Contacts of the strand formed by residues 97 - 102 (chain Y) in PDB entry 2OTT
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 LYS 97 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23Y THR* 4.8 10.5 - - + +
24Y VAL 5.9 0.7 - - - +
34Y ALA* 3.5 32.8 - - + +
35Y LEU 3.5 7.6 - - - +
37Y ASP* 4.9 0.3 - - - +
64Y VAL* 3.6 6.2 - - - +
65Y LEU* 2.9 42.3 + - + -
66Y ASP* 3.4 18.8 + - - +
72Y SER* 3.6 20.3 + - - +
73Y ARG 3.8 17.1 + - - +
95Y CYS* 4.0 9.6 - - - +
96Y LYS* 1.3 78.2 - - - +
98Y VAL* 1.3 64.8 + - - +
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Residues in contact with VAL 98 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23Y THR* 3.1 5.0 - - - -
24Y VAL* 2.9 36.5 + - + +
35Y LEU* 4.1 14.1 + - + +
37Y ASP* 4.2 22.9 - - + +
47Y TRP* 3.5 41.5 - - + -
62Y TYR* 4.2 14.1 - - + -
63Y ARG 3.3 15.7 - - - +
64Y VAL* 4.8 1.8 - - + +
65Y LEU* 3.9 4.9 - - - -
97Y LYS* 1.3 82.3 - - - +
99Y PHE* 1.3 70.6 + - - +
100Y VAL* 4.0 2.9 - - + -
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Residues in contact with PHE 99 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14Y VAL 5.2 0.9 - - - -
15Y GLY 5.4 2.0 - - - -
16Y GLY* 4.9 7.2 - - - -
21Y GLU* 4.1 20.0 - - - -
22Y GLY* 3.4 31.9 - - - -
23Y THR* 4.0 12.6 - - + -
62Y TYR* 3.1 7.6 - - - +
63Y ARG* 2.8 80.5 + - + +
65Y LEU* 3.8 13.6 - - + +
98Y VAL* 1.3 74.3 - - - +
100Y VAL* 1.3 67.4 + - - +
101Y THR* 3.6 26.9 - - + -
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Residues in contact with VAL 100 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13Y LEU* 4.1 8.1 - - + +
20Y CYS 4.1 0.7 - - - +
21Y GLU* 3.2 3.1 - - - -
22Y GLY 2.8 34.2 + - - +
24Y VAL* 3.6 27.4 - - + -
47Y TRP* 4.0 35.7 - - + +
50Y VAL* 5.2 2.7 - - + -
51Y CYS* 3.9 28.5 - - - -
59Y VAL* 4.5 3.1 - - + -
61Y SER 3.8 7.4 - - - +
62Y TYR* 4.2 6.5 - - + -
98Y VAL* 4.0 3.6 + - + -
99Y PHE* 1.3 76.8 - - - +
101Y THR* 1.3 66.2 + - - +
102Y CYS* 4.1 4.5 - - - -
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Residues in contact with THR 101 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20Y CYS 3.8 2.0 - - - -
21Y GLU* 3.7 25.2 + - - +
59Y VAL* 3.9 1.6 - - - -
60Y ASN* 3.0 38.8 + - - -
61Y SER* 3.1 28.5 + - - +
62Y TYR* 5.8 0.2 - - - -
63Y ARG* 5.1 4.7 - - - +
99Y PHE* 3.6 22.9 - - + +
100Y VAL* 1.3 79.2 - - - +
102Y CYS* 1.3 63.1 + - - +
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Residues in contact with CYS 102 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13Y LEU* 4.1 11.0 - - - -
20Y CYS* 2.8 27.8 + - - +
21Y GLU* 5.3 1.9 - - - +
51Y CYS* 2.1 53.6 - - + -
54Y GLN* 5.3 0.2 - - - -
56Y CYS* 3.7 22.2 - - + -
58Y SER 3.6 9.9 - - - +
59Y VAL* 4.0 0.4 - - - +
60Y ASN* 4.6 2.9 - - - +
100Y VAL* 4.1 7.4 - - - -
101Y THR* 1.3 78.3 + - - +
103Y GLN* 1.3 63.4 + - - +
104Y ASP 3.8 0.7 + - - -
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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