Contacts of the strand formed by residues 276 - 279 (chain A) in PDB entry 5M7R
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 VAL 276 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61A LEU* 4.5 13.9 - - + +
213A LEU* 4.8 4.5 - - + -
246A GLU* 4.2 17.5 - - + -
247A VAL 2.9 8.6 + - - +
248A LEU* 3.2 26.6 - - + -
249A TRP 3.0 23.4 + - - -
275A PRO* 1.3 72.1 - - - +
277A ILE* 1.3 72.3 + - - +
308A LYS* 3.7 28.5 - - + -
309A GLY* 3.5 19.5 - - - +
311A LEU* 4.1 17.5 - - + -
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Residues in contact with ILE 277 (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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249A TRP* 3.2 17.3 - - + +
250A THR* 4.9 0.9 - - - -
251A GLY 5.3 0.2 - - - +
259A ILE* 4.2 25.4 - - + -
264A ILE* 4.1 18.4 - - + -
275A PRO* 4.0 0.9 - - + -
276A VAL* 1.3 78.6 - - - +
278A TRP* 1.3 68.6 + - - +
279A ASP* 3.8 21.3 - - + +
296A TYR* 4.9 0.7 - - - +
299A ARG* 6.5 0.2 - - + -
303A LEU* 5.2 1.1 - - + -
307A LEU* 3.3 42.2 - - + -
309A GLY 2.8 14.5 + - - +
310A VAL* 3.5 12.3 - - + -
311A LEU* 2.8 31.9 + - - +
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Residues in contact with TRP 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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65A VAL* 3.9 21.1 - - + -
67A GLY* 3.5 36.3 - - - -
94A LEU* 4.5 4.5 - - + -
96A ALA* 4.4 4.7 - - + -
98A LYS* 3.8 21.1 - - - -
172A LEU* 4.2 23.3 - - + -
174A ASP* 4.0 9.4 - - - -
215A CYS* 4.9 9.2 - - - -
248A LEU* 4.1 31.9 - - + -
249A TRP 2.8 10.7 + - - +
250A THR* 3.2 31.8 - - + +
276A VAL 3.5 1.4 + - - -
277A ILE* 1.3 70.8 - - - +
279A ASP* 1.3 60.3 + - - +
280A ASN* 2.9 35.3 + - - +
311A LEU* 3.5 6.1 - - - -
313A ASN* 3.7 11.8 - - + +
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Residues in contact with ASP 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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250A THR* 5.2 1.8 - - - +
259A ILE* 4.1 5.1 - - - +
277A ILE* 3.9 12.2 - - + +
278A TRP* 1.3 71.2 - - - +
280A ASN* 1.3 60.3 + - - +
281A ILE* 2.9 25.1 + - - +
296A TYR* 2.5 30.1 + - - +
299A ARG* 2.6 39.3 + - - -
310A VAL* 4.4 3.4 - - + -
311A LEU 3.0 10.0 + - - +
312A THR* 3.6 17.6 + - - +
313A ASN* 2.8 29.8 + - - +
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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