Contacts of the strand formed by residues 269 - 277 (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 TYR 269 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B ILE* 3.7 19.5 - - + -
131B PRO* 3.9 17.6 + - + +
134B ALA* 3.2 33.2 - - + +
135B GLU* 4.5 4.5 + - - +
138B LYS* 4.4 11.8 + - - -
143B TYR* 4.1 6.2 + - - -
148B ILE* 6.4 0.2 - - + -
259B PHE* 3.6 28.8 - - + -
260B VAL 3.2 6.5 - - - +
261B LYS* 3.6 37.3 - - + +
262B SER 4.1 0.2 - - - +
267B CYS* 3.4 14.8 - - - +
268B THR* 1.3 102.2 - - + +
270B PHE* 1.3 66.9 + - - +
305B LEU* 4.9 1.4 - - - +
309B ILE* 3.6 19.0 - - + +
313B GLU* 4.0 13.8 + - - -
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Residues in contact with PHE 270 (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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179B ILE* 4.4 7.2 - - + -
180B GLY* 3.7 26.5 - - - -
188B ILE* 5.0 3.1 - - + -
259B PHE* 3.7 8.2 - - - -
260B VAL* 2.9 32.0 + - - +
262B SER* 3.6 21.4 - - - +
264B GLU* 4.8 1.1 - - + -
265B THR* 3.8 38.1 - - + +
267B CYS* 4.1 10.1 - - + +
269B TYR* 1.3 74.8 - - - +
271B SER* 1.3 85.3 + - - +
272B THR* 3.8 19.9 + - + -
287B ILE* 4.1 13.7 - - + -
298B ILE* 4.5 14.1 - - + -
301B ALA* 6.1 0.7 - - + -
302B ILE* 5.2 2.7 - - + -
305B LEU* 3.8 22.2 - - + -
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Residues in contact with SER 271 (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* 3.6 14.5 + - - -
178B VAL 3.8 11.7 + - - -
179B ILE* 3.1 11.9 - - - +
180B GLY 2.8 46.2 + - - -
181B GLY 5.6 0.7 - - - -
257B CYS* 3.9 0.2 - - - +
258B SER* 3.1 36.0 + - - -
259B PHE* 3.7 8.7 - - - -
270B PHE* 1.3 76.8 - - - +
272B THR* 1.3 59.1 + - - +
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Residues in contact with THR 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B ILE* 4.1 4.9 - - + +
257B CYS* 3.3 19.1 - - - -
258B SER 3.4 3.7 + - - -
262B SER* 5.0 0.5 + - - -
264B GLU* 4.1 5.9 - - + +
270B PHE* 3.8 23.1 + - + -
271B SER* 1.3 78.3 - - - +
273B PRO* 1.4 74.6 - - + +
274B LEU* 3.3 12.5 - - - +
284B ASN* 2.4 37.5 + - - +
286B GLY* 3.6 26.2 - - - +
287B ILE* 3.9 9.0 - - + +
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Residues in contact with PRO 273 (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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177B PRO* 4.4 15.5 - - + -
179B ILE* 4.0 13.5 - - + -
190B LEU* 6.0 0.4 - - + -
193B GLN* 5.4 3.6 - - - +
255B VAL* 3.8 17.7 - - + -
256B GLU 3.9 4.7 - - - +
257B CYS* 3.9 19.5 - - - +
272B THR* 1.4 90.0 - - - +
274B LEU* 1.3 61.5 + - - +
284B ASN* 3.8 1.4 - - - +
285B LEU* 3.1 35.6 + - + +
286B GLY 3.5 15.3 - - - +
287B ILE 5.8 0.4 - - - +
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Residues in contact with LEU 274 (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* 4.3 4.7 - - + -
255B VAL* 3.1 8.9 - - - -
256B GLU 2.9 33.2 + - - +
258B SER* 3.7 19.3 - - - +
260B VAL* 3.5 38.4 - - + -
272B THR* 3.3 14.1 - - - +
273B PRO* 1.3 81.9 - - - +
275B LEU* 1.3 61.1 + - - +
276B LEU* 3.5 14.0 + - + +
281B ILE* 4.2 21.5 - - + -
283B LYS 3.5 3.6 - - - +
284B ASN* 3.6 34.5 - - + +
285B LEU* 4.5 0.2 - - - -
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Residues in contact with LEU 275 (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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253B GLY* 3.8 28.0 - - - +
254B VAL 3.4 17.0 - - - +
255B VAL* 4.0 9.9 - - + -
274B LEU* 1.3 71.7 - - - +
276B LEU* 1.3 58.9 + - - +
281B ILE* 3.7 2.6 - - - -
282B GLU* 2.7 45.7 + - + -
283B LYS* 2.7 33.5 + - + +
285B LEU* 4.1 18.7 - - + +
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Residues in contact with LEU 276 (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* 3.9 29.2 - - + -
240B PHE* 4.8 7.2 - - + -
243B SER 4.2 0.4 - - - -
244B LEU* 4.0 34.8 - - + +
247B ALA* 3.6 18.8 - - + +
251B LYS 4.7 4.9 - - - +
253B GLY 5.6 0.5 + - - -
254B VAL* 2.8 31.7 + - + +
256B GLU* 4.4 19.7 - - + +
274B LEU* 4.1 18.6 - - + +
275B LEU* 1.3 85.5 - - - +
277B GLY* 1.3 59.6 + - - +
280B GLY 3.4 11.7 - - - +
281B ILE* 4.2 5.4 - - - -
282B GLU* 3.7 5.0 - - - +
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Residues in contact with GLY 277 (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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244B LEU* 5.4 0.9 - - - +
247B ALA* 3.6 23.0 - - - +
248B MET* 4.0 4.9 + - - +
251B LYS 5.4 1.3 - - - -
276B LEU* 1.3 75.7 - - - +
278B LYS* 1.3 65.4 + - - -
279B LYS 3.1 4.5 + - - -
280B GLY* 2.8 18.0 + - - +
282B GLU* 3.4 18.0 - - - +
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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