Contacts of the strand formed by residues 270 - 276 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137D THR* 4.9 0.2 - - - +
263D VAL* 4.0 5.1 - - - +
264D GLY* 2.8 37.4 + - - +
265D GLY* 3.9 24.7 - - - +
268D VAL 3.5 2.4 - - - -
269D ASN* 1.3 85.4 - - - +
271D ILE* 1.3 67.0 + - - +
272D ASP* 3.0 34.5 + - - +
290D ASN* 3.6 6.6 + - + +
291M TYR* 4.1 20.2 + - - -
295M SER* 4.0 34.3 + - - +
299M PHE* 4.7 17.0 - - + -
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Residues in contact with ILE 271 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137D THR* 4.8 13.2 - - + +
140D LEU* 4.6 10.1 - - + -
261D VAL* 5.1 0.4 - - + -
262D ARG 3.8 2.7 - - - +
263D VAL* 4.4 19.5 - - + +
270D ARG* 1.3 73.8 - - - +
272D ASP* 1.3 61.7 + - - +
273D GLU 3.4 24.5 - - - +
274D TRP* 3.9 37.7 - - + -
286D ILE* 3.9 35.6 - - + +
290D ASN* 3.1 31.4 + - - +
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Residues in contact with ASP 272 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262D ARG* 2.8 36.8 + - + +
264D GLY* 3.4 21.9 + - - -
270D ARG* 3.0 42.2 + - - +
271D ILE* 1.3 76.7 - - - +
273D GLU* 1.3 72.8 - - + +
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Residues in contact with GLU 273 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248C LEU* 3.5 25.8 - - + +
260D THR* 4.1 10.8 - - + +
261D VAL* 3.6 5.7 - - - +
262D ARG* 3.2 39.6 + - + +
271D ILE* 3.4 9.2 - - - +
272D ASP* 1.3 86.8 - - - +
274D TRP* 1.3 65.1 + - - +
275D LYS* 3.5 34.4 + - - -
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Residues in contact with TRP 274 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140D LEU* 3.5 31.6 - - + -
141D VAL* 3.8 24.0 - - + -
144D ALA* 4.3 6.7 - - + -
149D ARG* 3.8 13.9 - - - -
260D THR 3.5 4.9 - - - -
261D VAL* 4.0 20.9 - - + +
271D ILE* 3.9 25.4 - - + -
273D GLU* 1.3 77.8 + - - +
275D LYS* 1.3 63.4 + - - +
276D PHE* 3.2 27.1 - + - -
282D ASP* 4.8 11.4 - - + -
283D ASP* 3.0 27.1 + - + +
286D ILE* 3.1 36.2 - - + +
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Residues in contact with LYS 275 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244C TYR* 4.0 19.2 + - + +
245C PRO* 4.0 26.7 - - + +
246C GLN* 5.1 11.5 + - - +
247C ASN 5.4 2.2 + - - -
248C LEU* 4.3 14.8 - - - +
259D GLY* 3.0 5.0 - - - -
260D THR* 3.0 40.3 + - - +
273D GLU* 3.5 33.4 + - - +
274D TRP* 1.3 78.8 - - - +
276D PHE* 1.3 65.6 + - - +
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Residues in contact with PHE 276 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244C TYR* 3.9 7.4 + - - -
144D ALA* 3.9 14.1 - - + -
149D ARG* 3.4 61.7 - - + +
150D PHE* 3.8 32.8 - + - -
258D LYS 3.3 5.8 - - - +
259D GLY* 3.7 8.5 - - - -
261D VAL* 3.4 23.6 - - + -
274D TRP* 3.2 41.9 - + - -
275D LYS* 1.3 75.0 - - - +
277D ALA* 1.3 64.6 + - - +
278D GLU 3.3 9.3 + - - +
279D PRO* 5.4 0.5 - - - +
283D ASP* 5.2 0.4 - - - +
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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