Contacts of the strand formed by residues 285 - 291 (chain A) in PDB entry 2I69
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 HIS 285 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A VAL* 3.7 21.1 - - + -
25A LEU 3.1 16.2 - - - +
26A GLU* 4.5 11.9 - - - +
48A MET* 4.0 3.5 - - - +
137A TYR* 3.8 10.6 + - - -
194A SER* 2.7 46.3 + - - -
195A GLY* 3.8 29.2 - - - -
284A GLY* 1.3 76.3 - - - +
286A LEU* 1.3 56.1 + - - +
287A LYS* 4.7 9.3 - - + +
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Residues in contact with LEU 286 (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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24A VAL* 3.0 5.4 - - - -
25A LEU* 2.7 40.4 + - + +
45A MET* 4.0 17.5 - - + +
137A TYR* 3.7 40.8 - - + -
139A VAL* 4.5 7.9 - - + -
169A ILE* 3.9 16.6 - - + -
190A CYS* 3.9 8.7 - - + -
191A GLU 4.1 0.9 - - - +
192A PRO* 3.9 34.1 - - + -
194A SER* 4.2 0.7 - - - -
285A HIS* 1.3 75.8 - - - +
287A LYS* 1.3 64.5 + - - +
288A CYS* 3.7 22.8 + - - -
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Residues in contact with LYS 287 (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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23A LEU 3.4 7.9 - - - +
24A VAL* 4.1 13.5 - - + +
190A CYS* 3.1 3.5 - - - +
191A GLU* 3.1 73.0 + - + +
193A ARG 5.8 2.6 + - - -
194A SER* 4.6 14.1 + - - -
285A HIS* 4.7 7.2 - - + +
286A LEU* 1.3 73.1 - - - +
288A CYS* 1.3 61.5 + - - +
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Residues in contact with CYS 288 (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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22A ASP* 3.3 5.6 - - - +
23A LEU* 2.8 43.9 + - + +
25A LEU* 4.9 11.4 - - - -
139A VAL* 6.1 0.7 - - - -
188A VAL* 4.4 6.7 - - + -
189A ASP 3.2 5.8 - - - +
190A CYS* 2.1 46.0 - - - -
286A LEU* 3.7 17.2 + - - -
287A LYS* 1.3 76.1 - - - +
289A ARG* 1.3 65.4 + - - +
290A VAL* 4.0 9.6 - - + -
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Residues in contact with ARG 289 (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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20A TRP* 3.2 44.9 - - + -
21A VAL 3.3 4.0 - - - -
22A ASP* 2.8 39.8 + - - +
187A THR 4.0 0.2 - - - +
188A VAL* 3.7 2.1 - - - -
189A ASP* 2.7 41.7 + - + +
288A CYS* 1.3 74.0 - - - +
290A VAL* 1.3 63.4 + - - +
291A LYS* 3.8 29.6 + - + +
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Residues in contact with VAL 290 (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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20A TRP* 3.3 3.0 - - - -
21A VAL* 2.7 33.7 + - + +
23A LEU* 3.2 31.4 - - + -
33A ILE* 4.6 7.4 - - + -
41A ILE* 4.2 17.7 - - + -
43A VAL* 4.7 12.8 - - + -
186A VAL* 3.6 27.6 - - + -
187A THR 3.6 2.7 - - - -
188A VAL* 3.9 17.3 - - + -
288A CYS* 4.5 4.3 - - + -
289A ARG* 1.3 73.8 - - - +
291A LYS* 1.3 60.6 + - - +
292A MET* 3.6 9.6 - - + +
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Residues in contact with LYS 291 (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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19A THR* 5.5 0.2 - - - +
20A TRP* 4.1 13.0 - - + -
185A GLU 4.5 1.0 - - - +
186A VAL* 3.7 4.7 - - - +
187A THR* 2.8 49.3 + - + +
189A ASP* 2.9 30.5 + - - -
289A ARG* 4.1 26.5 - - + +
290A VAL* 1.3 72.2 - - - +
292A MET* 1.3 64.5 + - - +
293A GLU* 3.6 30.0 + - + +
294A LYS 5.2 0.2 + - - -
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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