Contacts of the strand formed by residues 244 - 250 (chain A) in PDB entry 4CQ8
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 PHE 244 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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217A PHE* 3.4 26.2 - + + -
221A PHE 4.0 0.7 - - - -
222A GLY* 3.1 25.5 - - - -
223A VAL* 3.1 20.4 + - - +
238A LEU* 3.6 9.2 - - - +
242A PHE* 3.4 5.7 - - - +
243A SER* 1.3 100.1 + - - +
245A ILE* 1.3 66.0 + - - +
307A ILE* 3.1 29.2 - - + +
338A TYR* 3.5 24.2 - + - -
427A PHE* 6.2 0.2 - + - -
503A ILE* 4.5 7.0 - - + -
524A VAL* 3.8 21.1 - - + -
525A CYS 3.8 7.0 - - - -
526A GLN* 3.5 41.5 - - + -
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Residues in contact with ILE 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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223A VAL* 3.6 24.2 - - + +
224A ALA 5.1 0.2 - - - +
228A ASP* 3.8 32.3 - - + +
234A ILE* 3.8 29.6 - - + -
237A ILE* 3.8 30.7 - - + -
238A LEU* 4.0 13.0 - - + -
244A PHE* 1.3 81.2 - - - +
246A GLU* 1.3 69.9 + - - +
247A ILE* 3.9 5.8 + - + -
307A ILE 3.2 1.6 + - - -
308A VAL* 3.4 13.8 - - + -
309A GLY 2.9 24.4 + - - +
338A TYR* 4.5 0.2 + - - -
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Residues in contact with GLU 246 (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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223A VAL 3.1 9.5 + - - +
224A ALA 3.7 4.3 - - - +
225A ALA* 3.3 51.6 + - + +
226A GLY 4.4 0.9 + - - -
227A PHE 5.2 1.0 + - - -
228A ASP 4.7 1.7 + - - +
244A PHE* 4.8 0.2 - - - -
245A ILE* 1.3 74.1 - - - +
247A ILE* 1.3 64.2 - - - +
309A GLY 3.4 4.7 - - - -
311A SER* 3.9 16.1 + - - +
338A TYR* 2.7 34.2 + - + +
340A ALA* 3.6 21.4 - - + +
429A LYS* 4.5 5.0 + - - +
455A ILE* 3.4 20.1 - - - +
526A GLN* 2.9 19.3 + - - +
800A FMN 4.5 2.9 - - - +
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Residues in contact with ILE 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A ASP* 3.5 17.7 - - + +
231A GLY* 3.9 11.7 - - - +
234A ILE* 3.9 26.9 - - + -
245A ILE* 4.5 12.8 - - + -
246A GLU* 1.3 74.8 - - - +
248A GLY* 1.3 63.1 + - - +
286A VAL* 3.8 26.9 - - + +
290A LEU* 4.2 25.6 - - + -
308A VAL* 4.4 8.1 - - + -
309A GLY 2.9 19.7 + - - +
310A VAL* 3.8 21.3 - - + -
311A SER* 2.9 26.5 + - - -
332A ILE* 4.4 1.1 - - + -
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Residues in contact with GLY 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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225A ALA* 4.4 2.5 - - - -
226A GLY* 2.8 28.0 + - - -
228A ASP 3.6 1.4 + - - -
229A LYS* 3.1 37.4 + - - -
247A ILE* 1.3 77.2 - - - +
249A THR* 1.4 66.9 + - - -
250A ILE* 3.5 7.8 - - - +
311A SER 3.9 0.7 - - - -
800A FMN 3.9 0.2 - - - -
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Residues in contact with THR 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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229A LYS* 4.5 2.8 + - - +
248A GLY* 1.4 69.6 + - - -
250A ILE* 1.3 63.7 + - - +
278A PHE* 3.6 30.8 - - + +
279A ASN 4.9 1.7 - - - +
280A ASN* 3.8 18.4 + - - +
311A SER* 2.7 22.8 + - - +
312A ILE 3.5 7.2 - - - +
313A GLY* 3.4 32.3 - - - +
342A ASN* 2.8 16.8 + - - +
800A FMN 2.8 29.7 + - - +
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Residues in contact with ILE 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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229A LYS 3.6 23.3 - - - +
247A ILE 5.1 0.2 - - - -
248A GLY* 3.7 6.7 - - - -
249A THR* 1.3 71.7 - - - +
251A THR* 1.3 65.5 + - - +
280A ASN* 3.5 8.5 - - - +
283A CYS* 3.9 30.7 - - + -
286A VAL* 3.6 26.9 - - + -
310A VAL* 3.8 20.0 - - + -
311A SER 3.0 17.6 + - - +
312A ILE* 3.7 10.0 - - + -
313A GLY 3.0 25.6 + - - +
328A CYS* 4.3 3.7 - - - -
332A ILE* 3.9 21.8 - - + -
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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