Contacts of the strand formed by residues 20 - 24 (chain Y) in PDB entry 5JBT
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 ARG 20 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18Y MET 3.5 4.4 + - - +
19Y PRO* 1.4 74.6 - - - +
21Y TRP* 1.3 59.1 + - - +
32Y ARG* 3.4 5.6 - - - +
33Y PHE* 2.7 53.9 + - + +
45Y PHE* 3.4 50.2 - - + +
48Y GLU* 2.8 42.7 + - - +
52Y MET* 3.7 5.6 - - - -
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Residues in contact with TRP 21 (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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5X CYS* 3.9 17.3 - - + -
6X SER 3.3 30.3 - - - -
7X GLN* 4.2 3.6 - - - -
19Y PRO* 4.5 10.8 - - - +
20Y ARG* 1.3 81.0 - - - +
22Y TYR* 1.4 65.1 + - - +
30Y CYS* 3.7 11.9 - - + -
31Y VAL 3.1 26.7 - - - -
32Y ARG* 3.4 42.4 - - + +
48Y GLU* 3.3 28.4 - - - +
51Y CYS* 3.9 21.5 - - + +
52Y MET* 3.4 23.2 - - + +
55Y CYS* 3.4 43.0 + - + -
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Residues in contact with TYR 22 (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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10X MET* 3.0 28.1 - - + +
11X THR 4.7 0.2 + - - -
12X GLY 4.2 4.2 + - - -
21Y TRP* 1.4 77.3 - - - +
23Y PHE* 1.3 74.8 + - - +
24Y ASP* 4.5 5.8 + - + -
30Y CYS* 3.3 0.2 - - - -
31Y VAL* 2.8 60.6 + - + +
33Y PHE* 4.0 23.1 - + + -
43Y ASN* 3.2 35.2 + - - -
44Y ASN 3.6 15.9 - - - -
45Y PHE* 3.8 29.4 - + + -
46Y GLU 3.6 11.2 - - - +
48Y GLU* 4.5 2.5 - - - +
51Y CYS* 3.6 11.0 - - - -
101Y SO4 3.9 8.4 + - - -
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Residues in contact with PHE 23 (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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4X VAL* 4.7 8.5 - - + -
22Y TYR* 1.3 85.1 - - - +
24Y ASP* 1.3 66.5 + - - +
25Y LEU* 3.8 21.9 + - + +
28Y GLY* 3.3 44.2 - - - -
29Y LYS* 3.6 14.1 - - - -
30Y CYS* 4.0 3.8 - - - -
44Y ASN 4.7 1.0 - - - +
46Y GLU* 2.8 34.6 + - + +
47Y SER* 4.0 14.6 - - - +
50Y TYR* 5.5 4.9 - + - -
51Y CYS* 3.6 14.9 - - - -
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Residues in contact with ASP 24 (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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10X MET* 4.1 3.1 - - - -
11X THR* 2.6 39.6 + - - -
12X GLY 4.7 0.9 + - - -
22Y TYR* 3.7 7.1 + - + -
23Y PHE* 1.3 72.9 - - - +
25Y LEU* 1.3 59.1 + - - +
26Y SER* 2.8 25.8 + - - -
27Y LYS* 3.1 17.6 + - + +
28Y GLY* 2.8 30.8 + - - -
29Y LYS 2.9 15.9 + - - +
31Y VAL* 3.9 19.0 - - + +
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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