Contacts of the helix formed by residues 273 - 294 (chain B) in PDB entry 2YVC
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 ARG 273 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B TYR* 4.7 17.2 + - - -
252B ASP 4.4 5.7 - - - +
253B LYS* 4.6 8.0 - - - +
271B ALA* 3.0 22.0 + - - +
272B PRO* 1.3 82.6 - - + +
274B LEU* 1.3 75.0 + - - +
275B ARG* 3.4 56.9 - - - +
276B ILE* 3.8 20.2 + - + +
277B ASN* 3.9 1.4 + - - +
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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
----------------------------------------------------------
250B PHE* 3.7 28.5 - - + -
252B ASP* 3.8 40.8 + - - +
273B ARG* 1.3 84.0 - - - +
275B ARG* 1.3 67.5 + - - +
277B ASN* 2.9 18.3 + - + +
278B LYS* 3.2 27.8 + - + +
7E MET 4.6 5.4 - - - +
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Residues in contact with ARG 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B TYR* 5.6 0.4 + - - -
51B ASP* 3.2 24.9 + - - +
53B LYS* 5.4 2.4 - - - +
55B TYR* 3.5 30.4 - - + +
57B THR* 3.2 33.3 + - - +
273B ARG* 3.4 44.2 - - - +
274B LEU* 1.3 78.1 - - - +
276B ILE* 1.3 64.1 + - + +
278B LYS* 3.0 18.7 + - + +
279B ARG* 2.9 57.0 + - + +
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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
----------------------------------------------------------
55B TYR* 6.1 5.4 - - + -
206B PHE* 3.9 30.1 - - + -
207B GLU 5.0 2.0 - - - +
208B ILE* 5.8 1.1 - - + -
271B ALA* 3.8 15.7 - - + -
272B PRO* 4.5 14.6 - - + -
273B ARG* 3.8 28.7 + - + +
274B LEU 3.2 0.2 + - - -
275B ARG* 1.3 79.4 - - + +
277B ASN* 1.3 61.1 + - - +
279B ARG* 3.2 22.3 - - - +
280B ILE* 2.9 32.2 + - + +
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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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250B PHE* 3.6 28.9 - - + +
253B LYS* 3.2 32.6 + - - +
254B LYS 4.1 0.2 - - - +
255B PHE* 3.1 34.2 - - - +
269B PHE* 4.2 4.6 - - - -
271B ALA* 3.3 22.7 - - - +
273B ARG 3.9 1.7 + - - +
274B LEU* 2.9 14.4 + - + +
276B ILE* 1.3 75.7 - - - +
278B LYS* 1.3 64.9 + - - +
280B ILE* 3.1 19.2 + - - +
281B LEU* 3.1 14.2 + - - +
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Residues in contact with LYS 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250B PHE* 4.2 28.4 - - + -
274B LEU* 3.5 29.9 - - + +
275B ARG* 3.0 18.8 + - + +
277B ASN* 1.3 74.9 - - - +
279B ARG* 1.3 62.8 - - - +
281B LEU* 3.3 5.1 + - - +
282B ALA* 3.1 22.2 + - - +
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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
----------------------------------------------------------
55B TYR* 4.0 11.5 - - - +
56B SER 3.8 12.9 + - - -
57B THR* 3.5 33.3 + - - +
58B TRP* 4.3 11.8 - - - +
206B PHE* 3.9 22.2 - - + -
275B ARG* 2.9 58.8 + - + +
276B ILE* 3.2 24.4 - - - +
278B LYS* 1.3 76.4 - - - +
280B ILE* 1.3 63.7 + - - +
282B ALA* 3.2 8.5 + - - +
283B LEU* 3.1 28.3 + - + +
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Residues in contact with ILE 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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206B PHE* 3.3 51.6 - - + -
208B ILE* 5.7 0.9 - - + -
218B LEU* 3.9 24.5 - - + -
220B VAL* 4.0 9.4 - - + +
225B LEU* 5.4 2.5 - - + -
255B PHE* 3.7 24.5 - - + -
269B PHE* 5.1 5.2 - - + -
276B ILE* 2.9 17.9 - - + +
277B ASN* 3.4 17.5 - - - +
279B ARG* 1.3 73.4 - - - +
281B LEU* 1.3 58.7 + - - +
283B LEU* 3.1 7.8 + - - +
284B CYS* 2.9 38.1 + - - -
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Residues in contact with LEU 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B ILE* 3.4 41.1 - - + +
250B PHE* 4.0 27.4 - - + -
255B PHE* 4.6 6.9 - - + -
277B ASN 3.1 8.3 + - - +
278B LYS 3.3 8.2 + - - +
280B ILE* 1.3 80.0 - - - +
282B ALA* 1.3 56.1 + - - +
284B CYS* 3.5 5.0 + - + +
285B MET* 3.0 59.5 + - + +
8E ASP* 5.4 2.9 - - + -
9E ILE* 4.3 11.0 - - - +
10E THR* 3.9 15.9 - - - +
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Residues in contact with ALA 282 (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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83B LYS* 5.5 8.5 - - - +
84B PHE* 4.9 2.3 - - - -
278B LYS 3.1 11.7 + - - +
279B ARG* 3.4 11.0 - - - +
281B LEU* 1.3 73.8 - - - +
283B LEU* 1.3 61.4 + - + +
284B CYS 3.1 0.3 + - - -
285B MET* 3.1 20.9 + - + +
286B GLY* 2.9 27.5 + - - -
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Residues in contact with LEU 283 (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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58B TRP* 5.3 4.0 - - + +
83B LYS* 3.9 33.4 - - + +
84B PHE* 4.0 16.2 - - + -
204B ASN* 3.4 37.5 - - + +
206B PHE* 3.4 36.6 - - + -
220B VAL* 4.3 12.1 - - + +
279B ARG* 3.1 13.9 + - + +
280B ILE* 3.1 7.2 + - - +
282B ALA* 1.3 77.9 - - - +
284B CYS* 1.3 57.4 + - - +
287B ASN* 2.9 37.5 + - - +
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Residues in contact with CYS 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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220B VAL* 3.8 7.9 - - - -
225B LEU* 3.7 33.2 - - - -
242B TRP* 3.8 17.5 - - + -
248B ILE* 4.8 20.9 - - + -
255B PHE* 5.4 1.3 - - - -
280B ILE* 2.9 32.5 + - - +
281B LEU* 3.7 7.9 - - - +
282B ALA 3.1 0.2 - - - -
283B LEU* 1.3 74.8 - - - +
285B MET* 1.3 58.7 + - - +
288B HIS* 2.8 38.6 + - - +
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Residues in contact with MET 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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281B LEU* 3.0 37.1 + - + +
282B ALA* 3.1 27.6 + - + +
284B CYS* 1.3 74.6 - - - +
286B GLY* 1.3 57.5 - - - +
288B HIS* 3.8 4.6 - - - +
289B GLU* 2.8 34.4 + - - +
10E THR* 4.5 15.0 - - - -
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Residues in contact with GLY 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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84B PHE* 3.6 26.5 - - - -
282B ALA 2.9 11.5 + - - -
285B MET* 1.3 79.5 - - - +
287B ASN* 1.3 62.6 + - - +
289B GLU* 3.0 11.5 + - - +
290B LEU* 3.2 21.5 + - - +
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Residues in contact with ASN 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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83B LYS 5.2 0.7 - - - +
84B PHE* 3.6 28.5 - - - +
85B PHE 4.8 6.1 + - - +
204B ASN* 4.7 4.2 - - - +
220B VAL* 4.7 3.7 - - + +
221B ASP* 3.4 26.0 - - - +
222B ALA* 3.0 35.0 - - - +
242B TRP* 3.8 10.1 - - + -
283B LEU* 2.9 32.1 + - - +
286B GLY* 1.3 71.4 - - - +
288B HIS* 1.3 61.4 + - - +
290B LEU* 3.8 8.0 + - - +
291B TYR* 3.3 19.2 + - - +
294B ARG* 4.7 2.4 + - - +
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Residues in contact with HIS 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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242B TRP* 3.7 44.8 - + + +
284B CYS 2.8 22.6 + - - +
285B MET* 3.8 4.0 - - - +
287B ASN* 1.3 71.5 - - - +
289B GLU* 1.3 62.5 + - - +
291B TYR* 2.8 33.7 + + - +
292B MET* 3.0 49.9 + - + +
11E ASP 5.8 8.6 - - - -
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Residues in contact with GLU 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 MET 2.8 22.9 + - - +
286B GLY* 3.0 5.6 + - - +
288B HIS* 1.3 77.2 - - - +
290B LEU* 1.3 67.4 + - + +
292B MET* 3.6 5.2 + - - +
293B ARG* 2.9 53.9 + - - +
296B LYS* 4.7 5.9 + - - +
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Residues in contact with LEU 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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43B TRP* 4.3 35.2 - - + +
44B PHE* 4.5 4.0 - - + -
84B PHE* 3.7 36.6 - - + -
85B PHE 5.5 0.4 - - - +
286B GLY* 3.2 28.5 + - - +
287B ASN* 4.0 7.9 - - - +
288B HIS 3.1 0.6 - - - -
289B GLU* 1.3 89.5 - - + +
291B TYR* 1.3 59.8 + - - +
293B ARG* 3.8 8.3 - - + -
294B ARG* 3.0 56.5 + - - +
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Residues in contact with TYR 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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87B GLU* 3.9 5.4 - - - -
222B ALA 4.0 6.3 - - - +
223B LEU* 4.1 16.8 - - + -
242B TRP* 3.5 32.9 + + + -
243B SER* 3.8 25.5 + - - -
287B ASN 3.3 12.9 + - - +
288B HIS* 2.8 31.6 + + - +
290B LEU* 1.3 78.2 - - - +
292B MET* 1.3 69.0 + - + +
294B ARG* 3.4 19.0 + - - +
295B ARG* 3.0 68.7 + - - -
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Residues in contact with MET 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 HIS* 3.0 50.7 + - + +
289B GLU* 3.9 7.2 - - + +
291B TYR* 1.3 80.3 - - + +
293B ARG* 1.3 59.3 + - - +
295B ARG* 2.9 23.4 + - - +
296B LYS* 3.1 35.4 + - - +
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Residues in contact with ARG 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 GLU* 2.9 42.0 + - - +
290B LEU* 3.9 9.2 - - + +
292B MET* 1.3 78.2 - - - +
294B ARG* 1.3 56.7 + - - +
295B ARG 3.1 5.0 + - - -
296B LYS* 3.6 41.8 + - + +
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Residues in contact with ARG 294 (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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44B PHE* 4.7 2.6 - - - -
85B PHE 4.0 12.1 + - - -
86B PRO* 4.0 1.2 - - - +
87B GLU* 3.1 48.0 + - - +
92B GLU* 2.6 40.0 + - + +
222B ALA* 4.6 8.7 + - - +
287B ASN* 4.7 2.6 + - - +
290B LEU* 3.0 58.9 + - - +
291B TYR* 3.4 21.2 - - - +
293B ARG* 1.3 73.6 - - - +
295B ARG* 1.3 62.8 + - - +
296B LYS 5.3 0.9 - - - -
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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
------------------------------------------------------------
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