Contacts of the strand formed by residues 255 - 260 (chain K) in PDB entry 1DU3
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 255 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173K GLU* 3.0 29.2 + - + +
174K LEU 3.3 6.3 - - - +
175K VAL* 3.4 27.6 - - + -
212K LYS* 3.0 3.8 - - - -
213K TYR* 2.6 90.0 + - + +
214K THR 5.3 3.0 + - - -
253K ASN 3.9 13.4 + - - +
254K ASP* 1.3 77.8 - - - +
256K ILE* 1.3 62.6 + - - +
257K PHE* 4.6 2.4 - - - -
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Residues in contact with ILE 256 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167K LEU* 5.4 0.4 - - + -
173K GLU* 3.4 1.8 - - - -
174K LEU* 2.8 55.0 + - + +
176K ILE* 4.4 18.8 - - + -
184K ILE* 4.3 21.5 - - + -
210K ILE* 5.5 1.3 - - + -
211K TYR 3.3 13.5 - - - +
212K LYS* 3.9 12.3 - - + -
222K LEU* 4.5 2.0 - - + -
250K LEU* 4.1 21.3 - - + -
255K ARG* 1.3 77.9 - - - +
257K PHE* 1.3 62.3 + - - +
275K PHE* 3.6 17.2 - - + -
277K ALA* 4.1 24.5 - - + -
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Residues in contact with PHE 257 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146K ALA* 4.1 17.9 - - + -
150K LYS* 3.5 28.7 - - + -
172K GLY 3.9 7.9 - - - +
173K GLU* 3.7 20.9 - - + -
210K ILE* 3.5 3.3 - - - +
211K TYR* 2.9 74.9 + + + +
212K LYS 4.5 0.2 - - - -
213K TYR* 3.4 42.2 - + - -
219K PRO* 4.1 4.9 - - + -
255K ARG 4.6 2.7 - - - -
256K ILE* 1.3 76.4 - - - +
258K VAL* 1.3 70.0 + - - +
259K SER* 4.2 7.4 - - - -
275K PHE* 4.1 8.0 - - - -
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Residues in contact with VAL 258 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150K LYS* 3.6 1.4 - - - +
151K ILE* 3.1 40.2 + - + +
154K TRP* 4.3 12.1 - - + +
172K GLY 4.8 2.4 + - - -
186K SER* 3.6 24.2 - - - +
188K THR* 4.1 1.3 - - + -
208K GLN* 4.0 9.0 - - + -
209K TYR 3.3 10.8 - - - +
210K ILE* 4.1 7.4 - - + -
257K PHE* 1.3 83.0 - - - +
259K SER* 1.3 70.5 + - - +
260K VAL* 4.0 5.2 - - + -
275K PHE* 3.5 40.5 - - + -
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Residues in contact with SER 259 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146K ALA* 5.2 0.9 - - - -
147K LEU 2.4 30.2 + - - -
148K GLY 3.3 4.6 + - - -
149K ARG 3.2 12.3 - - - -
150K LYS* 3.7 9.2 - - - -
151K ILE 4.2 1.6 - - - +
209K TYR* 2.7 41.2 + - - +
211K TYR* 4.3 6.1 - - - -
257K PHE* 4.2 14.6 - - - -
258K VAL* 1.3 75.4 - - - +
260K VAL* 1.3 63.3 + - - +
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Residues in contact with VAL 260 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148K GLY* 4.0 1.8 - - - -
149K ARG* 2.8 36.4 + - - +
151K ILE* 3.4 30.3 - - + -
188K THR* 3.9 22.0 - - + +
190K PHE* 4.0 5.4 - - + -
207K VAL 3.3 13.2 - - - +
208K GLN* 4.5 2.5 - - - -
209K TYR* 4.5 1.3 - - - -
258K VAL* 4.0 2.5 - - + -
259K SER* 1.3 81.0 - - - +
261K THR* 1.3 75.0 + - - +
263K GLU* 3.9 14.6 + - + -
266K ILE* 3.9 21.3 - - + -
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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