Contacts of the strand formed by residues 255 - 261 (chain B) in PDB entry 2DFD
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 VAL 255 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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239B ARG* 5.1 1.7 + - - -
243B SER* 5.3 0.2 + - - -
253B GLY* 3.5 12.1 + - - +
254B VAL* 1.3 80.1 - - - +
256B GLU* 1.3 75.9 + - - +
273B PRO* 3.8 27.4 - - + -
274B LEU 3.1 10.5 - - - +
275B LEU* 4.0 11.9 - - + -
285B LEU* 3.8 24.0 - - + -
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Residues in contact with GLU 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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153B THR* 4.6 6.8 + - - +
156B ILE* 5.4 2.4 - - - +
239B ARG* 2.9 47.5 + - - +
240B PHE* 3.7 32.0 - - + -
243B SER* 2.9 39.6 + - - -
254B VAL 4.3 0.2 - - - -
255B VAL* 1.3 80.2 - - - +
257B CYS* 1.3 63.9 + - - +
258B SER* 4.7 0.3 - - - -
273B PRO* 4.2 1.1 - - - -
274B LEU* 2.9 35.5 + - - +
276B LEU* 4.4 9.7 - - + +
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Residues in contact with CYS 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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152B THR* 3.5 7.9 + - - -
153B THR* 4.4 8.1 + - - -
156B ILE* 3.8 23.4 - - + +
177B PRO* 4.1 6.3 - - - -
178B VAL 3.4 42.6 - - - +
240B PHE* 4.2 3.8 - - - -
255B VAL* 5.2 0.4 - - - +
256B GLU* 1.3 81.7 + - - +
258B SER* 1.3 61.6 + - - +
271B SER* 3.9 4.0 - - - +
272B THR 3.3 8.1 - - - +
273B PRO* 3.9 28.3 - - - -
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Residues in contact with SER 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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149B PHE* 3.5 28.7 - - - +
150B GLY 2.9 19.3 + - - -
151B VAL* 4.6 0.3 - - - -
152B THR* 3.6 6.1 - - - -
240B PHE* 3.9 12.8 - - - -
256B GLU 3.8 0.6 + - - -
257B CYS* 1.3 74.5 - - - +
259B PHE* 1.3 61.9 + - - +
260B VAL* 3.3 12.4 + - - +
270B PHE 3.6 1.4 - - - +
271B SER* 3.1 24.8 + - - -
272B THR 3.4 7.4 + - - +
274B LEU* 3.7 18.3 - - - +
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Residues in contact with PHE 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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126B VAL* 3.7 25.1 - - + -
127B ASN* 3.7 32.8 - - + -
130B ILE* 3.8 24.2 - - + +
131B PRO* 4.3 0.9 - - + -
149B PHE* 3.8 0.7 - - - -
150B GLY* 2.8 44.8 + - - +
152B THR* 3.9 13.8 - - + +
180B GLY 3.4 26.0 - - - -
181B GLY* 4.1 6.5 - - - -
258B SER* 1.3 69.1 + - - +
260B VAL* 1.3 59.1 + - - +
269B TYR* 3.6 40.4 - - + -
270B PHE* 3.7 2.0 - - - -
271B SER* 3.7 8.8 + - - -
305B LEU* 4.2 10.3 - - + -
309B ILE* 4.7 3.8 - - + -
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Residues in contact with VAL 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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130B ILE* 4.9 1.8 - - - -
145B PRO 5.2 0.2 - - - +
148B ILE 3.7 19.5 - - - +
149B PHE* 3.8 13.7 - - + -
258B SER* 3.7 9.0 - - - +
259B PHE* 1.3 80.1 - - - +
261B LYS* 1.3 74.9 - - - +
262B SER* 4.7 0.2 - - - -
269B TYR* 3.2 7.1 - - - -
270B PHE 2.9 39.3 + - - +
274B LEU* 3.5 42.4 - - + -
281B ILE* 3.9 13.5 - - + -
284B ASN* 4.3 6.7 - - - +
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Residues in contact with LYS 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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130B ILE* 5.1 0.8 - - - +
138B LYS* 6.0 2.7 - - - +
143B TYR* 3.4 30.1 - - + +
145B PRO* 4.1 26.4 + - + +
148B ILE 5.0 1.2 + - - -
260B VAL* 1.3 80.9 - - - +
262B SER* 1.3 68.4 + - - +
263B GLN* 2.8 32.8 + - - +
268B THR* 2.9 42.2 + - - +
269B TYR* 3.6 19.7 - - + +
281B ILE* 5.2 3.1 - - - +
284B ASN* 4.7 2.4 + - - -
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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