Contacts of the strand formed by residues 20 - 24 (chain B) in PDB entry 5JTM
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 ASP 20 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A PHE* 3.2 10.1 - - - -
24A GLU* 3.5 25.3 - - - +
18B THR* 3.5 3.7 - - - +
19B LYS* 1.3 82.3 - - - +
21B ILE* 1.3 91.4 + - - +
22B SER* 5.0 1.2 - - - -
77B GLU* 4.3 10.3 - - - +
78B VAL* 4.7 0.4 - - - -
79B GLN* 2.9 59.6 + - - +
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Residues in contact with ILE 21 (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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21A ILE* 3.9 27.8 - - + -
22A SER* 3.3 23.1 + - - -
23A PHE* 2.8 27.9 + - + +
117A MET* 4.0 8.5 - - + -
120A ARG* 6.2 0.2 - - - -
18B THR* 3.5 18.6 - - + -
20B ASP* 1.3 90.6 + - - +
22B SER* 1.3 71.4 + - - +
77B GLU 3.4 5.2 - - - +
78B VAL* 3.6 19.1 - - + -
113B CYS* 3.3 32.3 - - - -
117B MET* 4.4 13.7 - - + -
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Residues in contact with SER 22 (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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21A ILE 3.3 8.3 + - - -
22A SER* 4.5 2.7 - - - +
20B ASP* 5.0 1.3 - - - -
21B ILE* 1.3 79.5 - - - +
23B PHE* 1.3 63.1 + - - +
24B GLU* 4.3 17.8 + - - +
75B LEU* 6.2 0.2 - - - +
76B CYS* 3.3 4.6 - - - -
77B GLU* 2.7 61.3 + - - +
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Residues in contact with PHE 23 (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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18A THR* 3.2 35.0 - - - -
19A LYS 4.4 3.6 - - - -
20A ASP* 3.1 11.4 - - - +
21A ILE* 2.8 49.1 + - + -
22B SER* 1.3 75.4 + - - +
24B GLU* 1.3 61.8 + - - +
25B ALA* 3.8 15.5 - - + -
74B PHE* 3.6 34.5 - + + -
75B LEU 3.1 23.8 - - - -
76B CYS* 3.8 7.6 - - + -
117B MET* 3.3 44.0 - - + -
118B VAL* 4.0 2.9 - - - -
121B GLY* 3.9 11.4 - - - -
123B PHE* 4.3 3.4 - + - -
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Residues in contact with GLU 24 (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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19A LYS 3.7 5.2 - - - -
20A ASP* 4.0 17.2 - - - +
22B SER* 4.3 14.5 + - - +
23B PHE* 1.3 78.5 - - - +
25B ALA* 1.3 56.5 + - - +
26B PRO* 3.2 11.2 - - + +
75B LEU* 2.7 64.7 + - + +
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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