Contacts of the helix formed by residues 278 - 295 (chain B) in PDB entry 3ER8
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 278 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276B PHE* 3.6 9.9 - - - +
277B PRO* 1.3 85.1 - - + +
279B THR* 1.3 61.9 + - - +
280B LYS* 3.7 11.0 + - - +
281B ALA* 3.1 32.9 + - - +
282B LYS* 3.5 3.8 + - - +
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Residues in contact with THR 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B TYR* 3.6 17.5 - - + +
268B ARG* 4.0 20.4 - - + +
278B THR* 1.3 71.3 - - - +
280B LYS* 1.3 56.8 + - - +
281B ALA 2.8 4.5 - - - -
282B LYS* 2.5 39.7 + - - +
283B VAL* 2.8 29.0 + - + -
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Residues in contact with LYS 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B ASP* 3.2 42.1 + - - +
253B TYR* 4.1 13.8 - - + +
254B PRO* 4.2 21.4 - - - +
264B TYR* 3.8 21.7 + - + +
278B THR* 3.9 10.3 - - - +
279B THR* 1.3 77.7 - - - +
281B ALA* 1.3 62.1 + - - +
283B VAL* 4.2 0.4 - - - +
284B LEU* 3.0 37.4 + - + +
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Residues in contact with ALA 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B PHE* 3.6 18.2 - - + -
277B PRO* 3.8 12.3 - - + -
278B THR* 3.1 34.9 + - - +
279B THR 2.7 0.6 + - - -
280B LYS* 1.3 81.9 - - - +
282B LYS* 1.3 54.2 + - - +
284B LEU* 4.0 4.5 - - - +
285B PHE* 3.3 23.2 + - - +
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Residues in contact with LYS 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B LEU 4.4 6.7 - - - -
268B ARG* 3.6 19.0 + - - +
270B VAL 3.2 26.3 + - - +
271B TYR* 5.2 2.0 - - - +
272B CYS* 4.2 20.2 - - + +
276B PHE* 3.6 34.3 - - + -
278B THR 3.5 1.7 + - - +
279B THR* 2.5 30.0 + - - +
281B ALA* 1.3 72.4 - - - +
283B VAL* 1.3 70.0 + - - +
284B LEU 3.1 1.1 - - - -
285B PHE* 2.7 4.9 + - - +
286B LEU* 2.7 35.8 + - + +
260C ASP* 5.7 3.4 + - - -
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Residues in contact with VAL 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B TYR* 3.4 17.0 - - + +
263B MET* 5.8 0.4 - - + -
264B TYR* 3.5 63.7 - - + +
267B LEU* 4.2 11.8 - - + +
268B ARG* 3.8 15.9 - - - +
279B THR* 2.8 28.5 + - + +
280B LYS 4.2 0.4 - - - +
282B LYS* 1.3 74.6 - - - +
284B LEU* 1.3 55.7 + - - +
286B LEU* 3.0 8.3 + - - +
287B GLN* 2.8 34.0 + - - +
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Residues in contact with LEU 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B TYR* 3.0 30.3 - - + +
254B PRO* 4.0 26.7 - - + -
280B LYS* 3.0 28.8 + - + +
281B ALA* 4.0 4.7 - - - +
283B VAL* 1.3 79.5 - - - +
285B PHE* 1.3 58.3 + - - +
287B GLN* 4.6 8.1 - - + +
288B GLN* 2.9 40.9 + - + +
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Residues in contact with PHE 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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272B CYS* 4.8 10.3 - - - -
274B LYS* 4.2 25.1 - - + -
276B PHE* 3.5 30.3 - + + -
281B ALA 3.3 14.7 + - - +
282B LYS 2.7 14.7 + - - +
284B LEU* 1.3 71.3 - - - +
286B LEU* 1.3 84.5 + - + +
288B GLN* 3.0 21.3 + - + +
289B SER* 2.9 27.1 + - - -
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Residues in contact with LEU 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B LEU* 5.6 2.9 - - + -
77B TYR* 5.1 7.9 - - - +
81B HIS* 5.0 7.6 - - + +
267B LEU* 3.4 53.2 - - + +
270B VAL* 3.9 17.7 - - + -
272B CYS* 4.6 16.4 - - + -
282B LYS* 2.7 35.2 + - + +
283B VAL* 3.4 6.1 - - - +
285B PHE* 1.3 84.0 - - + +
287B GLN* 1.3 56.3 + - - +
289B SER* 2.4 34.5 + - - -
290B ILE* 3.0 15.5 + - + -
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Residues in contact with GLN 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B TYR* 2.5 46.0 + - - +
255B ASN* 5.5 0.7 - - - +
260B TYR* 3.9 18.7 - - - -
263B MET* 3.4 20.3 - - + +
267B LEU* 3.9 15.1 - - + +
283B VAL* 2.8 19.3 + - + +
284B LEU* 4.1 8.1 - - + +
286B LEU* 1.3 72.9 - - - +
288B GLN* 1.3 66.9 + - - +
290B ILE* 4.5 6.7 - - - -
291B PHE* 2.8 47.5 + - + +
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Residues in contact with GLN 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B LEU* 2.9 32.5 + - + +
285B PHE* 3.0 20.1 + - + +
286B LEU 2.8 1.6 + - - -
287B GLN* 1.3 80.7 - - - +
289B SER* 1.3 54.9 + - - +
291B PHE* 4.4 3.9 - - - +
292B ARG* 3.2 28.6 + - - +
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Residues in contact with SER 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B TYR* 3.2 25.2 + - - -
285B PHE* 2.9 22.3 + - - -
286B LEU* 2.4 28.2 + - - -
288B GLN* 1.3 67.2 - - - +
290B ILE* 1.3 58.4 + - - -
292B ARG* 2.9 13.1 - - - +
293B PHE* 2.8 28.2 + - - +
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Residues in contact with ILE 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B LEU* 4.0 15.9 - - + -
43B LEU* 3.5 26.0 - - + -
44B LEU* 4.1 12.6 - - + -
47B LEU* 4.0 13.9 - - + -
77B TYR* 3.7 29.4 - - + +
263B MET* 6.2 0.7 - - - -
267B LEU* 3.9 33.7 - - + -
286B LEU* 3.0 12.9 + - + +
287B GLN* 3.7 7.2 - - - +
289B SER* 1.3 71.0 + - - +
291B PHE* 1.3 66.7 + - + +
292B ARG 2.9 4.8 + - - -
293B PHE* 3.1 2.4 + - - +
294B LEU* 3.0 35.9 + - + +
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Residues in contact with PHE 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B LEU* 4.5 2.5 - - + -
40B LEU* 3.8 40.6 - - + -
200B PHE* 4.4 0.9 - + - -
260B TYR* 3.8 39.5 - + - -
263B MET* 3.9 18.2 - - + -
287B GLN* 2.8 39.5 + - + +
288B GLN* 4.6 3.6 - - - +
290B ILE* 1.3 76.6 - - + +
292B ARG* 1.3 57.3 + - - +
295B ASN 3.1 3.7 + - - -
296B ILE* 2.6 78.2 + - + +
297B PRO* 4.9 8.1 - - - +
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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 GLN* 3.2 21.9 + - - +
289B SER* 2.9 17.2 + - - +
290B ILE 2.9 0.2 - - - -
291B PHE* 1.3 78.0 - - - +
293B PHE* 1.3 61.9 + - - +
295B ASN* 2.9 24.2 + - - +
296B ILE 5.1 0.7 - - - -
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Residues in contact with PHE 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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43B LEU* 5.2 0.4 - - + -
73B THR* 3.7 35.9 - - + -
74B HIS* 4.1 8.1 - - - -
76B ARG* 3.8 15.7 - - + -
77B TYR* 3.5 58.8 - + + -
80B ASP* 5.0 1.1 - - - -
102B ILE* 4.2 9.0 - - + -
289B SER 2.8 8.4 + - - +
290B ILE 3.6 4.3 - - - +
292B ARG* 1.3 77.7 - - - +
294B LEU* 1.3 76.3 + - + +
295B ASN* 3.4 9.5 + - - -
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Residues in contact with LEU 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B TYR* 3.6 26.0 - - + -
39B GLN* 3.5 35.0 - - + +
40B LEU* 3.8 26.9 - - - +
43B LEU* 4.3 4.7 - - + -
73B THR* 5.8 2.5 - - + -
74B HIS* 4.6 7.4 - - + +
290B ILE* 3.0 30.7 + - + +
293B PHE* 1.3 92.8 - - + +
295B ASN* 1.3 70.4 + - - +
296B ILE* 3.6 32.1 - - + -
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Residues in contact with ASN 295 (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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35B PRO* 4.8 0.5 - - - +
36B TYR* 4.2 21.2 + - + -
291B PHE 3.1 1.1 + - - -
292B ARG* 2.9 21.7 + - - +
293B PHE 3.9 8.6 + - - -
294B LEU* 1.3 83.0 + - - +
296B ILE* 1.3 61.5 + - - +
297B PRO* 3.5 9.2 - - - +
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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
------------------------------------------------------------
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