - + +
513B LEU* 3.1 32.3 + - + +
531B ILE* 4.3 9.0 - - + -
535B ALA* 5.3 0.9 - - + -
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Residues in contact with ILE 510 (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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504B LEU 5.8 0.9 - - - +
506B ASP 5.2 2.5 - - - +
507B PRO* 3.5 20.4 - - + +
508B ARG 3.2 0.4 - - - -
509B LEU* 1.3 77.8 - - + +
511B THR* 1.3 58.0 + - - +
513B LEU* 3.4 9.9 + - + +
514B ALA* 3.0 26.5 + - - +
541B PHE* 3.8 34.1 - - + -
542B PRO* 4.0 22.7 - - + +
545B VAL* 3.8 24.0 - - + +
546B LEU* 3.5 36.1 - - + +
549B SER* 4.0 8.5 - - - -
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Residues in contact with THR 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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458B ILE* 3.5 27.5 - - + +
459B ASP* 5.7 1.6 - - - -
465B LYS* 3.6 26.9 + - + +
507B PRO 4.7 0.6 + - - -
508B ARG* 3.8 3.9 + - - -
510B ILE* 1.3 76.1 - - - +
512B PRO* 1.3 67.4 - - - +
514B ALA* 3.3 1.7 + - - +
515B PHE* 3.0 62.1 + - + -
549B SER* 4.1 13.3 + - - -
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Residues in contact with PRO 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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453B PHE* 4.4 11.0 - - + -
458B ILE* 4.1 6.7 - - + -
476B ALA* 3.7 36.5 - - + +
479B ILE* 4.6 5.4 - - + -
480B LEU* 3.3 27.6 - - + +
508B ARG 3.1 19.3 - - - +
509B LEU* 3.3 10.1 - - + +
511B THR* 1.3 94.6 - - + +
513B LEU* 1.3 56.6 + - - +
515B PHE* 3.5 3.1 + - + +
516B ALA* 3.1 28.1 + - - +
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Residues in contact with LEU 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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480B LEU* 4.4 8.1 - - + -
509B LEU* 3.1 39.5 + - + +
510B ILE* 3.6 12.3 - - + +
512B PRO* 1.3 72.6 - - - +
514B ALA* 1.3 60.4 + - - +
516B ALA* 3.3 1.4 + - - +
517B LEU* 2.9 40.6 + - + +
528B GLY* 3.4 31.6 - - - +
531B ILE* 4.0 14.6 - - + -
532B LEU* 4.0 21.1 - - + +
535B ALA* 5.3 1.1 - - + -
541B PHE* 4.5 25.1 - - + -
546B LEU* 4.0 9.9 - - + -
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Residues in contact with ALA 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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510B ILE 3.0 13.1 + - - +
511B THR 3.3 4.0 + - - +
513B LEU* 1.3 72.5 - - - +
515B PHE* 1.3 58.0 + - - +
518B THR* 2.7 39.0 + - - +
546B LEU* 4.2 0.6 - - + +
549B SER* 3.2 40.2 - - - +
550B ILE* 3.9 16.8 - - + +
553B ASN* 3.6 13.2 - - - +
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Residues in contact with PHE 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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458B ILE* 5.0 1.8 - - + -
465B LYS* 4.0 13.0 - - + -
466B VAL 3.6 8.7 - - - -
467B ALA* 3.4 30.3 - - + -
472B CYS* 3.6 31.6 - - + -
473B LYS* 4.1 10.3 - - + -
476B ALA* 3.7 20.2 - - + -
511B THR* 3.0 40.7 + - + -
512B PRO* 3.6 9.0 - - + +
513B LEU 3.3 0.2 - - - -
514B ALA* 1.3 76.0 - - - +
516B ALA* 1.3 61.3 + - - +
518B THR* 3.4 7.4 + - - -
519B SER* 3.4 9.0 + - - -
524B GLN* 4.6 5.8 - - - +
553B ASN* 3.3 26.5 - - - -
557B ARG* 3.2 25.3 + - - +
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Residues in contact with ALA 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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480B LEU* 3.5 32.8 - - + -
512B PRO 3.1 7.4 + - - +
513B LEU 3.6 4.3 - - - +
514B ALA 3.3 0.2 - - - -
515B PHE* 1.3 76.2 - - - +
517B LEU* 1.3 61.3 + - - +
519B SER* 3.2 18.9 + - - -
524B GLN* 3.7 32.7 - - - +
525B VAL* 3.4 15.5 + - - +
528B GLY* 3.9 6.5 - - - -
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Residues in contact with LEU 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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517A LEU 5.2 3.1 - - - +
518A THR* 5.1 0.7 - - - +
550A ILE* 3.4 19.1 - - + +
554A ASN* 2.9 17.4 + - - +
513B LEU* 2.9 34.6 + - + +
514B ALA 4.3 2.0 - - - +
516B ALA* 1.3 74.3 - - - +
518B THR* 1.3 58.6 + - - +
519B SER 3.4 0.2 - - - -
525B VAL* 4.0 12.7 - - + +
528B GLY 4.5 3.8 - - - +
529B LEU* 3.6 45.3 - - + +
532B LEU* 3.6 26.5 - - + -
546B LEU* 4.8 2.2 - - + -
550B ILE* 3.9 28.9 - - + -
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Residues in contact with THR 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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517A LEU 5.1 0.4 - - - +
554A ASN* 3.4 9.1 - - - +
558A GLN* 2.8 30.8 + - - -
514B ALA 2.7 22.6 + - - +
515B PHE* 3.4 2.4 + - - -
517B LEU* 1.3 75.9 - - - +
519B SER* 1.3 58.1 + - - +
550B ILE* 3.4 30.7 - - + +
553B ASN* 3.6 11.7 - - + +
554B ASN* 3.2 26.2 - - - +
557B ARG* 2.9 30.8 + - - -
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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