Contacts of the strand formed by residues 246 - 251 (chain A) in PDB entry 4IXU
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 246 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130A HIS* 4.2 2.7 - - - -
138A CYS* 3.6 21.8 - - - +
140A VAL* 4.2 20.0 - - + -
235A PHE* 4.1 13.9 - - + -
239A ILE* 4.4 9.0 - - + -
244A ARG 3.8 7.0 - - - +
245A PRO* 1.3 75.6 - - - +
247A HIS* 1.3 72.8 + - - +
248A LEU 4.2 1.6 - - - +
283A ILE* 4.2 15.0 - - + +
286A THR* 3.5 38.4 - - + +
288A LEU* 2.9 21.2 + - + +
289A LEU* 3.6 8.2 - - + +
290A SER* 2.8 27.5 + - - -
291A ALA 3.3 6.8 + - - +
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Residues in contact with HIS 247 (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 THR* 3.4 29.2 - - - -
127A ILE* 3.3 29.7 - - + +
130A HIS* 2.9 27.5 + - + +
137A LEU* 4.5 4.9 - - + +
138A CYS 2.8 17.2 + - - +
139A VAL* 3.3 11.6 - - + +
140A VAL 2.8 27.4 + - - +
245A PRO 4.0 0.2 + - - -
246A ILE* 1.3 73.7 - - - +
248A LEU* 1.3 68.3 + - - +
249A SER* 4.0 3.6 - - - -
291A ALA* 3.4 16.8 - - + +
293A ASP* 2.6 33.6 + - - -
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Residues in contact with LEU 248 (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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140A VAL* 3.4 28.5 - - + +
142A VAL* 3.7 23.6 - - + -
246A ILE* 3.9 1.6 - - + -
247A HIS* 1.3 72.6 - - - +
249A SER* 1.3 59.6 + - - +
250A PHE* 3.7 23.2 + - + -
279A ILE* 4.9 2.5 - - + -
280A ALA* 5.3 2.0 - - - -
283A ILE* 4.2 26.2 - - + -
289A LEU* 4.0 16.4 - - + +
291A ALA 2.9 9.3 + - - +
292A LEU* 3.2 17.2 - - + -
293A ASP 2.8 24.9 + - - +
318A VAL* 5.0 0.4 - - + -
322A SER* 3.7 23.8 - - - +
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Residues in contact with SER 249 (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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120A HIS* 2.8 28.5 + - - -
123A ALA* 3.9 0.5 - - - +
127A ILE* 5.0 0.2 - - - -
139A VAL* 4.7 0.9 - - - -
140A VAL 2.8 11.0 + - - -
141A TRP* 3.5 31.1 - - - -
142A VAL 2.9 27.0 + - - +
247A HIS* 3.7 8.5 + - - -
248A LEU* 1.3 72.1 - - - +
250A PHE* 1.3 57.6 + - - +
251A ASP 3.9 0.4 + - - -
293A ASP* 2.8 26.4 + - - +
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Residues in contact with PHE 250 (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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142A VAL* 3.6 39.7 - - + -
248A LEU* 4.2 18.4 - - + -
249A SER* 1.3 72.7 + - - +
251A ASP* 1.3 79.3 + - - +
252A ILE* 3.7 2.7 + - + -
254A ALA* 4.3 1.6 - - + -
255A PHE* 3.6 41.3 - + - -
271A LEU* 4.5 6.3 - - + -
276A GLY* 4.7 6.7 - - - -
279A ILE* 4.6 11.9 - - + -
280A ALA* 5.6 1.1 - - + -
292A LEU* 5.5 0.7 - - + -
293A ASP* 2.8 18.5 + - - +
294A LEU* 3.4 18.4 - - + +
295A VAL* 3.0 28.0 + - - +
318A VAL* 3.6 25.1 - - + -
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Residues in contact with ASP 251 (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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120A HIS* 3.7 4.7 - - - +
142A VAL 2.8 8.1 + - - +
143A ASP* 3.3 22.4 - - - +
249A SER 3.9 1.2 + - - -
250A PHE* 1.3 74.4 - - - +
252A ILE* 1.3 65.8 + - - +
253A ASP* 3.0 26.8 + - - +
254A ALA* 2.9 22.9 + - - +
295A VAL* 3.6 6.7 - - - +
296A GLU* 3.3 21.2 - - - +
401A MN 2.3 18.7 + - - +
402A MN 2.2 25.8 + - - -
406A 38I 2.8 5.0 + - - -
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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