Contacts of the strand formed by residues 193 - 197 (chain A) in PDB entry 1F44
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 MET 193 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185A ILE* 3.6 27.1 - - + -
186A SER 3.4 4.9 - - - +
187A ARG* 3.4 22.0 - - - +
188A THR* 4.1 0.9 - - - +
191A GLY 3.5 0.2 + - - -
192A ARG* 1.3 74.8 - - - +
194A LEU* 1.3 63.2 + - - +
195A ILE* 4.3 1.6 - - + -
212A ALA* 3.6 2.3 - - - -
213A LEU* 2.9 40.9 + - + +
218A THR* 2.9 24.6 + - + +
221A VAL* 3.5 27.1 - - - -
222A GLU* 3.2 40.8 - - + +
225A ILE* 4.1 17.3 - - + -
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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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184A ASP 3.5 1.2 - - - +
185A ILE* 3.4 5.2 - - - +
186A SER* 2.8 49.5 + - - +
187A ARG 4.1 2.5 - - - +
188A THR* 3.0 44.6 - - + +
193A MET* 1.3 72.0 - - - +
195A ILE* 1.3 63.0 + - - +
210A GLU* 3.9 25.6 - - + +
211A LYS 3.3 3.6 - - - +
212A ALA* 3.5 28.9 - - + +
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Residues in contact with ILE 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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166A ILE* 3.9 32.3 - - + -
170A THR* 4.9 3.4 - - + -
172A LEU* 5.5 0.7 - - + -
180A ILE* 3.7 36.8 - - + -
184A ASP* 3.6 6.7 - - + +
185A ILE* 4.5 13.5 - - + -
193A MET* 5.9 0.2 - - - -
194A LEU* 1.3 78.6 - - - +
196A HIS* 1.3 70.0 + - - +
197A ILE* 3.7 13.2 + - + -
210A GLU* 3.3 3.5 - - - -
211A LYS* 2.6 52.2 + - + +
213A LEU* 4.1 26.7 - - + -
221A VAL* 6.0 0.4 - - + -
238A LEU* 5.1 2.7 - - + -
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Residues in contact with HIS 196 (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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180A ILE* 5.6 0.9 - - - +
184A ASP* 2.9 49.7 + - + +
195A ILE* 1.3 73.6 - - - +
197A ILE* 1.3 75.3 + - - +
198A GLY* 3.7 18.0 + - - -
199A ARG* 6.2 0.2 - - - -
208A GLY* 4.3 12.8 - - - -
209A VAL 3.5 8.2 + - - -
210A GLU* 2.9 29.1 + - - +
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Residues in contact with ILE 197 (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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172A LEU* 3.5 33.7 - - + -
176A GLU* 3.9 30.7 - - + +
179A ARG* 6.3 0.7 - - + +
180A ILE* 4.5 9.0 - - + -
195A ILE* 3.9 15.5 - - + +
196A HIS* 1.3 82.7 - - - +
198A GLY* 1.3 68.3 + - - +
208A GLY* 2.8 6.6 + - - +
209A VAL* 2.8 51.3 + - + +
211A LYS* 3.6 23.8 - - + -
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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