Contacts of the strand formed by residues 179 - 184 (chain A) in PDB entry 1FSU
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 GLU 179 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A GLU* 3.4 1.8 - - - +
174A ASP* 2.9 25.8 + - + +
177A SER* 3.4 32.6 + - - +
178A HIS* 1.3 79.8 - - - +
180A ARG* 1.3 61.9 - - - +
181A CYS* 5.6 2.7 - - - -
192A CYS* 4.9 10.8 - - + +
193A ALA* 3.3 16.0 - - - +
194A LEU* 4.2 20.9 + - + +
207A LYS* 6.6 0.2 - - - -
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Residues in contact with ARG 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A ILE* 6.1 0.6 - - - +
115A TRP* 4.3 14.8 - - - -
116A PRO* 3.3 30.7 - - - +
170A LEU* 3.9 22.3 - - + +
171A GLY* 5.6 2.8 - - - +
172A SER* 3.2 47.0 + - - +
173A GLU* 4.1 7.0 - - + +
179A GLU* 1.3 74.7 - - - +
181A CYS* 1.3 76.4 + - - +
182A THR* 3.2 28.5 - - - +
191A ARG 3.5 0.3 - - - +
192A CYS* 3.4 0.9 - - - -
193A ALA 3.0 19.4 + - - +
195A ASP* 5.0 0.9 - - + -
529A TRP* 3.0 28.9 + - + +
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Residues in contact with CYS 181 (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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179A GLU* 5.6 2.9 - - - -
180A ARG* 1.3 96.4 + - - +
182A THR* 1.3 61.3 + - - +
190A THR* 3.9 13.0 - - + -
191A ARG 3.2 4.0 - - - -
192A CYS* 2.0 46.9 - - - -
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Residues in contact with THR 182 (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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115A TRP* 5.7 2.9 - - + -
116A PRO* 3.8 19.4 - - + +
117A CYS* 5.8 2.2 - - - -
180A ARG* 3.2 38.5 - - - +
181A CYS* 1.3 71.5 - - - +
183A LEU* 1.3 67.7 + - - +
184A ILE* 3.6 5.1 + - - +
190A THR* 3.3 7.0 - - - -
191A ARG* 3.0 29.0 + - - +
517A GLN* 6.2 0.4 - - - +
529A TRP* 3.2 30.5 - - - -
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Residues in contact with LEU 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A CYS* 5.6 0.7 - - - -
182A THR* 1.3 78.7 - - - +
184A ILE* 1.3 60.1 + - - +
185A ASP* 3.4 21.1 + - - +
188A ASN* 4.1 15.7 - - - +
189A VAL 3.5 32.3 - - - +
190A THR* 3.9 12.3 + - - +
517A GLN* 3.1 23.6 + - - -
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Residues in contact with ILE 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A CYS* 4.2 11.0 - - - -
182A THR* 4.3 7.2 - - - +
183A LEU* 1.3 72.4 - - - +
185A ASP* 1.3 67.2 + - - +
186A ALA 4.7 1.1 - - - +
187A LEU* 3.1 28.9 + - + +
188A ASN* 2.9 18.7 + - - -
189A VAL* 2.9 18.6 + - + +
191A ARG* 3.5 30.5 - - + -
517A GLN* 3.4 9.2 - - - +
519A PRO* 3.9 23.3 - - + -
521A CYS* 4.0 8.1 - - - -
522A ASP* 3.8 29.6 - - - +
523A PRO* 4.2 2.0 - - + -
529A TRP* 4.7 2.9 - - + -
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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