Contacts of the helix formed by residues 285 - 302 (chain B) in PDB entry 3E7O
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 285 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284B SER* 1.3 70.1 - - - +
286B ARG* 1.3 60.5 + - - +
287B ASP 3.1 4.9 - - - -
288B LYS* 3.3 57.4 + - - +
289B ILE* 4.4 1.9 + - - +
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Residues in contact with ARG 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B SER* 3.3 12.0 + - - +
285B GLU* 1.3 75.0 - - - +
287B ASP* 1.3 62.4 + - - +
288B LYS 3.3 0.2 - - - -
289B ILE* 3.3 26.5 - - + +
290B LYS* 3.4 34.6 - - - +
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Residues in contact with ASP 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B ASP* 6.1 0.9 - - - +
125B HIS* 3.5 18.7 + - + +
281B PRO* 3.4 30.8 - - - +
282B SER* 4.2 2.9 - - - -
283B GLU* 3.4 21.8 + - - +
284B SER* 3.4 24.4 + - - +
285B GLU 3.1 0.4 - - - -
286B ARG* 1.3 76.9 - - - +
288B LYS* 1.3 57.9 + - + +
290B LYS* 3.3 17.3 + - - -
291B THR* 2.9 35.4 + - - -
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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
----------------------------------------------------------
284B SER 4.7 3.1 - - - +
285B GLU* 3.3 52.1 + - - +
287B ASP* 1.3 79.1 - - - +
289B ILE* 1.3 60.4 + - - +
291B THR* 3.5 7.6 + - - +
292B SER* 3.3 23.4 + - - -
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Residues in contact with ILE 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 4.4 1.0 + - - +
286B ARG* 3.3 26.4 - - + +
288B LYS* 1.3 76.2 - - - +
290B LYS* 1.3 69.1 + - + +
291B THR 3.2 0.2 - - - -
292B SER* 3.3 8.7 + - - -
293B GLN* 3.0 48.4 + - + +
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Residues in contact with LYS 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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125B HIS* 3.5 40.9 - - + +
126B GLU* 5.6 3.3 - - - +
286B ARG* 3.4 41.5 + - - +
287B ASP* 3.3 25.9 + - - +
289B ILE* 1.3 81.6 - - + +
291B THR* 1.3 57.3 + - - +
293B GLN* 3.4 15.9 + - - +
294B ALA* 2.9 30.3 + - - +
320B TYR* 3.5 12.9 - - + -
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Residues in contact with THR 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B HIS* 3.1 18.4 + - - -
277B ASP* 3.7 27.8 - - + +
280B PHE* 3.4 36.5 - - + +
281B PRO 3.8 4.2 + - - -
287B ASP 2.9 20.5 + - - -
288B LYS* 3.5 8.1 - - - +
290B LYS* 1.3 74.1 - - - +
292B SER* 1.3 63.9 + - - +
294B ALA* 3.9 2.7 - - - +
295B ARG* 3.1 30.8 + - - +
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Residues in contact with SER 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 3.3 11.6 + - - -
289B ILE* 3.6 13.1 - - - -
291B THR* 1.3 78.2 - - - +
293B GLN* 1.3 58.4 + - - +
295B ARG* 4.0 14.4 + - - +
296B ASP* 3.1 28.8 + - - +
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Residues in contact with GLN 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 ILE* 3.0 40.7 + - + +
290B LYS* 3.6 21.3 - - - +
291B THR 3.3 0.2 - - - -
292B SER* 1.3 75.9 - - - +
294B ALA* 1.3 59.4 + - - +
296B ASP* 3.3 3.6 + - - +
297B LEU* 3.0 23.9 + - - +
318B HIS* 3.0 17.7 - - + -
319B PRO* 3.7 31.2 + - + +
320B TYR* 4.0 25.9 + - + +
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Residues in contact with ALA 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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215B MET* 3.2 21.0 - - + +
219B VAL* 5.8 0.2 - - + -
280B PHE* 3.6 26.2 - - + -
290B LYS 2.9 20.0 + - - +
291B THR 3.9 1.3 - - - +
292B SER 3.4 0.2 - - - -
293B GLN* 1.3 72.8 - - - +
295B ARG* 1.3 63.6 + - - +
297B LEU* 3.3 2.2 + - - -
298B LEU* 3.0 22.5 + - - +
320B TYR* 3.7 30.2 - - + +
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Residues in contact with ARG 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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271B PHE* 3.5 37.8 + - + +
272B GLU* 3.6 26.2 + - - +
275B PHE* 2.8 32.6 + - + +
276B PRO* 3.6 1.6 - - - +
277B ASP* 2.6 40.8 + - - +
280B PHE* 4.2 7.4 - - + -
291B THR* 3.1 33.3 + - - +
292B SER* 4.0 13.8 + - - +
294B ALA* 1.3 76.0 - - - +
296B ASP* 1.3 57.5 + - - +
298B LEU* 3.5 11.4 + - - +
299B SER* 3.0 27.4 + - - -
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Residues in contact with ASP 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B SER 3.1 19.9 + - - +
293B GLN* 3.5 8.3 - - - +
294B ALA 3.3 0.2 - - - -
295B ARG* 1.3 78.3 - - - +
297B LEU* 1.3 60.4 + - - +
299B SER* 2.6 27.1 + - - -
300B LYS* 2.6 43.6 + - - +
318B HIS* 2.9 14.5 + - - +
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Residues in contact with LEU 297 (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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132B LEU* 5.1 0.7 - - + -
215B MET* 3.9 22.4 - - + -
293B GLN 3.0 13.6 + - - +
294B ALA* 3.3 7.2 + - - +
296B ASP* 1.3 73.6 - - - +
298B LEU* 1.3 66.5 + - - +
300B LYS* 2.9 14.2 + - - +
301B MET* 3.0 45.0 + - + +
310B ILE* 4.2 15.9 - - + -
315B ALA* 4.3 3.6 - - - -
318B HIS* 3.7 35.8 + - + +
320B TYR* 4.4 4.5 - - + -
321B ILE* 3.7 32.5 - - + -
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Residues in contact with LEU 298 (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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212B GLY* 3.5 26.7 - - - +
215B MET* 3.8 21.3 - - + +
216B GLY* 3.6 18.6 - - - +
219B VAL* 5.0 2.9 - - + -
271B PHE* 3.9 10.3 - - + -
275B PHE* 3.7 35.9 - - + -
280B PHE* 4.4 14.6 - - + -
294B ALA 3.0 16.5 + - - +
295B ARG* 3.6 10.1 - - - +
297B LEU* 1.3 75.2 - - - +
299B SER* 1.3 56.5 + - - +
301B MET* 4.5 3.6 - - - +
302B LEU* 2.9 48.1 + - + +
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Residues in contact with SER 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B PHE* 3.7 36.1 - - - -
295B ARG* 3.0 14.7 + - - -
296B ASP* 2.6 28.0 + - - -
298B LEU* 1.3 75.4 - - - +
300B LYS* 1.3 60.8 + - - +
302B LEU 4.5 2.0 - - - +
303B VAL* 3.3 17.0 - - - +
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Residues in contact with LYS 300 (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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296B ASP* 2.6 41.4 + - - +
297B LEU* 2.9 8.7 + - - +
299B SER* 1.3 82.0 + - - +
301B MET* 1.3 61.2 + - - +
303B VAL* 3.4 15.4 - - - +
308B LYS 4.7 1.0 - - - +
309B ARG* 3.7 0.7 - - - +
310B ILE* 3.1 56.3 + - + +
318B HIS* 3.9 14.8 + - + -
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Residues in contact with MET 301 (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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132B LEU* 6.0 1.1 - - + -
136B LEU* 4.3 6.3 - - + -
208B ILE* 3.7 22.4 - - + +
209B TRP* 4.0 8.3 - - - -
211B VAL* 4.0 20.6 - - + -
212B GLY* 3.9 31.6 - - - -
215B MET* 4.6 8.1 - - - +
297B LEU* 3.0 51.3 + - + +
298B LEU* 4.1 2.9 - - - +
300B LYS* 1.3 76.5 - - - +
302B LEU* 1.3 59.9 + - - +
303B VAL 2.9 11.2 + - - -
309B ARG* 3.4 20.8 + - - +
310B ILE* 3.5 13.7 - - + -
315B ALA* 3.6 21.1 - - + -
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Residues in contact with LEU 302 (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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209B TRP* 3.8 24.0 - - + +
212B GLY* 3.6 37.0 - - - +
213B CYS* 3.7 16.6 - - - +
224B ILE* 4.5 6.1 - - + -
225B PHE* 4.0 22.7 - - + -
241B LEU* 3.3 26.2 - - + +
271B PHE* 4.0 16.1 - - + -
275B PHE* 4.4 18.8 - - + -
298B LEU* 2.9 28.5 + - + +
299B SER 4.5 0.2 - - - +
301B MET* 1.3 71.7 - - - +
303B VAL* 1.3 63.0 + - - +
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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