Contacts of the strand formed by residues 105 - 109 (chain F) in PDB entry 1M54
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 LEU 105 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92F ILE* 2.8 62.3 + - + +
95F ILE* 5.4 0.9 - - + -
96F GLY* 4.1 14.1 - - - -
101F LEU* 3.5 31.9 - - + -
103F CYS 3.6 2.4 + - - +
104F GLU* 1.3 77.4 - - - +
106F LEU* 1.3 63.8 + - - +
354F VAL* 5.1 11.7 - - + -
357F ALA* 4.6 9.4 - - + -
358F VAL* 5.4 2.9 - - + -
370F CYS* 3.1 34.5 - - + +
372F VAL* 4.5 14.4 - - + -
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Residues in contact with LEU 106 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76E ILE* 3.3 34.5 - - + -
89F MET* 3.2 39.9 - - + +
90F VAL 3.8 5.2 - - - +
91F ARG* 4.0 9.2 - - + -
104F GLU* 3.1 42.5 - - + +
105F LEU* 1.3 78.0 - - - +
107F ALA* 1.3 63.3 + - - +
244F CYS* 5.3 2.7 - - - -
369F ARG* 4.4 10.3 - - + -
370F CYS 3.0 9.6 + - - +
371F VAL* 3.9 15.9 - - + -
372F VAL* 3.0 23.2 + - - +
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Residues in contact with ALA 107 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89F MET* 3.4 6.2 - - - -
90F VAL 2.9 36.5 + - - +
92F ILE* 3.9 18.4 - - + -
106F LEU* 1.3 80.1 - - - +
108F LYS* 1.3 64.3 + - - +
109F CYS* 3.3 8.7 - - - -
344F LEU* 5.2 0.2 - - + -
372F VAL* 3.3 15.5 - - + +
374F LEU* 3.6 22.0 - - + -
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Residues in contact with LYS 108 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87F THR* 3.0 39.5 + - - +
88F PRO 3.8 3.6 - - - +
89F MET* 3.6 21.5 - - + +
107F ALA* 1.3 67.9 - - - +
109F CYS* 1.3 60.4 + - - +
110F GLU* 3.2 20.2 + - - +
121F ARG* 3.4 1.1 - - - +
236F THR* 4.8 1.6 - - + -
239F GLU* 2.7 48.3 + - - +
240F ILE* 3.6 22.4 - - + +
243F GLN* 3.5 17.2 + - - +
371F VAL* 4.3 5.3 - - + +
372F VAL 2.9 10.9 + - - +
373F ILE* 4.8 7.4 - - + -
374F LEU* 3.1 27.2 + - - +
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Residues in contact with CYS 109 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87F THR* 2.8 24.0 - - - +
88F PRO* 2.9 21.2 + - + +
90F VAL* 4.2 17.5 - - - -
107F ALA* 3.3 16.6 - - - -
108F LYS* 1.3 73.2 - - - +
110F GLU* 1.3 61.0 + - - +
111F PHE* 3.3 28.6 + - + +
112F PHE* 3.9 14.2 + - + -
344F LEU* 4.1 12.3 - - - -
374F LEU* 3.5 23.1 - - - -
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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