Contacts of the strand formed by residues 6194 - 6196 (chain B) in PDB entry 1Y1S
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 ASN6194 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6095B THR* 2.7 30.4 + - - +
6096B GLY 3.3 13.0 - - - +
6097B ALA* 4.0 0.2 - - - -
6098B ILE* 4.3 5.1 - - - +
6108B LEU* 3.2 27.7 - - + +
6110B THR* 4.8 2.0 + - - -
6156B THR* 2.7 37.5 + - - +
6157B ALA* 2.9 30.0 + - - +
6192B VAL* 3.7 4.2 - - - +
6193B MET* 1.3 89.6 - - - +
6195B TYR* 1.3 65.0 + - - +
6196B GLU* 4.6 3.2 - - - +
6215B MET* 5.5 1.0 - - - +
6217B ALA* 4.9 4.0 - - - +
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Residues in contact with TYR6195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6095B THR* 2.5 25.6 + - - -
6096B GLY* 2.8 19.4 + - - +
6098B ILE* 3.5 24.0 - - + -
6116B LEU* 4.9 2.9 - - + -
6157B ALA* 3.3 31.2 - - + -
6159B SER* 5.0 2.0 - - - -
6165B GLY 4.1 7.7 + - - -
6166B GLN* 3.3 55.3 - - + +
6183B SER* 4.4 2.6 + - - -
6184B MET* 3.0 40.4 + - + +
6187B TRP* 3.5 23.6 + + - -
6194B ASN* 1.3 73.7 - - - +
6196B GLU* 1.3 61.3 + - - +
6223B ARG* 3.7 16.8 - - + -
8006B URA 3.8 4.8 - - - +
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Residues in contact with GLU6196 (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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6091B ARG* 3.1 28.8 + - - +
6094B THR 4.3 8.1 - - - +
6095B THR* 4.3 4.9 - - - +
6156B THR* 3.4 24.2 - - + -
6157B ALA 3.2 2.8 + - - +
6158B SER* 2.7 22.0 + - - -
6159B SER* 2.9 24.8 + - - -
6166B GLN* 4.3 0.3 + - - -
6194B ASN* 4.6 0.7 - - - +
6195B TYR* 1.3 75.3 - - - +
6197B MET* 1.3 64.3 + - - +
6198B GLU 2.8 14.5 + - - -
6199B SER* 2.5 42.4 + - - +
6215B MET* 4.3 8.1 - - + -
8006B URA 3.3 10.3 - - - -
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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
------------------------------------------------------------
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