Contacts of the helix formed by residues 495 - 505 (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 GLY 495 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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442B THR* 4.0 6.4 - - - +
493B VAL 3.6 0.6 + - - -
494B PRO* 1.3 69.9 - - - +
496B MET* 1.3 63.0 + - - +
497B GLU* 3.2 7.6 + - - +
498B VAL* 3.5 17.9 + - - +
499B SER* 3.3 20.1 + - - -
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Residues in contact with MET 496 (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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440B LEU* 4.3 4.0 - - + +
441B THR 4.0 7.6 - - - +
442B THR* 3.3 49.1 + - + +
445B CYS* 4.3 14.4 - - - -
486B ILE* 3.6 31.4 - - + +
489B LEU* 3.7 37.5 - - + +
490B LYS* 4.4 6.1 - - - +
493B VAL* 3.5 27.6 - - + +
494B PRO 3.3 3.0 - - - -
495B GLY* 1.3 72.5 - - - +
497B GLU* 1.3 65.9 + - - +
499B SER* 3.9 0.4 - - - -
500B PHE* 3.0 23.4 + - - +
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Residues in contact with GLU 497 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490B LYS* 3.6 42.5 + - - +
491B PRO* 4.3 5.5 - - - +
493B VAL 4.3 3.0 + - - +
495B GLY* 4.2 5.4 - - - +
496B MET* 1.3 80.6 - - - +
498B VAL* 1.3 68.1 + - + +
500B PHE* 3.6 3.1 - - - +
501B TYR* 3.2 54.5 + - + -
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Residues in contact with VAL 498 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495B GLY* 3.5 17.0 + - - +
497B GLU* 1.3 81.8 - - + +
499B SER* 1.3 64.7 + - - +
501B TYR* 3.5 7.6 + - - +
502B LYS* 3.0 28.6 + - - +
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Residues in contact with SER 499 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442B THR* 3.5 24.6 - - - +
446B THR* 3.1 31.5 - - - +
495B GLY 3.3 6.6 + - - -
496B MET* 3.9 2.2 - - - -
497B GLU 3.4 0.2 - - - -
498B VAL* 1.3 79.2 - - - +
500B PHE* 1.3 59.7 + - - +
502B LYS* 3.3 8.7 + - - +
503B ILE* 3.0 33.2 + - - +
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Residues in contact with PHE 500 (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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483B LEU* 3.5 32.5 - - + -
486B ILE* 3.5 27.3 - - + +
487B ASN* 3.7 31.2 - - + -
490B LYS* 3.6 21.5 - - + -
496B MET 3.0 19.3 + - - +
497B GLU 3.6 4.0 - - - +
499B SER* 1.3 76.4 - - - +
501B TYR* 1.3 68.0 + + - +
503B ILE* 3.2 8.6 + - - +
504B LEU* 3.1 58.7 + - + +
531B ILE* 4.5 8.1 - - + -
534B GLU* 3.7 22.7 - - + -
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Residues in contact with TYR 501 (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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490B LYS* 3.2 23.2 + - - -
497B GLU* 3.2 45.1 + - + -
498B VAL* 3.5 9.0 + - - +
499B SER 3.4 0.2 - - - -
500B PHE* 1.3 85.8 - + - +
502B LYS* 1.3 63.1 + - - +
504B LEU* 3.9 6.7 - - + -
505B GLN* 3.0 27.6 + - - +
534B GLU* 3.3 32.7 + - + -
538B LEU* 3.3 36.8 - - + +
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Residues in contact with LYS 502 (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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498B VAL 3.0 17.5 + - - +
499B SER* 3.5 9.6 - - - +
500B PHE 3.2 0.2 - - - -
501B TYR* 1.3 76.1 - - - +
503B ILE* 1.3 67.9 + - + +
505B GLN* 3.3 29.4 + - + +
506B ASP* 3.6 15.2 + - - +
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Residues in contact with ILE 503 (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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446B THR* 4.0 26.2 - - + -
449B ILE* 4.4 27.6 - - + -
453B PHE* 5.4 3.4 - - + -
483B LEU* 3.8 25.8 - - + -
486B ILE* 4.3 22.7 - - + -
499B SER* 3.0 26.1 + - - +
500B PHE* 3.6 7.6 - - - +
502B LYS* 1.3 78.4 - - + +
504B LEU* 1.3 58.2 + - - +
506B ASP* 3.0 31.2 + - + +
509B LEU* 3.9 9.4 - - + +
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Residues in contact with LEU 504 (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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483B LEU* 3.6 26.2 - - + -
500B PHE* 3.1 47.5 + - + +
501B TYR* 3.9 15.7 - - + +
502B LYS 3.3 0.6 - - - -
503B ILE* 1.3 76.1 - - - +
505B GLN* 1.3 58.5 + - - +
506B ASP 3.6 2.6 + - - +
509B LEU* 3.7 21.7 - - + +
510B ILE* 5.8 1.0 - - - +
531B ILE* 4.3 9.0 - - + +
534B GLU* 3.8 14.6 - - + +
535B ALA* 3.7 39.6 - - + +
538B LEU* 4.2 5.6 - - + -
541B PHE* 4.1 19.7 - - - -
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Residues in contact with GLN 505 (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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501B TYR* 3.0 24.6 + - - +
502B LYS* 3.3 23.6 + - - +
503B ILE 3.2 0.8 - - - -
504B LEU* 1.3 74.8 - - - +
506B ASP* 1.3 64.5 + - - +
507B PRO* 3.3 9.7 - - - +
538B LEU* 3.7 23.1 - - + +
539B PRO* 3.8 31.1 - - - +
540B ASP* 4.9 16.1 - - + +
541B PHE* 5.4 6.5 - - + +
542B PRO* 5.0 6.8 - - - +
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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