Contacts of the strand formed by residues 270 - 276 (chain G) in PDB entry 3Q2K
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 ARG 270 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137G THR* 4.2 0.2 - - - +
263G VAL* 4.2 2.2 - - - -
264G GLY* 2.8 32.3 + - - +
265G GLY* 3.6 26.8 - - - +
268G VAL 3.7 1.0 - - - -
269G ASN* 1.3 88.0 - - - +
271G ILE* 1.3 64.8 + - - +
272G ASP* 2.6 40.4 + - - +
290G ASN* 3.7 23.1 - - + +
294G THR* 4.6 1.8 - - - +
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Residues in contact with ILE 271 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137G THR* 4.1 29.7 - - + +
140G LEU* 4.2 11.4 - - + -
141G VAL* 4.9 0.7 - - + -
261G VAL* 5.3 0.4 - - + -
262G ARG 3.7 5.4 - - - +
263G VAL* 4.1 13.2 - - + +
270G ARG* 1.3 68.8 - - - +
272G ASP* 1.3 63.4 + - - +
273G GLU 3.9 17.7 - - - +
274G TRP* 3.8 39.9 - - + -
286G ILE* 3.9 28.4 - - + +
289G ALA* 5.0 0.7 - - + -
290G ASN* 2.8 36.1 + - - +
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Residues in contact with ASP 272 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262G ARG* 2.7 31.3 + - + -
264G GLY* 3.8 10.0 - - - -
270G ARG* 2.6 56.8 + - - +
271G ILE* 1.3 74.9 - - - +
273G GLU* 1.3 70.9 + - + +
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Residues in contact with GLU 273 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260G THR* 4.0 7.2 - - + +
261G VAL* 3.2 7.6 - - - +
262G ARG* 2.7 48.9 + - + +
271G ILE* 3.9 3.3 - - - +
272G ASP* 1.3 86.3 - - - +
274G TRP* 1.3 61.0 + - - +
275G LYS* 3.4 35.7 + - + -
248H LEU* 3.8 23.6 - - + +
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Residues in contact with TRP 274 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140G LEU* 3.9 30.5 - - + -
141G VAL* 4.0 19.7 - - + -
144G ALA* 4.3 5.8 - - + -
149G ARG* 3.5 22.0 - - - -
260G THR 3.6 3.8 + - - -
261G VAL* 3.8 20.9 - - + -
271G ILE* 3.8 34.3 - - + -
273G GLU* 1.3 76.3 + - - +
275G LYS* 1.3 65.0 + - - +
276G PHE* 3.5 20.3 - + + -
282G ASP* 5.1 4.7 - - + -
283G ASP* 3.1 31.8 + - + +
286G ILE* 3.2 32.7 - - + +
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Residues in contact with LYS 275 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259G GLY* 3.3 4.3 - - - -
260G THR* 2.9 45.1 + - + +
273G GLU* 3.4 29.3 + - + -
274G TRP* 1.3 82.3 - - - +
276G PHE* 1.3 66.6 + - - +
244H TYR* 4.1 18.3 + - + +
245H PRO* 4.4 20.5 - - + +
246H GLN* 5.4 7.9 + - - +
247H ASN 5.4 1.8 + - - -
248H LEU* 3.4 23.8 - - - +
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Residues in contact with PHE 276 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144G ALA* 3.9 13.0 - - + -
149G ARG* 3.2 64.6 - - + +
150G PHE* 3.8 15.7 - + - -
258G LYS 3.5 8.5 - - - -
259G GLY* 3.6 12.8 - - - -
261G VAL* 3.7 27.6 - - + -
274G TRP* 3.5 43.5 - + - -
275G LYS* 1.3 75.6 - - - +
277G ALA* 1.3 65.0 + - - +
278G GLU 3.4 7.8 + - - +
279G PRO* 5.8 0.9 - - - +
283G ASP* 5.4 2.2 - - - +
244H TYR* 3.6 10.4 + - - -
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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