Contacts of the strand formed by residues 277 - 282 (chain A) in PDB entry 3U78
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 SER 277 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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197A VAL* 3.8 1.6 - - - -
222A VAL* 3.6 11.4 - - - +
223A LEU 3.9 0.7 + - - -
224A ASN* 3.4 30.7 + - - +
274A VAL* 2.7 42.5 + - - +
275A GLN 3.2 1.2 + - - -
276A ASP* 1.3 79.6 - - - +
278A TYR* 1.3 60.9 + - - +
357A LEU* 3.6 2.1 - - - +
358A THR* 2.8 42.6 + - - -
701A AKG 5.7 0.2 - - - -
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Residues in contact with TYR 278 (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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117A ALA* 4.4 4.7 - - + -
118A GLY* 4.0 11.9 - - - -
122A PHE* 3.4 35.7 - + - -
123A ILE* 4.1 11.0 - - + -
126A LEU* 3.7 27.4 - - + -
195A ILE* 5.2 2.1 - - - +
197A VAL* 3.3 19.6 - - + +
200A GLN* 3.3 22.3 + - - -
224A ASN* 4.4 2.7 + - - +
276A ASP 4.0 4.3 - - - +
277A SER* 1.3 78.3 - - - +
279A THR* 1.3 76.5 + - - +
280A ASP* 2.7 37.9 + - + -
281A PHE* 4.0 8.1 - - - -
302A TYR* 5.1 1.8 - + - -
327A PHE* 4.0 2.8 - + - -
355A ALA* 3.6 19.5 - - + +
356A VAL 3.1 21.5 - - - -
357A LEU* 4.5 1.3 - - + -
701A AKG 5.4 0.2 - - - -
707A E67 4.3 1.7 - - - +
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Residues in contact with THR 279 (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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195A ILE* 5.5 1.7 - - - +
224A ASN* 3.8 6.6 + - - -
226A ILE* 4.0 9.9 - - + +
278A TYR* 1.3 79.3 + - - +
280A ASP* 1.3 67.0 + - - +
282A HIS* 3.5 28.5 - - + +
355A ALA* 3.2 5.2 - - - +
356A VAL* 2.9 32.4 + - - -
701A AKG 2.7 36.3 + - + +
707A E67 3.8 28.3 - - - +
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Residues in contact with ASP 280 (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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117A ALA* 3.8 17.4 - - - +
122A PHE* 5.0 1.4 - - - -
200A GLN* 3.8 14.1 + - - +
278A TYR* 2.7 35.4 + - + -
279A THR* 1.3 79.6 - - - +
281A PHE* 1.3 70.0 + - - +
282A HIS* 2.7 32.9 + - - +
317A TRP* 3.8 23.4 - - + -
323A GLN* 4.5 14.0 + - - +
324A SER* 4.9 1.6 - - - -
326A VAL 5.3 0.9 - - - +
327A PHE* 5.4 1.7 - - - -
328A PHE 5.6 0.7 + - - -
355A ALA* 4.1 1.1 - - - -
707A E67 3.6 11.6 - - + +
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Residues in contact with PHE 281 (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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278A TYR* 4.0 0.7 - - - -
280A ASP* 1.3 87.0 + - - +
282A HIS* 1.3 59.4 + - - +
302A TYR* 3.6 17.5 - - + -
304A ILE* 3.6 15.0 - - + -
314A TYR* 3.4 5.8 + - - -
317A TRP* 3.2 32.2 - - + -
323A GLN* 5.5 0.3 + - - -
327A PHE* 3.6 31.9 - + - -
328A PHE* 3.8 21.3 - + + -
329A GLY 3.7 11.4 - - - -
335A CYS* 3.9 19.1 - - - -
353A ILE* 3.9 22.7 - - + -
354A HIS* 3.5 5.8 - - - -
355A ALA* 3.4 33.1 - - + +
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Residues in contact with HIS 282 (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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279A THR* 3.5 24.5 - - + +
280A ASP 2.7 19.5 + - - +
281A PHE* 1.3 75.5 - - - +
283A ILE* 1.3 65.6 + - - +
284A ASP* 3.3 8.1 - - - -
314A TYR* 3.2 13.7 - - - +
353A ILE* 3.6 2.0 - - - -
354A HIS* 3.2 42.9 + + - +
355A ALA* 5.1 1.1 - - - -
356A VAL* 5.2 0.2 - - + -
392A ASP* 5.1 1.8 - - - +
701A AKG 3.3 11.2 + - + -
702A NI 2.2 43.4 - - + +
707A E67 3.8 31.6 - - + +
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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