Contacts of the strand formed by residues 45 - 50 (chain F) in PDB entry 1SMK
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 45 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44F GLY* 1.3 82.1 - - - -
46F LYS* 1.3 62.8 + - - +
47F VAL* 4.8 0.9 - - + -
69F LEU* 2.8 28.1 + - + +
70F VAL* 3.5 6.5 - - - +
71F SER* 2.8 28.3 + - - -
72F VAL 3.5 2.3 + - - +
114F ASP* 3.3 20.9 - - + +
283F LEU* 4.0 28.9 - - + -
286F LEU* 3.4 32.1 - - + -
287F ARG* 3.4 43.5 - - + -
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Residues in contact with LYS 46 (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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44F GLY 5.4 0.7 - - - +
45F PHE* 1.3 76.5 - - - +
47F VAL* 1.3 60.9 + - - +
71F SER* 3.9 5.2 - - - +
72F VAL* 3.3 38.3 - - + +
112F GLY* 3.0 26.5 + - - +
113F MET* 3.4 16.0 - - + -
114F ASP* 2.5 45.1 + - - +
115F LEU 3.1 8.7 + - - +
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Residues in contact with VAL 47 (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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45F PHE 4.7 1.8 - - - +
46F LYS* 1.3 77.5 - - - +
48F ALA* 1.3 67.5 - - - +
49F ILE* 4.3 1.3 - - + -
64F MET* 4.2 12.3 - - + -
70F VAL* 4.1 23.8 - - + -
72F VAL 2.9 10.3 + - - +
73F LEU* 3.2 16.8 - - + +
74F HIS 2.8 25.1 + - - -
113F MET* 3.7 3.5 - - - +
115F LEU* 3.2 30.5 - - + +
117F ILE* 3.8 31.2 - - + -
283F LEU* 4.3 9.2 - - + -
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Residues in contact with ALA 48 (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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47F VAL* 1.3 74.7 - - - +
49F ILE* 1.3 60.1 + - - +
50F LEU* 3.9 6.1 - - + -
74F HIS* 3.5 8.5 - - + -
76F TYR* 6.3 0.2 - - + -
109F ALA* 3.8 11.0 - - + +
110F LEU* 4.2 16.8 - - + -
113F MET* 3.6 28.1 - - + -
115F LEU 3.0 7.8 + - - +
116F ILE* 3.3 7.4 - - + +
117F ILE 2.9 25.5 + - - +
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Residues in contact with ILE 49 (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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47F VAL* 4.3 4.9 - - + -
48F ALA* 1.3 74.4 - - - +
50F LEU* 1.3 63.1 + - - +
52F ALA* 3.8 26.5 - - + +
57F GLY 4.6 4.5 - - - +
60F LEU* 4.3 7.2 - - + -
61F ALA* 3.4 36.6 - - + +
64F MET* 3.9 14.8 - - + -
73F LEU* 3.9 16.2 - - + -
74F HIS 2.8 11.9 + - - +
75F LEU* 3.9 7.0 - - + -
76F TYR* 3.0 26.9 + - - +
117F ILE* 3.3 22.0 - - + +
119F PRO* 4.2 14.8 - - + -
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Residues in contact with LEU 50 (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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48F ALA* 4.5 7.4 - - + -
49F ILE* 1.3 74.3 - - - +
51F GLY* 1.3 57.3 + - - +
76F TYR* 3.6 29.6 - - + -
106F LEU* 4.2 4.3 - - + -
109F ALA* 5.3 1.1 - - + -
110F LEU* 3.9 26.0 - - + -
116F ILE* 3.9 25.8 - - + -
117F ILE 2.9 11.8 + - - +
118F VAL* 4.0 12.3 - - + -
119F PRO* 3.1 22.1 - - - +
120F ALA* 3.1 12.1 + - - -
144F LEU* 3.6 42.4 - - + +
148F ILE* 4.6 6.3 - - + -
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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