Contacts of the strand formed by residues 239 - 245 (chain A) in PDB entry 1I72
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 TYR 239 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71A PHE* 3.8 32.3 - + + -
76A ARG* 3.9 18.6 - - - -
78A ILE* 3.5 25.4 - - + +
176A THR* 3.9 12.8 + - - +
232A GLY 3.2 11.0 - - - +
238A THR* 1.3 72.6 - - - +
240A TRP* 1.3 64.0 + - - +
241A THR* 4.8 1.6 - - + -
256A GLU* 2.6 45.4 + - + +
257A THR* 2.7 32.4 + - - -
258A ASN* 2.9 51.8 + - + -
15B GLU* 4.2 3.7 + - - -
60B GLN* 3.4 17.9 - - - +
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Residues in contact with TRP 240 (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 PHE* 4.0 1.6 - - - -
209A ILE* 3.3 27.8 - - + -
210A ARG 3.8 6.7 - - - -
212A LEU* 4.1 7.2 - - + -
213A ILE* 3.5 43.1 - - + +
216A SER* 2.8 32.3 + - - -
218A ILE* 4.0 8.7 - - + -
230A MET* 3.5 34.0 - - + +
231A ASN* 3.5 0.7 - - - -
232A GLY* 2.6 52.8 + - - +
233A MET* 4.2 1.1 - - - -
234A LYS* 5.4 0.2 - - + -
238A THR* 4.7 4.0 - - + -
239A TYR* 1.3 83.4 - - - +
241A THR* 1.3 62.8 + - - +
242A ILE* 3.9 15.7 - - + -
255A PHE* 4.0 18.8 - + + -
256A GLU 3.1 11.4 - - - +
257A THR* 3.4 13.7 - - - +
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Residues in contact with THR 241 (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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69A SER* 3.2 1.6 + - - +
71A PHE* 3.9 15.0 - - + -
78A ILE* 6.6 0.2 - - + -
80A LYS* 4.2 9.1 + - + +
230A MET* 2.9 18.8 + - - -
231A ASN* 3.0 17.1 + - - -
239A TYR* 4.8 1.6 - - + -
240A TRP* 1.3 76.4 - - - +
242A ILE* 1.3 65.9 + - - +
243A HIS* 2.9 27.6 + - - +
254A SER 3.8 0.9 - - - +
255A PHE* 3.6 1.6 - - - -
256A GLU* 2.9 58.2 + - + +
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Residues in contact with ILE 242 (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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209A ILE* 3.8 27.8 - - + -
212A LEU* 4.0 8.7 - - + -
228A TYR* 4.5 6.2 - - + -
229A SER* 3.3 4.0 - - - -
230A MET* 2.9 41.6 + - + -
240A TRP* 3.9 14.8 - - + -
241A THR* 1.3 78.4 + - - +
243A HIS* 1.3 67.9 + - - +
244A ILE* 3.8 29.2 - - + -
253A VAL* 4.4 1.1 - - + -
254A SER 3.3 11.7 - - - +
255A PHE* 3.6 28.7 - - + -
275A PHE* 4.1 14.1 - - + -
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Residues in contact with HIS 243 (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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68A PYR 3.4 22.6 - - + +
69A SER* 2.9 30.9 + - - -
80A LYS* 4.3 10.0 - - + +
228A TYR 3.5 3.4 - - - -
229A SER* 2.9 26.1 + - - -
230A MET 4.5 1.3 - - - -
241A THR* 2.9 23.7 + - + +
242A ILE* 1.3 81.3 + - - +
244A ILE* 1.3 63.6 + - - +
245A THR* 5.6 0.4 - - - -
252A TYR* 3.9 4.3 - - + +
253A VAL* 3.3 4.2 - - - -
254A SER* 3.1 31.6 + - - -
368A MAO 3.5 18.3 + - - -
9B GLY 5.8 0.4 - - - +
11B GLU* 3.6 25.8 - - - +
64B VAL* 6.1 0.2 - - + -
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Residues in contact with ILE 244 (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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189A MET* 3.8 10.3 - - - -
192A PHE* 3.6 45.5 - - + -
209A ILE* 4.1 0.9 - - + -
228A TYR* 2.7 50.3 + - + +
242A ILE* 3.8 12.6 - - + -
243A HIS* 1.3 80.1 - - - +
245A THR* 1.3 64.2 + - - +
246A PRO* 3.4 10.5 - - + +
252A TYR 3.5 2.0 - - - -
253A VAL* 3.7 22.9 - - + -
275A PHE* 3.6 26.0 - - + -
368A MAO 3.3 12.2 - - - +
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Residues in contact with THR 245 (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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189A MET* 4.4 0.7 - - - +
243A HIS 4.4 0.5 + - - -
244A ILE* 1.3 72.8 - - - +
246A PRO* 1.3 60.2 - - - +
247A GLU* 3.2 16.6 - - - +
250A PHE* 3.6 32.1 - - + +
251A SER* 3.1 7.3 - - - -
252A TYR* 2.8 47.9 + - - -
368A MAO 3.2 25.0 - - - +
7B PHE* 3.9 8.2 - - + +
9B GLY* 3.5 18.8 - - - -
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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