Contacts of the helix formed by residues 108 - 112 (chain C) in PDB entry 1FS2
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 108 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137A LYS* 3.0 30.0 + - - +
142B LYS* 6.1 2.2 - - - +
144B ASP* 3.3 29.6 + - - -
106C GLY 3.2 7.4 + - - -
107C VAL* 1.3 72.7 - - - +
109C TRP* 1.3 63.1 + - - +
110C ASP* 3.2 4.7 - - - +
111C SER* 2.6 32.5 + - - -
101D PHE* 3.5 16.3 - - - -
140D ASN* 5.3 0.9 - - - +
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Residues in contact with TRP 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107C VAL* 2.9 37.5 + - + +
108C SER* 1.3 67.5 - - - +
110C ASP* 1.3 52.7 + - - +
111C SER 2.7 17.1 + - - -
112C LEU* 2.9 47.2 + - + +
117C LEU* 5.6 1.9 - - - +
120C ILE* 5.6 0.2 - - + -
139C TRP* 5.5 5.0 + + + -
97D GLN* 3.0 35.7 + - + +
100D LEU* 4.4 9.2 - - + -
101D PHE* 3.7 47.1 - + + -
104D ILE* 4.9 4.7 - - + -
123D VAL* 4.1 29.8 - - + -
126D MET* 6.0 0.2 - - - -
139D PHE* 3.2 56.8 + + + +
141D ILE* 3.6 12.7 - - + +
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Residues in contact with ASP 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A ASP 5.0 3.1 - - - +
138A ARG* 4.7 1.6 + - - -
142B LYS* 5.3 12.2 + - + +
144B ASP* 5.6 2.7 - - - +
108C SER* 3.2 3.0 - - - +
109C TRP* 1.3 75.3 - - - +
111C SER* 1.3 49.8 + - - +
136C CYS* 5.1 3.8 - - - -
138C ARG* 2.7 28.2 + - - +
139C TRP* 6.1 1.1 - - - +
140D ASN 2.9 10.6 + - - +
141D ILE* 2.7 44.6 - - - +
142D LYS* 2.8 27.1 + - - +
144D ASP* 5.4 2.4 - - - +
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Residues in contact with SER 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A LYS* 4.0 5.0 - - - +
138A ARG* 4.1 7.8 - - - +
141A ARG* 2.6 51.3 + - - -
144B ASP* 3.7 25.8 - - - -
108C SER* 2.6 26.6 + - - -
109C TRP 2.7 1.4 + - - -
110C ASP* 1.3 78.4 - - - +
112C LEU* 1.3 65.4 + - - +
113C PRO 3.2 0.2 - - - -
138C ARG* 3.1 12.2 + - - +
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Residues in contact with LEU 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108C SER 3.9 0.6 + - - -
109C TRP* 2.9 33.4 + - + +
110C ASP 3.6 0.6 - - - -
111C SER* 1.3 76.0 + - - +
113C PRO* 1.3 80.3 - - + +
114C ASP 3.5 0.3 + - - -
116C LEU* 3.7 25.6 - - + -
117C LEU* 3.7 23.6 - - + +
120C ILE* 3.5 33.2 - - + -
138C ARG* 2.8 21.3 + - - -
101D PHE* 3.6 28.3 - - + -
104D ILE* 4.1 11.0 - - + -
105D LEU* 4.6 2.5 - - + -
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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