Contacts of the strand formed by residues 185 - 189 (chain A) in PDB entry 5I4A
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 ILE 185 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A LEU* 4.1 2.4 - - - +
180A SER* 3.9 2.1 + - - +
181A GLY* 3.6 2.6 - - - -
182A LEU* 3.0 32.7 + - + +
183A ASP* 4.1 11.7 - - + +
184A GLY* 1.3 80.5 - - - +
186A LEU* 1.3 61.2 + - - +
187A LYS* 4.0 16.5 + - + +
197A GLU* 4.1 38.8 - - + +
198A VAL 5.8 1.3 - - - -
201A PRO* 5.5 0.7 - - - -
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Residues in contact with LEU 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A ALA* 3.9 22.0 - - + -
158A LEU* 4.1 9.8 - - + +
167A LEU* 4.1 9.9 - - + -
178A TYR* 3.7 33.9 - - + -
180A SER 3.6 4.0 - - - +
181A GLY* 4.1 6.7 - - - -
184A GLY 4.1 2.0 + - - -
185A ILE* 1.3 72.8 - - - +
187A LYS* 1.3 60.6 + - - +
188A ILE* 4.7 2.0 - - + -
197A GLU* 3.4 3.5 - - - -
198A VAL* 3.1 34.9 + - + +
201A PRO* 3.8 36.8 - - + +
204A TYR* 3.8 33.2 - - + -
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Residues in contact with LYS 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A TYR* 4.1 4.0 - - - -
179A ILE* 3.1 37.4 + - + -
180A SER* 2.8 40.4 + - - +
185A ILE* 4.6 17.1 - - + +
186A LEU* 1.3 78.7 - - - +
188A ILE* 1.3 65.3 + - - +
195A ILE* 4.9 22.0 - - + +
196A VAL 3.3 7.4 - - - +
197A GLU* 3.8 31.2 + - + +
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Residues in contact with ILE 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A LEU* 3.5 28.7 - - + -
176A PHE* 4.1 14.8 - - + -
177A PRO 3.5 7.9 - - - +
179A ILE* 3.8 5.9 - - - +
186A LEU* 4.7 2.2 - - + -
187A LYS* 1.3 77.2 - - - +
189A ASP* 1.3 60.6 + - - +
190A ILE* 4.0 17.9 + - + -
194A GLN 3.7 0.2 - - - +
195A ILE* 3.5 6.6 - - - +
196A VAL* 3.1 36.1 + - + +
198A VAL* 3.7 19.3 - - + -
204A TYR* 3.6 34.5 - - + +
21B U 4.0 16.4 - - - +
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Residues in contact with ASP 189 (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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176A PHE* 3.3 24.9 - - - +
177A PRO* 3.1 44.0 + - + +
179A ILE* 3.8 17.6 - - + +
188A ILE* 1.3 72.7 - - - +
190A ILE* 1.3 88.9 + - - +
193A ASN* 3.4 24.9 - - - +
194A GLN 3.7 8.1 + - - +
195A ILE* 5.0 1.8 - - - +
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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