Contacts of the strand formed by residues 259 - 264 (chain B) 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 GLY 259 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244A TYR* 3.8 4.1 - - - +
150B PHE* 3.6 14.8 + - - -
256B GLY 2.8 36.6 + - - +
258B LYS* 1.3 80.9 - - - +
260B THR* 1.3 64.5 + - - -
275B LYS 3.2 11.2 - - - -
276B PHE* 3.9 11.9 - - - -
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Residues in contact with THR 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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243A THR* 4.1 1.3 - - + +
244A TYR 2.8 33.4 + - - +
248A LEU* 4.1 28.9 - - + -
150B PHE* 4.1 1.2 - - - -
254B ILE 3.6 4.7 - - - -
255B LEU* 3.8 21.8 - - + +
259B GLY* 1.3 77.3 + - - -
261B VAL* 1.3 64.3 + - - +
262B ARG* 6.2 0.2 - - + -
273B GLU* 4.4 9.4 - - + -
274B TRP* 3.7 4.3 + - - -
275B LYS* 2.9 38.4 + - + -
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Residues in contact with VAL 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B VAL* 4.1 9.4 - - + -
150B PHE* 3.3 30.3 - - + -
252B ILE* 5.3 0.9 - - + +
253B THR* 3.4 5.6 - - - +
254B ILE* 2.9 36.5 + - + +
260B THR* 1.3 81.5 - - - +
262B ARG* 1.3 68.2 + - - +
263B VAL* 4.0 20.0 - - + -
271B ILE* 5.3 0.4 - - + -
273B GLU* 3.4 12.1 - - - +
274B TRP* 3.8 26.0 - - + -
276B PHE* 3.5 20.4 - - + -
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Residues in contact with ARG 262 (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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159A ASN* 3.8 11.5 - - - +
161A PHE* 4.2 7.5 - - - -
248A LEU* 5.0 10.2 - - + +
249A GLU* 2.3 38.2 + - - +
262A ARG* 4.3 10.3 - - - +
249B GLU* 5.9 0.6 + - - -
251B SER* 5.4 4.7 + - - -
252B ILE 3.4 7.4 - - - +
253B THR* 3.0 30.6 + - + +
260B THR* 6.2 0.2 - - + -
261B VAL* 1.3 77.9 - - - +
263B VAL* 1.3 65.5 + - - +
264B GLY* 4.3 2.2 - - - +
271B ILE* 3.9 1.0 - - - -
272B ASP* 2.9 47.3 + - + +
273B GLU* 3.3 29.5 + - + +
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Residues in contact with VAL 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B THR* 3.7 15.3 - - - +
138B LEU* 5.0 2.5 - - + -
141B VAL* 3.6 31.2 - - + -
251B SER* 3.0 7.4 - - - -
252B ILE* 2.9 47.8 + - + -
261B VAL* 4.0 8.7 - - + -
262B ARG* 1.3 71.9 - - - +
264B GLY* 1.3 59.5 + - - +
268B VAL* 3.3 39.5 - - + +
270B ARG 3.7 10.3 - - - +
271B ILE* 4.5 11.4 - - + +
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Residues in contact with GLY 264 (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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249B GLU* 5.7 0.4 - - - -
250B GLY 4.0 1.8 - - - -
251B SER* 3.7 13.5 - - - -
262B ARG* 3.8 5.7 + - - -
263B VAL* 1.3 72.9 - - - +
265B GLY* 1.3 62.8 + - - -
268B VAL* 3.4 4.0 - - - -
269B ASN 3.3 10.7 + - - -
270B ARG* 2.9 32.7 + - - -
272B ASP* 3.6 14.7 + - - -
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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