Contacts of the strand formed by residues 268 - 275 (chain X) in PDB entry 2Q0Z
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 268 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127X GLY* 3.4 6.6 + - - -
129X LEU* 3.7 4.0 - - - +
262X GLY* 3.2 4.2 - - - -
263X ASP* 2.8 37.3 + - - -
266X SER* 3.7 18.6 - - - -
267X ASN* 1.3 76.9 - - - +
269X LEU* 1.3 62.4 + - - +
270X ILE* 3.6 12.9 + - - +
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Residues in contact with LEU 269 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124X SER* 3.6 30.3 - - - +
127X GLY* 2.8 37.1 + - - +
129X LEU* 3.8 19.9 - - + +
132X ALA* 3.5 30.1 - - + -
136X MSE 4.3 8.1 - - + -
260X VAL* 3.7 22.2 - - + -
261X ILE 4.2 1.6 - - - -
268X SER* 1.3 72.9 + - - +
270X ILE* 1.3 64.0 + - - +
271X SER 3.9 24.2 - - - +
272X ILE* 4.1 7.2 - - + -
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Residues in contact with ILE 270 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261X ILE* 3.0 14.4 + - + +
262X GLY* 4.3 2.5 - - - -
263X ASP* 4.3 13.2 - - + +
268X SER* 4.0 16.2 - - - +
269X LEU* 1.3 79.0 - - - +
271X SER* 1.3 64.0 + - - +
287X PHE* 3.3 39.2 - - + +
297X TYR* 3.5 39.5 - - + -
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Residues in contact with SER 271 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260X VAL* 3.3 9.2 - - - +
261X ILE* 2.9 40.4 + - - -
269X LEU* 3.9 2.0 - - - -
270X ILE* 1.3 82.9 + - - +
272X ILE* 1.3 61.9 + - - +
285X LEU* 4.3 18.2 - - - -
286X ASP 2.9 26.8 + - - -
287X PHE* 3.5 13.0 - - - +
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Residues in contact with ILE 272 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120X VAL* 4.4 3.1 - - + -
121X ASP* 6.1 0.4 - - - +
124X SER* 4.0 28.7 - - - +
125X SER* 6.3 0.2 - - - -
136X MSE 3.8 24.5 - - + -
258X TRP* 3.7 29.8 - - + +
259X VAL 3.4 5.8 - - - +
260X VAL* 3.8 12.6 - - + -
269X LEU* 4.1 13.0 - - + -
271X SER* 1.3 78.3 - - - +
273X LYS* 1.3 73.0 + - - +
274X ARG* 5.3 1.8 - - + -
285X LEU* 4.1 2.1 - - - +
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Residues in contact with LYS 273 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258X TRP* 3.3 3.8 - - - -
259X VAL* 2.9 34.2 + - + +
272X ILE* 1.3 80.4 - - - +
274X ARG* 1.3 67.7 + - - +
275X LEU* 5.4 0.2 - - - -
283X VAL* 3.9 21.1 - - + -
284X LYS* 2.7 38.7 + - - +
285X LEU* 3.4 17.9 - - + +
286X ASP* 5.8 3.1 + - - -
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Residues in contact with ARG 274 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117X GLN* 2.6 54.2 + - - +
121X ASP* 3.6 32.2 + - - -
257X TRP 3.3 8.5 - - - +
258X TRP* 3.4 32.4 - - + +
272X ILE* 5.3 2.2 - - + -
273X LYS* 1.3 79.9 - - - +
275X LEU* 1.3 64.9 + - - +
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Residues in contact with LEU 275 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234X LEU* 3.6 19.1 - - + -
256X GLY* 3.8 1.7 - - - -
257X TRP* 2.8 62.2 + - + +
259X VAL* 3.7 26.7 - - + -
273X LYS 4.8 0.9 - - - +
274X ARG* 1.3 76.9 - - - +
276X THR* 1.3 78.0 + - - +
277X LEU* 4.7 2.0 - - + +
281X ALA* 4.0 13.5 - - + -
283X VAL* 3.3 30.3 - - + -
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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