Contacts of the strand formed by residues 41 - 45 (chain B) in PDB entry 1N54
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 THR 41 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39B SER* 3.0 7.4 + - - +
40B CYS* 1.3 79.9 - - - +
42B LEU* 1.3 60.3 + - - +
70B ILE* 6.1 0.2 - - - +
85B PHE* 4.3 12.7 - - + +
86B VAL 3.2 19.9 + - - -
87B GLU* 3.8 18.6 - - - +
115B TRP* 4.4 3.0 - - - -
116B ASP* 3.1 42.1 + - + +
118B GLY* 3.7 23.8 - - - -
119B PHE* 4.4 7.2 - - - +
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Residues in contact with LEU 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B THR* 1.3 75.4 - - - +
43B TYR* 1.3 63.7 + - - +
44B VAL* 3.5 6.8 + - + +
60B PHE* 4.8 7.6 - - + -
85B PHE* 3.5 3.3 - - - -
86B VAL* 2.9 34.1 + - + +
88B TYR* 4.0 19.7 - - + -
94B ALA* 3.6 22.9 - - + +
97B ALA* 4.2 10.8 - - + -
98B MET* 3.2 38.6 - - + +
113B THR* 4.8 7.6 - - - +
114B ASP 3.4 10.8 - - - +
115B TRP* 3.7 29.6 - - + -
116B ASP* 4.5 1.6 - - - -
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Residues in contact with TYR 43 (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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42B LEU* 1.3 69.1 - - - +
44B VAL* 1.3 63.6 + - - +
45B GLY* 3.8 8.9 + - - -
83B PHE* 3.7 44.8 - + + +
84B CYS 3.8 5.4 - - - -
85B PHE* 3.7 28.0 - + + -
112B ARG* 4.1 14.0 + - - +
113B THR* 3.5 2.0 - - - -
114B ASP* 2.6 47.2 + - + +
115B TRP 5.1 0.7 - - - +
116B ASP* 3.6 27.3 - - + +
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Residues in contact with VAL 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B LEU* 3.9 6.5 - - + +
43B TYR* 1.3 77.8 - - - +
45B GLY* 1.3 60.7 + - - +
47B LEU* 3.6 23.3 - - + -
56B ILE* 5.9 0.4 - - + -
60B PHE* 3.8 23.3 - - + -
83B PHE* 3.2 4.6 - - - +
84B CYS* 2.8 45.1 + - - +
86B VAL* 3.6 31.2 - - + -
111B ILE* 4.2 8.7 - - + -
112B ARG 4.1 2.7 - - - +
113B THR* 4.0 20.0 - - + +
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Residues in contact with GLY 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 TYR* 3.8 13.9 + - - -
44B VAL* 1.3 74.8 - - - +
46B ASN* 1.3 71.6 + - - +
47B LEU* 3.6 2.2 - - - -
83B PHE* 3.9 9.4 - - - -
111B ILE* 4.1 4.3 - - - +
112B ARG* 3.1 38.4 + - - +
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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