Contacts of the strand formed by residues 40 - 45 (chain B) in PDB entry 5J12
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 PHE 40 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B HIS 3.5 14.8 - - - +
39B SER* 1.3 76.2 - - - +
41B TRP* 1.3 63.0 + - - +
42B CYS* 3.9 14.4 - - - -
58B ALA 3.2 16.2 - - - +
59B PHE* 4.0 2.0 - - + -
60B ASN* 3.7 11.8 + - - +
71B PHE* 3.2 32.3 - + + -
107B ILE* 3.5 40.2 - - + -
109B VAL* 3.6 20.9 - - + -
117B THR* 3.9 20.4 - - + -
119B LYS* 4.1 15.7 - - + -
121B MET* 4.5 8.3 - - + +
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Residues in contact with TRP 41 (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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40B PHE* 1.3 74.8 - - - +
42B CYS* 1.3 75.0 + - - +
43B HIS* 3.3 35.4 - + - -
56B THR* 3.6 28.9 - - + -
57B CYS* 3.1 6.6 - - - +
58B ALA* 2.9 67.6 + - + +
59B PHE 4.1 6.5 + - - -
60B ASN* 3.4 25.1 - - - +
91B ILE* 5.3 4.7 - - + -
121B MET* 6.2 0.9 - - - -
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Residues in contact with CYS 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B PHE* 3.9 16.6 - - - -
41B TRP* 1.3 79.4 - - - +
43B HIS* 1.3 63.9 + - - +
55B LEU* 4.1 3.6 - - + -
56B THR 3.1 5.6 - - - -
57B CYS* 2.0 47.6 - - - -
107B ILE* 3.8 15.9 - - - -
121B MET* 4.1 13.0 - - - +
126B ILE* 3.9 23.7 - - + +
217B PHE* 3.8 15.2 - - - -
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Residues in contact with HIS 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B TRP* 3.3 33.4 - + + -
42B CYS* 1.3 75.3 - - - +
44B SER* 1.3 59.4 + - - +
45B GLN* 4.0 24.2 + - + -
54B LEU 3.9 0.5 - - - +
55B LEU* 3.6 5.4 - - - +
56B THR* 2.8 48.0 + - + +
126B ILE* 3.3 14.8 - - - +
128B LYS* 4.1 18.3 - - + +
217B PHE* 3.9 15.7 - - + +
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Residues in contact with SER 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B HIS* 1.3 73.4 - - - +
45B GLN* 1.3 65.9 + - - +
46B LEU* 5.1 2.5 - - - -
53B HIS* 6.1 0.4 - - - -
54B LEU 3.1 9.9 - - - -
55B LEU* 4.4 5.2 - - - +
99B PHE* 5.8 0.4 - - - -
123B ILE* 2.9 45.7 + - - +
126B ILE* 2.8 20.0 + - - +
127B VAL* 3.4 11.9 - - - +
128B LYS 2.8 27.4 + - - -
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Residues in contact with GLN 45 (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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43B HIS* 4.0 21.7 + - + -
44B SER* 1.3 80.5 - - - +
46B LEU* 1.3 65.2 + - - +
48B VAL* 3.6 16.4 - - + +
53B HIS* 3.4 3.5 - - - +
54B LEU* 2.8 56.8 + - + +
56B THR* 4.5 2.4 + - - -
127B VAL* 4.8 0.9 - - - -
128B LYS* 3.5 26.0 - - + +
129B ALA 4.7 3.1 - - - +
130B GLU* 3.9 23.8 - - + +
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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