Contacts of the strand formed by residues 278 - 283 (chain M) in PDB entry 6D6Q
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 HIS 278 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154M ASN* 3.0 40.3 + - + +
155M GLN* 4.2 2.9 - - + -
156M SER 3.8 7.4 + - - +
247M ALA* 2.9 26.0 + - + +
248M TRP* 3.2 28.7 - + + -
249M VAL 3.0 10.4 + - - -
275M ASP 5.9 0.4 - - - -
276M ASN 4.8 6.9 + - - -
277M VAL* 1.3 77.3 + - - +
279M TYR* 1.3 72.6 + - - +
302M GLN* 2.8 32.8 + - + +
303M PRO* 6.6 0.2 - - + -
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Residues in contact with TYR 279 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156M SER* 2.0 42.7 + - - -
157M VAL 3.0 6.9 + - - +
248M TRP* 3.9 5.7 - - - -
249M VAL* 2.7 31.6 - - + +
251M PHE* 3.4 28.7 - + - -
270M ILE* 3.4 19.4 - - + +
273M LEU* 3.9 10.8 - - + -
277M VAL* 3.6 16.6 - - + -
278M HIS* 1.3 83.3 - - - +
280M VAL* 1.3 61.4 + - - +
281M PHE* 3.1 32.1 - + - -
296M ILE* 3.9 11.3 - - + +
300M HIS* 2.8 40.5 + + - -
302M GLN* 4.8 3.4 - - - -
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Residues in contact with VAL 280 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151M VAL* 4.5 8.7 - - + -
157M VAL* 3.4 27.8 - - + -
159M VAL* 4.9 0.4 - - + -
170M CYS* 4.1 20.0 - - - +
171M ALA* 5.8 1.1 - - - +
174M ALA* 5.0 3.1 - - + -
248M TRP* 4.6 9.2 - - + -
249M VAL 2.9 4.8 + - - -
250M ILE* 3.5 25.9 - - + -
251M PHE* 2.9 33.0 + - - -
279M TYR* 1.3 79.8 - - - +
281M PHE* 1.3 66.6 + - - +
282M LEU* 3.8 29.4 - - + -
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Residues in contact with PHE 281 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156M SER* 4.5 6.7 - - - -
157M VAL 2.9 26.5 + - - +
158M LEU* 3.2 21.8 - - + -
159M VAL* 2.9 31.2 + - - +
251M PHE* 3.4 33.4 - + - -
254M ILE* 3.7 20.6 - - + -
270M ILE* 4.1 9.9 - - + -
279M TYR* 3.1 30.1 - + - -
280M VAL* 1.3 72.7 - - - +
282M LEU* 1.3 62.4 + - - +
283M SER 3.9 0.9 - - - -
292M PHE* 3.4 37.5 - + - -
296M ILE* 3.6 20.6 - - + -
304M CYS* 5.2 2.5 - - - -
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Residues in contact with LEU 282 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159M VAL* 3.8 15.3 - - + -
167M LYS* 3.6 50.4 + - + +
168M THR* 5.0 2.7 - - + +
170M CYS* 5.0 6.1 - - + -
171M ALA* 4.5 20.2 - - + -
187M PHE* 5.6 0.9 - - + -
250M ILE* 5.4 4.3 - - + -
251M PHE* 2.9 12.4 + - - +
252M ASP* 2.8 29.6 - - - +
253M GLU* 3.2 24.3 + - - -
254M ILE* 4.2 3.1 + - - +
255M HIS* 5.0 0.5 + - - -
280M VAL* 3.8 20.6 - - + -
281M PHE* 1.3 79.7 - - - +
283M SER* 1.3 60.2 + - - +
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Residues in contact with SER 283 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158M LEU* 4.4 10.1 - - - -
159M VAL 2.9 20.3 + - - +
160M SER* 4.6 1.1 - - - -
161M ALA 3.5 8.8 + - - +
167M LYS* 3.3 20.3 + - - +
254M ILE* 3.3 37.0 - - - +
255M HIS* 4.0 11.2 - - - +
281M PHE 3.9 0.2 - - - -
282M LEU* 1.3 72.9 - - - +
284M ALA* 1.3 79.9 + - - +
286M ILE* 3.9 12.3 - - - +
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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