Contacts of the strand formed by residues 967 - 970 (chain B) in PDB entry 2OOQ
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 ALA 967 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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945B SER* 2.9 16.1 + - - -
951B VAL* 3.2 18.8 + - + -
965B ILE* 2.7 14.4 + - + +
966B ASN* 1.3 76.1 + - - +
968B ASN* 1.3 64.0 + - - +
980B ILE* 3.7 15.5 - - + -
981B ALA 3.3 7.0 - - - -
982B THR* 3.4 19.5 - - - +
996B MET* 3.8 16.6 - - - -
1145B ARG* 4.0 0.9 - - - +
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Residues in contact with ASN 968 (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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945B SER* 2.9 27.5 + - - -
946B TYR 3.1 19.1 + - - +
949B SER* 2.8 27.3 + - - +
951B VAL* 4.0 5.4 - - - -
967B ALA* 1.3 70.7 - - - +
969B TYR* 1.3 64.7 + - - +
970B ILE* 3.6 2.1 - - + +
980B ILE* 3.4 0.7 - - - -
981B ALA 2.9 31.5 + - - -
1144B GLN 3.4 19.5 + - - +
1145B ARG* 2.9 43.2 + - + +
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Residues in contact with TYR 969 (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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949B SER* 2.8 30.6 + - - +
950B ARG 3.6 16.6 - - - -
951B VAL* 3.7 20.3 - - + +
952B ARG 4.8 2.6 + - - -
968B ASN* 1.3 74.7 - - - +
970B ILE* 1.3 67.6 + - - +
977B ARG* 3.3 61.0 + - + +
979B TYR 3.4 4.7 - - - +
980B ILE* 3.7 17.9 - - + +
999B GLN* 5.1 0.3 + - - -
1000B GLU* 2.7 37.8 + - - -
1101B PRO* 4.3 6.7 - - + -
1144B GLN* 3.7 12.6 - - - +
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Residues in contact with ILE 970 (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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968B ASN 3.6 4.7 - - - +
969B TYR* 1.3 84.7 - - - +
971B ASP* 1.3 69.6 - - - +
977B ARG 4.1 2.0 - - - -
978B HIS 3.1 5.2 + - - -
979B TYR* 2.8 43.4 + - + +
981B ALA* 3.6 26.0 - - + +
1117B ILE* 4.1 15.0 - - + -
1141B LEU* 3.5 31.6 - - + -
1144B GLN* 3.3 25.6 - - + +
1145B ARG* 4.0 13.5 - - + -
1148B LEU* 3.7 20.2 - - + -
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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