Contacts of the strand formed by residues 286 - 292 (chain A) in PDB entry 4II9
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 LEU 286 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A VAL* 4.0 13.9 - - + -
150A LEU 3.4 3.4 - - - +
151A ASP* 3.8 24.9 - - - +
152A LEU* 4.3 4.1 - - - +
250A ARG* 3.0 48.9 + - + +
251A LYS* 3.2 18.5 - - + -
252A ILE* 3.0 24.1 + - - +
279A ALA* 4.7 0.3 - - - +
284A THR* 3.5 5.9 - - - +
285A ASP* 1.4 86.6 - - - +
287A TYR* 1.3 60.7 + - - +
314A ARG* 3.8 35.0 - - - +
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Residues in contact with TYR 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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149A VAL* 3.5 2.6 - - - -
150A LEU* 2.7 54.0 + - + +
152A LEU* 4.2 14.1 - - + +
252A ILE* 3.3 30.1 - - + -
254A TYR* 3.4 15.7 - - + +
272A GLN* 2.7 27.8 + - - -
275A MET* 3.2 50.7 - - + +
276A ILE* 3.5 30.1 - - + -
279A ALA* 4.6 3.4 - - + -
286A LEU* 1.3 74.3 - - - +
288A ASP* 1.3 59.2 + - - +
289A LEU* 3.5 31.3 + - + +
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Residues in contact with ASP 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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110A GLU* 3.9 6.8 - - - +
147A ASN* 4.2 5.7 + - - +
148A MET 3.9 2.2 - - - -
149A VAL* 3.6 26.1 - - + +
251A LYS* 2.9 45.0 + - + -
252A ILE 2.9 11.2 + - - +
253A TRP* 3.5 16.5 + - - -
254A TYR* 2.8 30.0 + - - +
286A LEU 4.1 0.4 - - - -
287A TYR* 1.3 71.9 - - - +
289A LEU* 1.3 60.2 + - - +
290A GLY* 2.8 29.3 + - - -
316A TYR* 5.3 1.1 - - - -
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Residues in contact with LEU 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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148A MET* 2.8 13.3 + - + +
150A LEU* 4.8 0.7 - - + -
254A TYR* 3.7 24.0 - - + +
272A GLN* 3.5 23.8 - - + +
287A TYR* 3.5 35.2 - - + +
288A ASP* 1.3 73.2 - - - +
290A GLY* 1.3 59.6 + - - +
304A PHE* 4.9 2.0 - - + -
305A LYS* 2.7 56.2 + - + +
308A PHE* 3.9 23.3 - - + -
309A VAL* 3.5 27.6 - - + -
10C A9Z 4.5 1.4 + - - +
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Residues in contact with GLY 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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147A ASN* 3.4 11.2 - - - -
148A MET* 2.9 25.4 + - - +
253A TRP* 4.3 12.6 - - - -
254A TYR 4.9 0.7 - - - -
288A ASP* 2.8 22.3 + - - -
289A LEU* 1.3 83.3 - - - +
291A GLY* 1.3 65.0 + - - +
305A LYS* 3.4 2.2 + - - -
10C A9Z 5.4 2.0 - - - -
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Residues in contact with GLY 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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144A PRO* 3.6 15.8 - - - +
146A LEU 3.3 11.2 - - - -
147A ASN* 3.3 8.4 - - - +
290A GLY* 1.3 74.3 - - - -
292A ILE* 1.3 63.7 + - - +
301A LEU* 3.8 3.5 - - - +
305A LYS* 2.7 27.1 + - - +
10C A9Z 3.5 22.8 - - - +
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Residues in contact with ILE 292 (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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138A MET* 3.5 17.8 - - - +
144A PRO* 4.2 1.0 - - - +
145A ARG 5.4 0.2 + - - -
146A LEU* 3.0 35.4 + - + +
148A MET* 3.6 22.9 - - + -
291A GLY* 1.3 80.6 - - - +
293A GLU* 1.3 62.1 + - - +
294A SER 3.7 24.2 - - - +
295A GLU 4.1 0.7 - - - +
299A ASP* 3.6 7.4 - - - +
301A LEU* 3.9 10.3 - - - -
302A TYR* 3.7 34.3 - - + +
305A LYS* 4.0 3.4 - - + -
313A PRO* 3.7 33.0 - - + -
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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