Contacts of the strand formed by residues 994 - 999 (chain B) in PDB entry 2O8C
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 TYR 994 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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527A CYS* 3.0 38.2 + - - -
528A LYS* 3.6 21.8 - - + +
530A GLU* 4.1 8.9 + - - -
993B GLU* 1.3 83.5 - - - +
995B GLU* 1.3 81.5 + - - +
996B LEU* 3.9 16.5 - - + +
1005B ARG* 3.2 10.4 - - - +
1006B TYR* 2.9 48.2 + - + +
1007B TRP* 4.6 4.0 - - - +
1008B THR* 4.7 21.1 - - + +
1012B GLU* 4.9 8.3 - - - -
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Residues in contact with GLU 995 (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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527A CYS* 3.8 15.4 - - - +
528A LYS* 5.9 0.6 - - - +
529A GLU 3.5 20.8 + - - +
530A GLU* 3.8 15.4 - - - +
533A LEU* 5.5 6.8 - - - +
544A ILE* 3.4 33.6 - - + +
549A VAL* 4.2 17.7 - - + +
994B TYR* 1.3 85.9 - - - +
996B LEU* 1.3 73.8 + - - +
1003B CYS* 4.3 12.6 - - - -
1004B LYS 4.0 6.5 - - - +
1005B ARG* 3.9 15.5 + - + +
1006B TYR 4.6 0.4 - - - +
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Residues in contact with LEU 996 (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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527A CYS* 4.3 14.1 - - + -
544A ILE* 3.4 29.7 - - - +
545A GLN* 4.5 6.3 + - - +
546A LYS* 3.8 39.5 - - + +
975B ASN* 5.1 5.4 - - - +
978B GLN* 3.5 16.4 - - - +
994B TYR* 3.9 20.4 - - + +
995B GLU* 1.3 83.3 - - - +
997B LYS* 1.3 69.1 + - + +
1004B LYS 3.7 5.9 + - - -
1005B ARG* 5.0 0.8 - - - +
1006B TYR* 3.6 32.7 - - + +
1012B GLU* 5.1 5.6 - - - +
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Residues in contact with LYS 997 (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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544A ILE* 4.9 7.4 - - - +
546A LYS* 4.8 5.4 - - - +
970B TRP* 3.7 29.4 - - + -
972B ILE* 6.2 1.8 - - - +
975B ASN* 4.4 24.4 - - - +
978B GLN* 4.2 10.0 + - - +
996B LEU* 1.3 86.3 - - + +
998B SER* 1.3 61.4 + - - +
1003B CYS* 4.9 0.2 - - - -
1004B LYS* 3.1 50.5 + - + +
6E G 4.1 35.4 - - - +
28F T 6.0 2.6 - - - -
29F T 5.2 2.0 - - - +
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Residues in contact with SER 998 (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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541A THR* 5.7 0.9 + - - -
542A VAL 5.3 0.7 + - - -
543A ASP* 3.7 17.7 + - - +
544A ILE* 3.6 39.6 + - - +
997B LYS* 1.3 77.9 - - - +
999B THR* 1.3 63.9 + - - +
1002B GLY 3.6 9.9 - - - -
1003B CYS* 4.4 13.0 - - - -
1004B LYS* 4.8 2.7 - - - -
29F T 5.3 2.1 - - - +
30F C 5.3 0.2 + - - -
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Residues in contact with THR 999 (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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980B GLU* 4.5 14.4 - - - +
983B GLU* 5.2 2.8 - - - +
998B SER* 1.3 78.0 - - - +
1000B LYS* 1.3 71.4 + - - +
1001B LYS 3.0 10.3 + - - +
1002B GLY* 3.0 32.3 + - - +
1004B LYS* 4.5 5.7 - - - +
29F T 3.5 33.5 + - - +
30F C 3.6 17.8 + - - -
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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