Contacts of the strand formed by residues 255 - 261 (chain B) in PDB entry 2QCU
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 ILE 255 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B ARG* 3.6 36.1 - - + +
96B ARG* 4.8 5.2 - - - +
247B ILE* 3.7 25.1 - - + -
248B LEU 3.1 11.2 - - - +
249B GLN* 4.4 9.4 - - + -
253B LYS 4.9 2.0 - - - +
254B ARG* 1.3 89.5 + - - +
256B VAL* 1.3 65.9 + - - +
257B PHE* 3.4 38.1 - - + -
269B GLY 4.9 0.2 - - - +
270B THR 4.9 2.8 + - - -
816B EDO 3.9 25.4 - - - +
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Residues in contact with VAL 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247B ILE* 3.7 0.4 - - - -
248B LEU* 2.7 42.7 + - + +
250B ASN* 4.8 3.1 - - + +
254B ARG* 4.1 3.1 - - - +
255B ILE* 1.3 79.9 - - - +
257B PHE* 1.3 72.2 + - - +
268B ILE* 3.9 8.5 - - + -
269B GLY 3.6 10.8 - - - +
270B THR 3.8 17.0 - - - +
291B TYR* 3.9 21.8 - - + +
292B LEU* 3.7 14.6 - - + -
295B VAL* 3.7 33.4 - - + -
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Residues in contact with PHE 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B SER* 4.6 14.1 - - - -
48B LEU* 3.7 32.3 - - + -
50B HIS* 4.8 15.7 - + - -
87B PHE* 4.2 15.9 - + - -
141B TYR* 4.7 2.2 - - - -
246B TYR 3.3 4.9 - - - -
247B ILE* 3.6 35.0 - - + -
255B ILE* 3.4 25.4 - - + -
256B VAL* 1.3 73.4 - - - +
258B VAL* 1.3 62.6 + - - +
259B ILE* 3.7 20.0 - - + -
267B ILE 3.6 0.4 - - - +
268B ILE* 3.2 9.9 - - - +
269B GLY 2.7 44.3 + - - +
270B THR 5.1 0.4 - - - -
803B PO4 5.5 5.8 - - - -
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Residues in contact with VAL 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239B VAL* 3.9 27.8 - - + -
240B HIS* 4.9 5.2 + - - +
244B GLN 4.5 0.5 - - - +
245B ALA* 3.3 4.5 - - - -
246B TYR* 2.8 40.6 + - + +
248B LEU* 3.7 28.9 - - + -
257B PHE* 1.3 75.8 - - - +
259B ILE* 1.3 60.2 + - - +
260B PRO* 3.9 1.4 - - - +
266B SER* 4.3 7.0 - - - +
267B ILE 3.4 4.0 - - - -
268B ILE* 4.2 20.9 - - + -
296B TYR* 4.2 10.3 - - + -
300B PHE* 4.1 15.7 - - + -
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Residues in contact with ILE 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B SER* 3.6 28.5 - - - +
48B LEU* 4.1 13.9 - - + -
85B MET* 4.0 9.9 - - - -
145B TRP* 3.8 26.0 - - + +
233B HIS* 5.8 0.7 - - + -
245B ALA* 4.2 8.7 - - + -
257B PHE* 3.7 27.6 - - + -
258B VAL* 1.3 76.5 - - - +
260B PRO* 1.3 83.4 - - + +
261B TRP* 5.6 0.2 - - - -
266B SER* 3.2 4.3 - - - -
267B ILE* 2.8 56.7 + - + +
269B GLY 6.1 0.2 - - - +
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Residues in contact with PRO 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B MET* 4.2 14.3 - - + +
145B TRP* 4.8 1.4 + - - -
238B ARG* 5.3 8.7 - - + -
240B HIS* 5.3 4.3 - - + -
242B GLN 4.0 10.8 - - - +
243B LYS* 3.5 27.8 - - - +
244B GLN 3.6 19.5 - - - +
245B ALA* 3.7 10.8 - - + +
258B VAL 3.9 1.3 - - - +
259B ILE* 1.3 99.7 - - + +
261B TRP* 1.3 59.3 + - - +
262B MET 4.3 0.2 - - - -
263B ASP* 6.0 2.2 - - - +
265B PHE 3.7 7.6 - - - +
266B SER* 4.5 4.0 - - - +
808B EDO 4.3 5.1 + - - -
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Residues in contact with TRP 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B LYS* 4.9 6.1 - - - +
145B TRP* 3.7 34.0 - + - -
235B VAL* 3.7 36.8 - - + -
259B ILE* 4.1 1.6 - - + +
260B PRO* 1.3 74.7 - - - +
262B MET* 1.3 107.1 + - + +
263B ASP 3.1 2.1 - - - +
265B PHE* 2.9 44.0 + - + +
267B ILE* 3.4 35.8 - - + +
311B TRP* 3.7 22.2 - + - -
472B LYS* 3.7 34.8 - - + +
475B MET* 3.9 18.8 - - + -
808B EDO 3.8 2.9 - - - -
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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