Contacts of the strand formed by residues 187 - 191 (chain A) in PDB entry 6U17
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 187 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132A LEU* 3.9 3.8 - - - -
134A ILE* 3.3 30.5 - - + +
136A ILE* 3.8 20.9 - - + -
159A PHE* 5.2 1.1 - - + -
163A LEU* 3.9 25.6 - - + -
168A LEU* 4.8 13.9 - - + +
181A LEU* 3.2 35.0 + - + +
182A PRO* 3.0 22.9 - - - +
185A TYR* 3.9 20.6 - - + +
186A GLY* 1.3 81.8 - - - +
188A GLY* 1.3 72.5 + - - +
189A PHE* 4.6 3.4 - - + -
296A ARG* 5.5 1.8 - - - +
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Residues in contact with GLY 188 (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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127A ILE 3.2 13.5 - - - -
132A LEU* 3.8 17.3 - - - +
134A ILE 2.8 10.1 + - - -
135A VAL* 3.5 4.7 - - - -
136A ILE* 2.8 27.8 + - - -
182A PRO* 4.5 1.8 - - - -
187A ILE* 1.3 79.6 - - - +
189A PHE* 1.3 66.1 + - - -
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Residues in contact with PHE 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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126A ASP* 3.6 1.9 - - - -
127A ILE* 2.8 58.0 + - + +
128A LEU* 3.7 6.1 - - - +
135A VAL* 4.4 0.4 - - - -
136A ILE* 3.4 24.9 - - + +
151A HIS* 3.5 33.9 - + + +
152A TYR* 3.9 16.4 - + - -
159A PHE* 3.7 31.9 - + - -
160A TRP* 4.1 9.0 - + - -
178A ASP* 3.9 20.4 - - + -
181A LEU* 3.7 34.5 - - + -
187A ILE* 4.6 2.0 - - + -
188A GLY* 1.3 76.1 - - - -
190A THR* 1.3 65.1 + - - +
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Residues in contact with THR 190 (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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126A ASP* 2.7 30.7 + - - -
128A LEU* 4.1 11.4 - - + -
135A VAL* 3.9 19.7 - - + -
136A ILE 3.0 9.6 + - - +
137A ILE* 4.0 7.0 - - + -
138A GLY 3.0 19.1 + - - -
151A HIS* 4.8 6.5 + - - -
152A TYR* 4.9 0.9 + - - -
189A PHE* 1.3 75.1 - - - +
191A ASN* 1.3 75.8 + - - +
215A LEU* 3.8 28.1 - - + +
218A LYS* 3.8 11.2 + - + +
219A LEU* 5.6 1.6 - - + -
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Residues in contact with ASN 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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124A LEU* 3.8 21.6 + - - +
126A ASP* 4.2 2.5 + - - +
137A ILE* 4.2 4.5 - - - -
138A GLY* 3.0 31.7 - - - +
139A ILE 3.7 2.2 - - - +
140A ASN* 4.0 4.9 - - - -
141A PRO* 3.9 16.4 - - - +
151A HIS* 4.5 2.6 - - - -
190A THR* 1.3 88.2 + - - +
192A MET* 1.4 66.3 + - - +
193A VAL 3.6 18.1 + - - +
194A GLU* 5.7 0.2 - - - -
215A LEU* 4.9 3.9 - - - +
218A LYS* 5.2 4.3 + - - -
17D 1FC 3.1 23.4 + - - -
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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