Contacts of the helix formed by residues 189 - 195 (chain A) in PDB entry 1FS6
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 GLY 189 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144A ILE* 5.4 0.5 - - - +
147A ASN* 3.4 12.7 + - - -
155A SER 3.4 13.2 - - - -
156A ARG 3.4 15.4 - - - -
158A ARG* 3.6 3.4 - - - -
188A VAL* 1.3 76.8 - - - +
190A VAL* 1.3 65.8 + - - -
191A GLY 3.2 2.0 - - - -
192A THR* 2.9 13.0 + - - -
193A LEU* 3.1 20.6 + - - +
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Residues in contact with VAL 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A ILE* 4.9 11.4 - - + -
147A ASN* 3.8 24.5 - - + +
151A SER* 4.0 6.3 - - - -
152A SER 3.6 9.2 - - - +
153A LEU* 3.9 11.7 - - + -
155A SER* 3.0 18.0 + - - +
189A GLY* 1.3 70.3 - - - -
191A GLY* 1.3 61.0 + - - +
193A LEU* 3.2 7.2 + - + +
194A LEU* 2.8 50.1 + - + +
225A THR* 3.8 33.7 - - + -
228A CYS* 6.2 0.2 - - + -
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Residues in contact with GLY 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A LEU 3.4 17.4 + - - -
154A ALA* 3.9 5.4 - - - -
155A SER 2.8 13.7 + - - +
156A ARG* 3.4 15.3 - - - -
190A VAL* 1.3 79.8 - - - +
192A THR* 1.3 61.1 + - - +
194A LEU* 3.2 3.1 + - - +
195A ASP* 3.0 30.6 + - - +
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Residues in contact with THR 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A GLU* 2.7 30.6 + - - +
125A ILE* 3.8 27.4 - - + -
131A ILE* 4.9 4.8 - - + +
134A PHE* 4.3 11.4 - - + -
155A SER 3.6 2.6 + - - -
156A ARG* 3.5 12.3 + - - +
157A THR 3.8 0.5 + - - -
188A VAL* 3.9 19.5 - - + -
189A GLY* 2.9 26.5 + - - -
190A VAL 3.2 0.2 - - - -
191A GLY* 1.3 76.7 - - - +
193A LEU* 1.3 61.8 + - - +
195A ASP* 3.4 12.7 + - - +
196A ALA* 3.8 3.5 + - - -
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Residues in contact with LEU 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A MET* 5.7 5.4 - - - -
134A PHE* 3.6 42.1 - - + +
135A MET 5.9 0.7 - - - -
136A GLY* 6.2 0.4 - - - -
144A ILE* 3.7 41.3 - - + -
188A VAL* 5.2 2.9 - - + +
189A GLY 3.1 10.0 + - - +
190A VAL* 3.2 10.3 + - + +
192A THR* 1.3 79.7 - - - +
194A LEU* 1.3 61.6 + - + +
196A ALA* 3.1 28.1 + - - +
199A VAL* 3.5 28.7 - - + +
201A ILE* 5.2 5.8 - - + -
229A LEU* 4.4 12.1 - - + -
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Residues in contact with LEU 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A ILE* 6.2 0.2 - - + -
153A LEU* 3.5 36.8 - - + +
190A VAL* 2.8 33.9 + - + +
191A GLY* 3.9 4.5 - - - +
193A LEU* 1.3 72.9 - - + +
195A ASP* 1.3 63.3 + - - +
196A ALA 3.1 5.9 - - - +
228A CYS* 4.8 11.9 - - + +
229A LEU* 3.5 32.3 - - + -
232A HIS* 3.2 35.5 + - + -
233A PRO* 5.3 1.2 - - - +
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Residues in contact with ASP 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A LYS* 3.4 22.7 + - - +
131A ILE* 4.5 1.8 + - - +
156A ARG* 2.7 30.0 + - - -
191A GLY* 3.0 18.5 + - - +
192A THR* 3.7 7.6 - - - +
193A LEU 3.2 0.6 - - - -
194A LEU* 1.3 75.9 - - - +
196A ALA* 1.3 66.5 + - - +
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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