Contacts of the helix formed by residues 257 - 277 (chain B) in PDB entry 3V4R
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 GLU 257 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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256B MET* 1.3 74.7 - - - +
258B LYS* 1.4 60.6 + - - +
260B ILE* 3.4 11.5 + - - +
261B GLN* 3.1 26.7 + - - +
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Residues in contact with LYS 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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256B MET 3.4 2.3 - - - +
257B GLU* 1.4 73.1 - - - +
259B ALA* 1.4 58.8 + - - +
261B GLN* 3.4 9.2 + - - +
262B ASN* 2.9 38.4 + - - +
315B LEU* 3.9 22.2 - - + -
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Residues in contact with ALA 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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256B MET* 3.4 19.2 + - - +
257B GLU 3.3 0.2 - - - -
258B LYS* 1.4 77.2 - - - +
260B ILE* 1.4 57.4 - - + +
262B ASN* 3.1 9.1 + - - +
263B ILE* 3.0 37.7 + - + +
312B HIS* 3.3 32.5 - - + +
313B LEU* 4.0 11.7 - - + +
315B LEU* 4.7 6.0 - - + +
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Residues in contact with ILE 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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256B MET* 3.2 23.2 + - + +
257B GLU* 3.4 10.5 + - - +
259B ALA* 1.4 75.7 - - + +
261B GLN* 1.4 61.0 + - - +
263B ILE* 3.5 2.9 + - + -
264B GLU* 3.3 23.1 + - + +
294B LEU* 3.7 28.1 - - + +
297B MET* 4.3 34.3 - - + +
298B ARG* 3.7 53.6 - - + +
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Residues in contact with GLN 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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257B GLU 3.1 13.4 + - - +
258B LYS* 3.5 12.8 - - - +
260B ILE* 1.4 76.0 - - - +
262B ASN* 1.4 59.8 - - - +
264B GLU* 3.5 7.0 + - - +
265B LYS* 3.1 26.4 + - - +
298B ARG* 5.5 2.9 - - - +
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Residues in contact with ASN 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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258B LYS* 2.9 28.3 + - - +
259B ALA* 3.1 8.0 + - - +
261B GLN* 1.4 76.3 - - - +
263B ILE* 1.4 62.7 + - - +
265B LYS* 3.4 9.3 + - - +
266B GLU* 3.1 17.3 + - - +
312B HIS* 3.6 27.4 + - + +
315B LEU* 4.8 12.3 - - - +
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Residues in contact with ILE 263 (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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259B ALA* 3.0 27.9 + - + +
260B ILE* 3.9 6.1 - - + +
261B GLN 3.5 0.4 - - - -
262B ASN* 1.4 71.3 - - - +
264B GLU* 1.4 54.8 + - - +
266B GLU* 2.9 7.6 + - - +
267B LEU* 2.8 31.9 + - - +
290B THR* 3.9 13.0 - - + -
294B LEU* 3.8 24.2 - - + -
297B MET* 4.5 8.5 - - + -
309B TYR* 3.8 30.7 - - + -
312B HIS* 3.6 35.4 - - + -
313B LEU 5.7 0.2 - - - +
368B LEU* 3.9 22.8 - - + +
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Residues in contact with GLU 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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260B ILE* 3.3 12.2 + - + +
261B GLN* 3.6 10.1 - - - +
263B ILE* 1.4 77.6 - - - +
265B LYS* 1.3 56.0 + - - +
267B LEU* 3.6 9.4 - - - +
268B GLU* 3.0 31.5 + - - +
291B ARG* 4.3 23.3 + - - +
294B LEU* 4.8 5.6 - - + +
298B ARG* 6.0 3.4 - - - +
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Residues in contact with LYS 265 (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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261B GLN 3.1 14.0 + - - +
262B ASN* 3.4 15.7 - - - +
263B ILE 3.2 0.2 - - - -
264B GLU* 1.3 76.0 - - - +
266B GLU* 1.4 59.1 + - - +
268B GLU* 3.7 5.5 + - - +
269B GLU* 3.3 21.8 + - - +
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Residues in contact with GLU 266 (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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262B ASN 3.1 11.7 + - - +
263B ILE* 2.9 8.9 + - - +
265B LYS* 1.4 72.9 - - - +
267B LEU* 1.4 59.6 + - - +
269B GLU* 3.4 7.2 + - + +
270B GLN* 2.9 28.1 + - + +
311B ARG* 4.1 6.7 + - - +
312B HIS* 3.1 15.1 + - + +
368B LEU* 3.4 25.9 - - + +
369B PRO* 3.6 12.6 - - + +
370B SER* 2.7 48.9 + - - -
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Residues in contact with LEU 267 (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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263B ILE 2.8 18.7 + - - +
264B GLU* 3.6 5.4 - - - +
266B GLU* 1.4 69.4 - - - +
268B GLU* 1.3 60.5 + - - +
270B GLN* 3.3 2.4 + - - -
271B LEU* 2.9 46.5 + - + +
286B LEU* 3.8 25.8 - - + +
287B GLU* 4.3 2.5 - - - -
290B THR* 3.6 41.5 - - + +
291B ARG* 3.7 42.6 - - + +
294B LEU* 4.5 4.3 - - + -
368B LEU* 3.7 12.5 - - + +
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Residues in contact with GLU 268 (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 GLU 3.0 17.8 + - - +
265B LYS* 4.0 5.6 - - - +
267B LEU* 1.3 74.7 - - - +
269B GLU* 1.4 62.7 + - - +
271B LEU* 3.3 12.4 + - - +
272B LYS* 3.2 21.7 + - - +
291B ARG* 5.5 5.8 - - - +
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Residues in contact with GLU 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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265B LYS 3.3 12.4 + - - +
266B GLU* 3.6 10.8 - - + +
267B LEU 3.3 0.4 - - - -
268B GLU* 1.4 77.7 - - - +
270B GLN* 1.3 61.0 + - - +
272B LYS* 3.5 7.4 + - - +
273B VAL* 3.3 27.9 + - - +
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Residues in contact with GLN 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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266B GLU* 2.9 18.6 + - + +
267B LEU 3.3 4.2 + - - +
269B GLU* 1.3 75.3 - - - +
271B LEU* 1.3 57.7 + - - +
273B VAL* 3.6 19.0 + - - +
274B MET* 3.2 46.4 + - + +
279B LYS* 5.9 1.8 - - - +
286B LEU* 3.7 20.6 - - + -
362B VAL* 4.4 9.5 + - - +
367B ARG 5.6 0.8 + - - +
368B LEU* 4.0 9.0 - - + -
369B PRO* 3.4 37.0 - - + +
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Residues in contact with LEU 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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267B LEU* 2.9 38.9 + - + +
268B GLU* 3.3 10.5 + - - +
270B GLN* 1.3 75.9 - - - +
272B LYS* 1.3 63.2 + - - +
274B MET* 4.1 3.1 - - - +
275B HIS* 3.2 24.8 + - - +
283B ALA* 3.8 31.7 - - + +
286B LEU* 3.7 27.8 - - + -
287B GLU* 4.3 15.3 - - + +
291B ARG* 5.3 5.2 - - - +
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Residues in contact with LYS 272 (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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268B GLU 3.2 11.2 + - - +
269B GLU* 3.5 9.6 + - - +
271B LEU* 1.3 73.7 - - - +
273B VAL* 1.4 64.4 + - + +
275B HIS* 3.4 5.9 + - - +
276B GLU* 3.1 40.2 + - - +
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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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269B GLU* 3.3 15.9 + - + +
270B GLN* 3.7 24.9 - - - +
271B LEU 3.3 0.2 - - - -
272B LYS* 1.4 77.6 - - + +
274B MET* 1.4 64.9 + - + +
276B GLU* 3.3 14.0 + - - +
277B ASN* 3.3 34.2 + - - +
279B LYS* 6.1 2.2 - - - +
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Residues in contact with MET 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 GLN* 3.2 36.2 + - + +
271B LEU* 4.1 3.1 - - - +
273B VAL* 1.4 77.7 - - + +
275B HIS* 1.3 63.2 - - - +
277B ASN* 3.4 4.8 + - - +
278B GLY 3.2 3.5 + - - -
279B LYS* 2.9 61.1 + - + +
282B GLU* 3.9 7.4 - - + +
283B ALA* 3.6 35.4 - - + -
286B LEU* 3.8 26.5 - - + -
362B VAL 4.3 7.4 - - - +
363B ASP 5.2 0.2 - - - +
365B GLY* 4.0 22.7 - - - +
367B ARG 5.7 0.2 - - - +
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Residues in contact with HIS 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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271B LEU 3.2 18.4 + - - +
272B LYS* 3.8 4.5 - - - +
274B MET* 1.3 76.8 - - - +
276B GLU* 1.3 60.2 + - + +
278B GLY* 3.0 20.1 + - - +
280B LEU* 3.7 29.2 - - + +
283B ALA* 5.1 6.8 - - + +
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Residues in contact with GLU 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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272B LYS* 3.1 33.2 + - - +
273B VAL* 3.6 12.4 - - - +
275B HIS* 1.3 76.4 - - + +
277B ASN* 1.3 66.3 + - - +
278B GLY 3.4 0.4 + - - -
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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* 3.3 27.6 + - - +
274B MET* 3.9 4.9 - - - +
275B HIS 3.1 0.8 - - - -
276B GLU* 1.3 83.0 + - - +
278B GLY* 1.3 61.2 + - - +
279B LYS* 3.3 25.0 + - + +
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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
------------------------------------------------------------
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