Contacts of the strand formed by residues 261 - 267 (chain A) in PDB entry 3DK9
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 LEU 261 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173A LEU* 3.8 43.5 - - + +
254A VAL* 4.2 14.8 - - + -
255A LYS 3.3 13.5 - - - +
256A LYS* 3.9 16.4 - - + -
257A THR* 3.7 6.1 - - - -
259A SER 3.3 0.6 + - - -
260A GLY* 1.3 80.8 - - - +
262A GLU* 1.3 60.8 + - - +
263A VAL* 4.1 2.0 - - + -
280A PRO 3.7 0.2 - - - -
281A ASP 3.2 8.7 + - - -
282A VAL* 2.8 43.0 + - + +
283A ASP 4.9 5.2 - - - +
285A LEU* 3.9 31.2 - - + +
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Residues in contact with GLU 262 (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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253A GLU 4.0 0.2 - - - +
254A VAL* 3.4 5.0 - - - +
255A LYS* 2.9 57.7 + - + +
257A THR* 3.7 19.7 - - + +
261A LEU* 1.3 73.3 - - - +
263A VAL* 1.3 62.9 + - - +
264A SER* 3.9 3.6 + - - +
278A MET* 3.3 54.2 - - + +
279A ILE 3.3 10.3 - - - +
280A PRO* 4.5 7.0 - - + +
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Residues in contact with VAL 263 (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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191A VAL* 5.1 2.5 - - + -
216A MET* 4.3 12.3 - - + -
251A VAL* 3.9 35.0 - - + -
253A GLU 3.8 2.9 - - - +
254A VAL* 4.5 5.4 - - + +
261A LEU* 4.8 1.8 - - + -
262A GLU* 1.3 76.8 - - - +
264A SER* 1.3 64.9 + - - +
265A MET 3.7 0.5 + - - -
277A THR 3.7 1.0 - - - +
278A MET* 3.5 1.4 - - - -
279A ILE* 2.8 48.9 + - + +
282A VAL* 4.2 24.5 - - + -
285A LEU* 4.3 28.9 - - + -
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Residues in contact with SER 264 (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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251A VAL* 3.5 4.7 - - - +
252A LYS* 2.8 30.6 + - - -
253A GLU* 2.9 37.9 + - - +
255A LYS* 5.7 1.9 - - - +
262A GLU* 3.9 5.1 + - - +
263A VAL* 1.3 71.5 - - - +
265A MET* 1.3 54.1 + - - +
276A MET* 3.7 22.7 - - - -
277A THR 3.8 4.3 - - - -
278A MET* 3.1 28.2 - - - +
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Residues in contact with MET 265 (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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216A MET* 3.8 24.2 - - + -
246A LEU* 3.9 24.7 - - + -
249A SER* 3.7 27.1 - - - +
250A GLN 3.3 11.2 - - - +
251A VAL* 4.6 0.2 - - - +
263A VAL* 5.1 0.2 - - + -
264A SER* 1.3 73.2 - - - +
266A VAL* 1.3 60.9 + - - +
267A THR* 3.9 16.8 - - - +
275A VAL 3.8 0.2 - - - +
276A MET* 3.2 9.2 - - - +
277A THR* 2.9 61.2 + - + +
279A ILE* 4.0 20.9 - - + -
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Residues in contact with VAL 266 (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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248A PHE 3.7 1.2 - - - +
249A SER* 3.3 2.3 - - - -
250A GLN* 2.9 46.7 + - + +
252A LYS* 3.3 42.8 - - + +
264A SER 4.4 0.4 + - - -
265A MET* 1.3 73.3 - - - +
267A THR* 1.3 70.4 + - - +
268A ALA* 4.3 4.7 + - + +
274A PRO* 4.6 14.6 - - + -
275A VAL 3.4 10.5 - - - +
276A MET* 4.5 5.2 - - + +
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Residues in contact with THR 267 (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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247A LYS 3.6 11.7 - - - +
248A PHE 3.2 3.6 - - - -
249A SER* 2.8 23.8 + - - +
265A MET* 3.9 15.9 - - - +
266A VAL* 1.3 73.5 - - - +
268A ALA* 1.4 62.4 + - - +
269A VAL* 3.9 18.3 + - + -
273A LEU 4.2 0.7 - - - +
274A PRO* 3.3 2.9 - - - +
275A VAL* 2.8 50.2 + - + +
277A THR* 4.9 2.7 + - - -
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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