Contacts of the helix formed by residues 268 - 280 (chain B) in PDB entry 3DVA
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 268 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B GLU* 4.5 2.2 - - + +
134B GLY* 4.1 7.6 - - - +
137B ALA* 3.7 30.7 - - + -
209B TYR* 3.6 29.1 + - + +
235B LEU* 3.8 14.6 - - + -
238B VAL* 3.8 29.8 - - + +
239B GLN* 6.0 0.2 - - - +
241B LEU* 4.7 2.7 - - + -
258B VAL* 5.4 1.3 - - + -
260B GLN* 3.1 2.6 + - - -
267B GLY* 1.3 78.8 - - - +
269B ALA* 1.3 68.0 + - - +
270B ALA* 3.3 3.1 - - - -
271B ASN* 3.2 14.6 + - + +
272B VAL* 3.2 35.4 + - + +
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Residues in contact with ALA 269 (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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209B TYR* 5.9 0.2 - - + -
258B VAL* 3.6 29.8 - - + +
260B GLN* 3.2 28.7 + - + +
266B ALA 4.8 0.2 + - - -
267B GLY 3.7 1.0 - - - -
268B ILE* 1.3 81.5 - - - +
270B ALA* 1.3 57.1 + - - +
272B VAL* 3.1 4.4 + - - +
273B VAL* 2.9 32.9 + - - +
290B ARG* 3.8 23.1 - - + +
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Residues in contact with ALA 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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264B ARG 5.7 1.8 - - - +
266B ALA 5.5 4.1 + - - +
267B GLY 5.5 0.2 - - - -
268B ILE* 3.3 1.2 - - - -
269B ALA* 1.3 77.5 - - - +
271B ASN* 1.3 57.7 + - - +
273B VAL* 3.3 5.5 + - - +
274B ALA* 2.9 30.8 + - - +
290B ARG* 4.0 26.0 - - - +
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Residues in contact with ASN 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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238B VAL 5.6 0.2 + - - -
239B GLN* 4.7 14.3 - - - +
241B LEU* 3.8 20.8 - - - +
268B ILE* 3.2 17.6 + - + +
270B ALA* 1.3 78.6 - - - +
272B VAL* 1.3 62.4 + - - +
274B ALA* 3.4 7.0 + - - +
275B GLU* 3.0 43.8 + - - +
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Residues in contact with VAL 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B ILE* 4.2 14.4 - - + -
235B LEU* 4.4 6.3 - - + -
241B LEU* 3.6 25.8 - - + -
246B ILE* 4.5 12.6 - - + -
258B VAL* 3.9 24.0 - - + -
268B ILE* 3.2 34.3 - - + +
269B ALA* 3.1 8.5 + - - +
271B ASN* 1.3 77.4 - - - +
273B VAL* 1.3 61.9 + - - +
275B GLU* 3.3 3.7 + - - +
276B ILE* 3.1 34.2 + - + +
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Residues in contact with VAL 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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258B VAL* 3.8 15.5 - - + -
269B ALA 2.9 20.0 + - - +
270B ALA* 3.6 6.5 - - - +
272B VAL* 1.3 77.0 - - - +
274B ALA* 1.3 55.2 + - - +
276B ILE* 3.9 5.5 - - - +
277B ASN* 2.7 56.2 + - - +
288B VAL* 3.9 28.3 - - + +
290B ARG* 3.7 29.8 - - + +
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Residues in contact with ALA 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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270B ALA 2.9 17.8 + - - +
271B ASN* 3.7 10.5 - - - +
273B VAL* 1.3 76.9 - - - +
275B GLU* 1.3 63.5 + - + +
277B ASN* 3.7 6.4 + - - +
278B GLU* 3.4 26.4 + - - +
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Residues in contact with GLU 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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241B LEU* 4.6 4.0 - - + -
243B ILE* 4.1 22.9 - - + -
246B ILE* 6.4 0.9 - - + -
247B ILE* 4.6 1.3 - - + -
271B ASN* 3.0 39.8 + - - +
272B VAL* 3.7 5.8 - - - +
274B ALA* 1.3 77.1 - - + +
276B ILE* 1.3 60.4 + - + +
278B GLU* 3.4 10.8 + - - +
279B ARG* 2.5 80.5 + - - +
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Residues in contact with ILE 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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207B ILE* 3.8 29.6 - - + -
246B ILE* 3.9 18.6 - - + -
247B ILE* 3.9 12.3 - - + -
250B VAL* 3.9 33.2 - - + -
256B ALA* 4.5 1.6 - - + -
258B VAL* 4.8 0.2 - - + -
272B VAL* 3.1 22.4 + - + +
273B VAL 3.9 3.4 - - - +
275B GLU* 1.3 73.9 - - + +
277B ASN* 1.3 58.4 + - - +
278B GLU 3.0 5.4 + - - -
280B ALA* 3.0 31.4 + - + -
284B LEU* 4.3 5.8 - - + +
288B VAL* 4.0 33.2 - - + -
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Residues in contact with ASN 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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273B VAL* 2.7 40.9 + - - +
274B ALA* 4.1 7.5 + - - +
276B ILE* 1.3 74.7 - - - +
278B GLU* 1.3 55.6 + - - +
281B ILE* 3.1 31.6 - - + +
284B LEU* 3.3 27.3 - - - +
287B PRO* 5.7 0.8 - - - +
288B VAL* 3.8 15.4 + - - +
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Residues in contact with GLU 278 (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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274B ALA 3.4 18.0 + - - +
275B GLU* 3.8 15.6 - - - +
276B ILE 3.0 0.6 - - - -
277B ASN* 1.3 80.8 - - - +
279B ARG* 1.3 79.0 + - + +
280B ALA 3.6 0.2 - - - -
281B ILE* 4.4 9.6 - - - +
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Residues in contact with ARG 279 (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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353A PHE* 4.9 0.6 - - - -
357A GLU* 2.7 44.4 + - - -
243B ILE* 3.4 40.1 - - - +
247B ILE* 4.0 19.4 - - + +
251B GLU* 5.2 2.6 - - - +
275B GLU* 2.5 48.8 + - - +
278B GLU* 1.3 94.0 + - + +
280B ALA* 1.3 60.2 + - - +
281B ILE* 3.7 1.3 - - - -
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Residues in contact with ALA 280 (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* 4.0 26.0 - - + -
250B VAL* 4.4 17.0 - - + -
251B GLU* 4.5 5.8 - - + -
276B ILE 3.0 13.3 + - - +
279B ARG* 1.3 79.7 - - - +
281B ILE* 1.3 55.8 + - - +
282B LEU* 3.0 7.9 - - - +
283B SER* 3.1 27.8 + - - +
284B LEU* 3.5 14.6 + - - +
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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