Contacts of the helix formed by residues 494 - 501 (chain B) in PDB entry 1YUC
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 494 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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492B GLN 3.2 1.2 - - - -
493B THR* 1.3 90.6 + - - +
495B LYS* 1.3 66.5 + - - +
496B PHE* 3.2 3.1 - - - -
497B GLY* 3.1 7.0 + - - +
498B GLN* 2.9 43.1 + - + +
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Residues in contact with LYS 495 (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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441B LEU* 3.0 23.0 + - + +
442B GLN 3.0 22.8 + - - -
447B GLU* 2.7 36.6 + - - +
485B THR* 4.3 11.4 - - + -
489B TYR* 3.2 42.0 - - + -
492B GLN* 3.1 28.5 + - + +
493B THR 3.5 0.8 + - - -
494B GLU* 1.3 76.7 - - - +
496B PHE* 1.3 64.0 + - - +
498B GLN* 3.1 12.4 + - - +
499B LEU* 2.8 39.7 + - + +
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Residues in contact with PHE 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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478B ASN* 3.5 35.4 - - + -
481B LEU* 4.0 19.1 - - + -
482B LEU* 3.6 44.4 - - + -
485B THR* 3.6 21.1 + - - +
486B MET* 6.1 0.2 - - + -
494B GLU 3.1 1.5 + - - -
495B LYS* 1.3 78.9 - - - +
497B GLY* 1.3 67.7 + - - +
499B LEU* 3.7 3.8 - - - +
500B LEU* 3.2 51.8 + - + +
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Residues in contact with GLY 497 (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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494B GLU* 3.1 7.6 + - - +
496B PHE* 1.3 88.2 - - - +
498B GLN* 1.3 62.3 + - - +
500B LEU* 3.5 7.0 + - - +
501B LEU* 3.1 29.3 + - - +
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Residues in contact with GLN 498 (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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441B LEU* 3.5 33.7 - - + +
492B GLN* 4.8 6.4 - - - +
494B GLU* 2.9 36.9 + - + +
495B LYS* 3.5 20.0 + - - +
497B GLY* 1.3 73.2 - - - +
499B LEU* 1.3 66.7 - - - +
501B LEU* 3.4 10.6 + - + -
502B ARG* 2.8 33.1 + - - +
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Residues in contact with LEU 499 (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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438B LEU* 4.1 8.5 - - + -
441B LEU* 4.1 22.2 - - + -
443B PHE* 3.6 31.4 - - + -
447B GLU* 3.8 37.5 - - + +
451B LEU* 4.8 16.4 - - + +
481B LEU* 4.6 7.6 - - + -
485B THR* 4.0 10.1 - - + -
495B LYS* 2.8 32.9 + - + +
496B PHE* 3.7 4.9 - - - +
498B GLN* 1.3 77.2 - - - +
500B LEU* 1.3 59.3 + - + +
502B ARG* 2.8 30.5 + - - +
503B LEU 4.0 1.0 + - - -
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Residues in contact with LEU 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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451B LEU* 4.0 9.6 - - + -
454B LEU* 3.7 23.1 - - + -
478B ASN* 3.8 8.5 - - - +
481B LEU* 4.1 7.6 - - + -
496B PHE* 3.2 52.3 + - + +
497B GLY* 3.9 6.7 - - - +
499B LEU* 1.3 76.4 - - - +
501B LEU* 1.3 56.5 + - - +
502B ARG 3.0 0.2 - - - -
503B LEU* 2.9 52.8 + - + +
504B PRO* 3.4 3.6 - - - +
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Residues in contact with LEU 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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497B GLY 3.1 18.8 + - - +
498B GLN* 3.6 8.7 - - + +
499B LEU 3.1 0.6 - - - -
500B LEU* 1.3 76.4 - - - +
502B ARG* 1.3 84.9 + - - +
503B LEU 3.3 0.4 - - - -
504B PRO* 3.3 21.3 - - + +
505B GLU* 3.5 15.1 - - - +
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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