Contacts of the helix formed by residues 283 - 293 (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 THR 283 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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281B GLU* 3.2 37.3 + - + +
282B ASN* 1.3 84.4 + - - +
284B PRO* 1.3 77.6 - - - +
285B GLU* 3.7 6.1 + - - +
286B ASN* 3.1 25.7 + - - +
287B LEU* 2.8 22.7 + - - +
322B GLU* 4.2 1.6 - - - -
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Residues in contact with PRO 284 (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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283B THR* 1.3 86.1 - - - +
285B GLU* 1.3 62.2 + - + +
287B LEU* 3.2 4.4 + - + +
288B LYS* 3.0 36.9 + - + +
318B VAL* 4.0 25.7 - - + +
322B GLU* 4.3 11.9 - - + +
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Residues in contact with GLU 285 (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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283B THR* 3.2 6.3 + - - +
284B PRO* 1.3 84.4 - - + +
286B ASN* 1.3 66.1 + - - +
288B LYS* 3.4 30.4 + - - +
289B ALA* 3.2 22.7 + - - +
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Residues in contact with ASN 286 (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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275B LEU* 3.4 5.6 - - + +
280B VAL* 3.0 24.6 - - + +
281B GLU* 2.9 36.5 + - - +
283B THR* 3.1 20.1 + - - +
285B GLU* 1.3 80.8 - - - +
287B LEU* 1.3 58.2 + - - +
289B ALA* 3.5 6.3 + - - +
290B TRP* 2.9 29.5 + - - +
297B MET* 4.0 7.4 - - + +
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Residues in contact with LEU 287 (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 39.9 - - + +
275B LEU* 3.9 16.9 - - + +
282B ASN* 4.9 2.2 - - - +
283B THR 2.8 16.2 + - - +
284B PRO* 3.5 5.6 - - + +
286B ASN* 1.3 74.5 - - - +
288B LYS* 1.3 60.0 + - - +
290B TRP* 3.3 4.8 + - + +
291B ILE* 2.9 53.4 + - + +
318B VAL* 4.0 17.5 - - + -
321B LEU* 3.8 26.5 - - + -
322B GLU* 3.8 10.8 - - - +
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Residues in contact with LYS 288 (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* 3.0 21.2 + - - +
285B GLU* 3.4 32.6 + - - +
286B ASN 3.3 0.2 - - - -
287B LEU* 1.3 72.9 - - - +
289B ALA* 1.3 59.9 + - - +
291B ILE* 3.1 6.5 + - - +
292B ARG* 2.8 45.7 + - - +
311B GLU* 2.7 28.3 + - - +
314B LEU* 3.9 28.4 - - + +
315B ASP* 2.8 29.7 + - - +
318B VAL* 3.9 16.4 - - + -
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Residues in contact with ALA 289 (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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285B GLU 3.2 14.7 + - - +
286B ASN* 3.8 3.1 - - - +
288B LYS* 1.3 78.4 - - - +
290B TRP* 1.3 61.7 + - - +
292B ARG* 3.3 10.1 + - - +
293B ASP* 3.0 24.8 + - - +
297B MET* 3.6 21.5 - - + +
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Residues in contact with TRP 290 (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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275B LEU* 3.8 30.7 - - + +
276B GLY* 4.2 17.9 - - - -
279B ILE* 5.0 0.7 - - + -
286B ASN 2.9 18.3 + - - +
287B LEU* 3.6 7.9 - - + +
289B ALA* 1.3 75.7 - - - +
291B ILE* 1.3 75.0 + - + +
293B ASP 3.2 0.4 + - - -
294B PRO* 3.0 74.6 - - + +
297B MET* 3.9 23.5 - - + +
298B LYS* 3.8 31.9 - - + -
301B VAL* 4.0 11.7 - - + -
303B MET* 3.7 27.2 - - + +
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Residues in contact with ILE 291 (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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287B LEU* 2.9 35.6 + - + +
288B LYS 3.6 3.4 - - - +
290B TRP* 1.3 83.4 - - + +
292B ARG* 1.3 60.1 + - - +
294B PRO* 4.1 0.5 - - - +
303B MET* 4.4 9.4 - - + -
304B PRO 4.6 0.2 - - - +
305B GLY* 3.6 4.2 - - - -
306B PHE* 2.9 46.9 + - + +
309B LEU* 4.5 1.6 - - + -
314B LEU* 3.7 31.9 - - + -
317B LEU* 3.9 21.5 - - + -
318B VAL* 4.4 4.5 - - + -
321B LEU* 4.0 21.3 - - + -
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Residues in contact with ARG 292 (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* 2.8 31.9 + - - +
289B ALA* 3.6 9.1 - - - +
290B TRP 3.1 0.4 - - - -
291B ILE* 1.3 79.6 - - + +
293B ASP* 1.3 62.8 + - + +
305B GLY* 3.6 3.5 - - - -
306B PHE 4.0 8.7 - - - +
307B PRO* 3.6 46.3 + - + +
309B LEU 4.7 7.3 + - - -
311B GLU* 2.5 42.8 + - - +
314B LEU* 3.6 29.6 - - + +
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Residues in contact with ASP 293 (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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289B ALA 3.0 12.8 + - - +
290B TRP 3.2 2.4 + - - -
292B ARG* 1.3 83.2 - - + +
294B PRO* 1.3 72.3 - - - +
295B ALA* 3.6 11.1 + - - +
296B GLY* 3.0 30.1 + - - -
297B MET* 3.9 6.4 + - - +
305B GLY* 4.4 2.0 + - - -
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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