Contacts of the strand formed by residues 107 - 113 (chain B) in PDB entry 1F5J
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 SER 107 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B ALA 3.4 3.0 + - - -
106B THR* 1.3 86.8 - - - +
108B LEU* 1.3 62.1 + - - +
109B GLY* 3.2 21.9 + - - -
119B ASP* 3.7 14.3 + - - +
120B ILE 3.6 6.4 + - - -
121B TYR* 3.6 19.7 - - - -
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Residues in contact with LEU 108 (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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106B THR* 4.3 13.9 - - + +
107B SER* 1.3 77.0 - - - +
109B GLY* 1.3 56.9 + - - +
120B ILE* 2.7 17.6 + - + +
121B TYR* 4.2 2.5 - - - -
122B ARG* 3.9 31.9 - - + +
165B ARG* 3.3 36.5 + - + +
167B LEU* 4.0 24.2 - - + -
1002B SO4 3.9 4.3 + - - -
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Residues in contact with GLY 109 (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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107B SER* 3.2 12.1 + - - -
108B LEU* 1.3 82.2 - - - +
110B GLN* 1.3 60.3 + - - -
119B ASP* 3.4 4.1 - - - -
120B ILE* 2.9 26.7 + - - +
165B ARG* 4.0 5.8 - - - -
1002B SO4 3.3 21.1 - - - -
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Residues in contact with GLN 110 (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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109B GLY* 1.3 74.1 - - - -
111B VAL* 1.3 68.5 + - - +
117B THR* 3.2 28.2 - - + +
118B TYR 3.2 16.2 - - - +
119B ASP* 3.0 28.5 + - - +
145B THR* 3.7 12.1 - - - +
165B ARG* 3.8 3.6 + - - -
1001B SO4 4.8 1.0 + - - -
1002B SO4 2.8 19.5 + - - +
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Residues in contact with VAL 111 (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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110B GLN* 1.3 73.2 - - - +
112B THR* 1.3 62.7 + - - +
113B ILE* 3.8 28.2 + - + -
116B GLY 3.6 0.7 - - - +
117B THR* 3.4 4.9 - - - +
118B TYR* 2.8 48.3 + - + +
120B ILE* 4.0 17.7 - - + -
158B HIS* 5.4 1.3 - - - +
161B ALA* 4.4 4.0 - - + -
165B ARG* 3.1 41.1 - - - +
1001B SO4 3.8 16.6 - - - +
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Residues in contact with THR 112 (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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111B VAL* 1.3 73.9 - - - +
113B ILE* 1.3 68.6 + - - +
115B GLY* 4.5 9.9 - - - +
116B GLY 3.1 19.3 - - - +
117B THR* 4.3 10.5 + - - +
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Residues in contact with ILE 113 (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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111B VAL* 3.8 24.1 + - + -
112B THR* 1.3 79.9 - - - +
114B ASP* 1.3 92.6 + - - +
115B GLY 3.2 1.6 - - - -
116B GLY 2.8 20.6 + - - +
118B TYR* 3.3 10.9 - - + -
157B ASP* 3.8 48.0 - - + +
158B HIS* 3.6 41.3 - - + +
161B ALA* 4.3 5.2 - - + -
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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