Contacts of the helix formed by residues 310 - 324 (chain B) in PDB entry 2YEV
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 SER 310 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238B ARG* 4.6 1.4 + - - -
292B ARG* 5.2 0.2 - - - -
308B GLN 3.4 3.7 + - - -
309B LEU* 1.3 76.3 - - - +
311B GLU* 1.3 59.2 + - - +
312B GLU* 3.6 7.4 + - - +
313B ASP* 3.1 31.3 + - - +
314B LEU* 2.9 29.0 + - - +
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Residues in contact with GLU 311 (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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288B LYS* 2.7 32.4 + - - +
292B ARG* 2.5 34.1 + - - +
309B LEU 4.0 0.4 + - - -
310B SER* 1.3 73.2 - - - +
312B GLU* 1.3 59.7 + - + +
314B LEU* 4.5 3.1 - - - -
315B ASP* 3.0 41.4 + - - +
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Residues in contact with GLU 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B ARG* 3.2 36.0 + - - +
310B SER* 3.2 5.2 + - - +
311B GLU* 1.3 77.6 - - + +
313B ASP* 1.3 59.7 + - - +
315B ASP* 3.3 5.0 + - - +
316B ALA* 2.9 30.5 + - - +
319B ARG* 4.7 1.6 + - - -
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Residues in contact with ASP 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B ARG* 2.9 29.8 + - - +
242B VAL* 3.8 25.2 - - + +
309B LEU* 4.1 19.3 - - + +
310B SER* 3.1 27.3 + - - +
312B GLU* 1.3 74.6 - - - +
314B LEU* 1.3 54.5 + - - +
316B ALA* 3.1 6.2 + - - +
317B LEU* 2.7 36.8 + - - +
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Residues in contact with LEU 314 (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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288B LYS* 3.9 25.1 - - + -
291B ILE* 3.7 41.1 - - + -
292B ARG* 3.6 48.9 - - + +
306B PHE 5.8 0.2 - - - +
309B LEU* 4.5 16.3 - - + +
310B SER 2.9 17.5 + - - +
311B GLU* 4.0 3.8 - - - +
313B ASP* 1.3 76.7 - - - +
315B ASP* 1.3 58.8 + - - +
317B LEU* 3.2 11.7 + - + +
318B VAL* 2.8 34.9 + - + +
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Residues in contact with ASP 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B LYS* 2.8 37.5 + - - +
311B GLU* 3.0 29.9 + - - +
312B GLU* 3.7 5.4 - - - +
313B ASP 3.2 0.2 - - - -
314B LEU* 1.3 73.7 - - - +
316B ALA* 1.3 66.1 + - - +
318B VAL* 3.2 6.7 + - - +
319B ARG* 3.0 43.0 + - - +
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Residues in contact with ALA 316 (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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236B ASP* 3.8 5.9 - - - +
238B ARG* 3.7 21.5 - - + -
239B GLY* 3.2 27.4 - - - +
242B VAL* 5.1 0.2 - - + -
312B GLU 2.9 17.8 + - - +
313B ASP* 3.5 4.7 - - - +
315B ASP* 1.3 75.7 - - - +
317B LEU* 1.3 63.0 + - - +
319B ARG* 3.2 26.4 + - - +
320B TYR 3.1 18.2 + - - -
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Residues in contact with LEU 317 (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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239B GLY* 3.6 22.9 - - - +
242B VAL* 3.9 18.8 - - + -
243B PHE* 3.8 35.7 - - + +
247B CYS* 4.3 11.7 - - - -
291B ILE* 3.9 24.0 - - + -
309B LEU* 4.4 9.4 - - + -
313B ASP 2.7 20.0 + - - +
314B LEU* 3.5 14.1 - - + +
316B ALA* 1.3 73.2 - - - +
318B VAL* 1.3 57.4 + - - +
320B TYR* 3.3 2.0 + - + +
321B LEU* 2.9 44.7 + - + +
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Residues in contact with VAL 318 (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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284B PRO* 4.0 32.1 - - + +
287B LEU* 4.0 24.9 - - + -
288B LYS* 3.9 24.9 - - + -
291B ILE* 4.4 10.1 - - + -
314B LEU* 2.8 20.5 + - + +
315B ASP* 3.2 6.3 + - - +
317B LEU* 1.3 75.0 - - - +
319B ARG* 1.3 68.1 + - + +
321B LEU* 3.4 5.5 + - - +
322B GLU* 2.9 29.5 + - + +
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Residues in contact with ARG 319 (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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235B ALA* 3.9 13.0 - - + +
236B ASP* 2.7 35.3 + - + -
238B ARG* 5.7 2.6 - - - +
312B GLU 4.7 1.6 + - - -
315B ASP* 3.0 27.4 + - - +
316B ALA* 3.3 30.2 - - - +
318B VAL* 1.3 76.8 - - + +
320B TYR* 1.3 63.2 + - - +
322B GLU* 3.5 4.5 + - - +
323B GLY* 3.2 16.6 + - - -
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Residues in contact with TYR 320 (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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233B PRO 4.1 8.3 - - - -
234B VAL* 4.2 17.7 - - + +
235B ALA* 4.3 2.8 + - - +
236B ASP* 3.7 16.9 - - - +
239B GLY 3.7 4.7 - - - -
240B GLN* 3.6 56.4 + - + +
243B PHE* 3.8 40.2 - + + -
244B GLN* 5.4 1.9 + - - -
253B VAL* 4.2 17.5 - - - +
316B ALA 3.1 7.3 + - - +
317B LEU 3.7 7.6 - - - +
319B ARG* 1.3 76.6 - - - +
321B LEU* 1.3 66.9 + - + +
323B GLY* 3.0 12.1 + - - -
324B LEU* 3.4 43.6 + - + +
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Residues in contact with LEU 321 (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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243B PHE* 3.8 31.9 - - + -
247B CYS* 6.3 0.7 - - - -
266B LEU* 4.2 15.7 - - + -
269B TRP* 3.3 28.2 - - + +
287B LEU* 3.8 25.4 - - + -
291B ILE* 4.0 21.3 - - + -
317B LEU* 2.9 32.9 + - + +
318B VAL 3.8 3.6 - - - +
320B TYR* 1.3 77.3 - - + +
322B GLU* 1.3 62.2 + - - +
324B LEU* 3.1 31.2 + - + +
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Residues in contact with GLU 322 (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 TRP* 3.6 15.1 + - - -
270B GLY* 3.6 22.6 - - - +
282B ASN* 2.7 38.8 + - - +
283B THR* 4.2 11.3 - - - -
284B PRO* 4.3 9.3 - - + -
287B LEU* 3.8 8.0 - - + +
318B VAL* 2.9 31.5 + - + +
319B ARG* 3.9 4.9 - - - +
321B LEU* 1.3 75.2 - - - +
323B GLY* 1.3 59.3 + - - +
324B LEU 3.3 0.2 - - - -
325B LYS* 3.9 13.3 + - - -
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Residues in contact with GLY 323 (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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233B PRO* 3.7 23.0 - - - +
235B ALA* 4.0 16.8 - - - -
319B ARG 3.2 10.0 + - - -
320B TYR 3.0 11.1 + - - -
322B GLU* 1.3 76.6 - - - +
324B LEU* 1.3 60.8 + - - +
325B LYS* 2.9 19.3 + - - +
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Residues in contact with LEU 324 (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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232B ALA* 3.8 18.2 - - + +
233B PRO* 3.6 16.8 - - - +
253B VAL* 3.8 20.9 - - + -
266B LEU* 3.1 26.9 - - + +
267B GLY 3.5 10.3 - - - +
268B LEU 3.3 0.5 - - - -
269B TRP* 3.0 9.5 + - + +
270B GLY 2.8 20.5 + - - -
320B TYR* 3.5 40.8 - - + +
321B LEU* 3.1 34.1 + - + +
322B GLU 3.3 0.4 - - - -
323B GLY* 1.3 73.6 - - - +
325B LYS* 1.3 58.9 + - - +
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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