Contacts of the helix formed by residues 136 - 144 (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 CYS 136 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110C ASP* 5.1 2.9 - - - -
134C GLY 3.4 1.6 - - - -
135C VAL* 1.3 82.2 - - - +
137C LYS* 1.3 62.7 + - - +
138C ARG* 4.0 7.0 - - - -
139C TRP* 3.2 42.0 + - - -
140C TYR* 2.8 27.4 + - - +
141D ILE* 3.7 17.3 - - + -
142D LYS 3.5 20.2 - - - +
144D ASP* 3.6 11.4 - - + +
145D PHE* 3.4 14.4 - - - -
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Residues in contact with LYS 137 (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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108A SER* 3.0 37.1 + - - +
111A SER* 4.0 10.1 - - - +
101B PHE* 5.4 4.9 - - + -
102B GLU* 6.0 0.4 + - - -
136C CYS* 1.3 72.1 - - - +
138C ARG* 1.3 62.5 + - - +
140C TYR* 3.1 8.1 + - - +
141C ARG* 3.0 41.6 + - - +
144D ASP* 3.0 36.0 + - + +
145D PHE* 3.7 27.7 - - + +
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Residues in contact with ARG 138 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A ASP 4.6 1.1 - - - +
111A SER* 4.0 7.0 - - - +
114A ASP* 3.2 9.5 + - - -
138A ARG* 2.4 81.1 - - - +
110C ASP* 2.7 34.8 + - - +
111C SER* 3.1 12.3 + - - +
112C LEU 2.8 26.9 + - - -
113C PRO* 3.7 6.7 - - - +
114C ASP* 3.0 13.3 + - - +
117C LEU* 4.2 12.7 - - + +
136C CYS* 3.4 9.3 - - - -
137C LYS* 1.3 75.9 - - - +
139C TRP* 1.3 65.8 + - + +
141C ARG* 3.5 13.5 + - - +
142C LEU* 3.2 29.5 + - + +
144D ASP* 3.6 4.9 + - - +
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Residues in contact with TRP 139 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109C TRP* 5.5 4.2 + + + -
110C ASP* 6.1 0.8 - - - +
117C LEU* 3.8 34.8 - - + +
120C ILE* 6.4 0.9 - - + -
121C PHE* 3.4 35.5 - + + -
132C VAL* 3.9 29.4 - - + +
133C SER* 4.6 1.1 - - - -
135C VAL* 3.9 13.2 - - + -
136C CYS* 3.2 27.7 + - - +
138C ARG* 1.3 80.5 - - + +
140C TYR* 1.3 60.6 + - - +
142C LEU* 3.7 0.8 - - - -
143C ALA* 2.8 35.1 + - - +
123D VAL* 6.2 1.1 - - + -
127D ILE* 4.0 23.3 - - + -
135D ILE* 3.9 28.0 - - + -
139D PHE* 5.1 9.4 - + + -
141D ILE* 4.4 25.9 - - + +
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Residues in contact with TYR 140 (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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49B ASN* 5.6 5.8 - - - -
133C SER* 3.1 38.6 + - - +
134C GLY* 5.2 0.7 - - - -
136C CYS 2.8 17.9 + - - +
137C LYS* 3.4 10.1 - - + +
139C TRP* 1.3 75.1 - - - +
141C ARG* 1.3 72.4 + - + +
143C ALA* 3.6 2.6 + - - +
144C SER* 3.0 31.8 + - - -
208C SER* 3.6 12.8 + - - -
209C THR* 3.2 48.3 - - + +
212C GLY* 5.9 1.0 - - - -
145D PHE* 4.2 16.8 - + + -
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Residues in contact with ARG 141 (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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111A SER* 2.6 52.8 + - - -
113A PRO* 4.0 19.4 - - + +
101B PHE* 3.5 21.4 - - - -
105B LEU* 3.8 27.3 - - - +
137C LYS* 3.0 30.9 + - - +
138C ARG* 3.9 8.1 - - - +
140C TYR* 1.3 83.7 - - + +
142C LEU* 1.3 61.1 + - + +
144C SER* 2.9 29.6 + - - -
145C ASP* 3.5 3.6 + - - -
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Residues in contact with LEU 142 (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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113A PRO* 6.6 0.4 - - + -
114C ASP* 3.7 34.3 - - + +
117C LEU* 3.4 46.0 - - + -
118C LEU* 3.8 25.3 - - + +
121C PHE* 3.9 13.0 - - + -
138C ARG* 3.2 19.1 + - + +
139C TRP 3.9 2.2 - - - +
141C ARG* 1.3 81.3 - - + +
143C ALA* 1.3 57.8 + - - +
145C ASP* 2.8 32.7 + - - +
148C LEU* 3.8 1.7 - - - +
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Residues in contact with ALA 143 (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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121C PHE* 3.9 16.5 - - + -
129C LEU* 4.0 18.2 - - + +
132C VAL* 4.3 4.0 - - + -
133C SER* 3.8 28.7 - - - -
139C TRP 2.8 22.4 + - - +
140C TYR 3.9 0.9 - - - +
142C LEU* 1.3 72.9 - - - +
144C SER* 1.3 56.5 + - - +
145C ASP 3.1 2.0 + - - -
148C LEU* 3.7 9.4 - - - +
149C TRP* 3.1 22.7 + - - -
213C ILE* 5.1 4.1 - - + +
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Residues in contact with SER 144 (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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133C SER* 5.7 1.4 - - - -
140C TYR* 3.0 26.4 + - - -
141C ARG* 2.9 12.3 + - - -
143C ALA* 1.3 75.4 - - - +
145C ASP* 1.3 67.2 + - - +
146C GLU 3.4 1.4 + - - -
149C TRP* 4.4 5.6 - - - +
209C THR 5.6 0.3 + - - -
212C GLY* 4.5 16.3 - - - -
213C ILE* 4.5 15.2 - - - +
216C GLN* 3.7 20.8 + - - +
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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