Contacts of the helix formed by residues 286 - 297 (chain S) in PDB entry 3EXG
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 ASP 286 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43S ARG* 2.8 33.1 + - - -
260S TYR* 2.9 20.6 + - - +
282S ARG* 3.1 26.4 + - + +
285S SER* 1.3 73.0 - - - +
287S PRO* 1.3 71.6 - - - +
288S ILE* 3.0 28.9 + - - +
289S MET* 3.1 26.2 + - + +
290S LEU* 3.1 25.7 + - - +
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Residues in contact with PRO 287 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39S MET* 3.4 13.0 - - - +
43S ARG* 3.9 4.9 - - - +
67S GLY 3.8 17.3 - - - +
69S GLU* 3.4 24.9 - - + +
70S ALA* 3.5 23.8 - - + +
228S MET* 3.4 30.9 - - + +
230S ILE* 4.8 2.9 - - - +
260S TYR* 3.9 6.7 - - - +
285S SER 3.7 3.7 - - - +
286S ASP* 1.3 94.5 - - - +
288S ILE* 1.3 59.4 + - + +
290S LEU* 3.8 3.3 - - + +
291S LEU* 3.4 16.5 + - - +
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Residues in contact with ILE 288 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36S TYR* 3.6 30.0 - - + +
39S MET* 3.5 53.6 - - + +
40S GLN* 3.8 20.4 - - + +
43S ARG* 3.8 34.3 - - + +
69S GLU* 4.6 2.5 - - + -
286S ASP* 3.0 9.4 + - - +
287S PRO* 1.3 77.0 - - + +
289S MET* 1.3 66.7 + - - +
291S LEU* 3.3 5.2 + - - +
292S LYS* 3.0 21.6 + - + +
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Residues in contact with MET 289 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282S ARG 4.0 9.2 - - - +
283S SER* 3.1 28.7 - - - +
284S LYS 4.0 2.9 - - - +
285S SER* 3.8 9.2 - - - +
286S ASP* 3.1 19.8 + - + +
288S ILE* 1.3 76.9 - - - +
290S LEU* 1.3 94.9 + - + +
292S LYS* 3.1 15.9 + - + +
293S ASP* 2.9 49.4 + - - +
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Residues in contact with LEU 290 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226S ASP* 5.9 0.9 - - - +
228S MET* 4.2 25.1 - - + +
229S ASP* 5.0 11.0 - - + +
230S ILE* 6.5 0.2 - - + -
284S LYS 4.3 7.4 - - - +
285S SER* 4.1 17.3 - - - -
286S ASP 3.1 20.9 + - - +
287S PRO* 3.8 4.9 - - + +
289S MET* 1.3 96.6 - - + +
291S LEU* 1.3 65.6 + - - +
293S ASP* 3.5 7.5 + - + +
294S ARG* 3.2 32.2 + - - +
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Residues in contact with LEU 291 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27S LEU* 4.4 18.6 - - + -
32S GLY* 3.9 8.1 - - - +
35S TYR* 4.1 8.3 - - + -
36S TYR* 3.6 40.2 - - + +
39S MET* 3.7 17.9 - - + -
230S ILE* 3.9 21.0 - - + +
231S LEU* 4.8 6.1 - - + -
287S PRO 3.4 11.0 + - - +
288S ILE 3.3 8.2 + - - +
290S LEU* 1.3 75.1 - - - +
292S LYS* 1.3 60.5 + - - +
294S ARG* 3.1 14.6 + - + +
295S MET* 2.9 45.0 + - + +
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Residues in contact with LYS 292 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36S TYR* 4.5 15.4 - - + +
288S ILE* 3.0 14.5 + - + +
289S MET* 3.1 17.0 - - + +
291S LEU* 1.3 77.0 - - - +
293S ASP* 1.3 65.9 + - - +
294S ARG 3.0 0.2 + - - -
295S MET* 3.1 2.6 + - - +
296S VAL* 2.8 35.1 + - + +
303S VAL* 3.5 30.7 - - - +
306S LEU* 3.6 36.8 - - + -
307S LYS* 5.7 5.8 - - - +
310S ASP* 5.2 5.2 - - - -
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Residues in contact with ASP 293 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289S MET* 2.9 42.7 + - - +
290S LEU* 4.1 7.4 + - + +
291S LEU 3.3 0.4 - - - -
292S LYS* 1.3 85.0 - - - +
294S ARG* 1.3 59.7 + - + +
296S VAL* 4.6 2.9 - - - +
297S ASN* 3.0 45.2 - - - +
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Residues in contact with ARG 294 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7S PHE* 3.4 40.1 - - + +
8S GLU 3.3 25.5 + - - -
9S ILE* 4.9 1.0 - - - +
27S LEU* 6.2 0.9 - - + -
229S ASP* 3.0 35.0 + - - -
230S ILE* 5.5 2.2 - - - +
231S LEU* 3.0 33.6 - - - +
290S LEU* 3.2 22.2 - - - +
291S LEU* 3.4 14.6 - - + +
292S LYS 3.0 0.4 - - - -
293S ASP* 1.3 79.3 - - + +
295S MET* 1.3 61.6 + - + +
296S VAL 3.2 1.3 - - - -
297S ASN* 5.0 1.3 - - - -
298S SER* 2.7 35.2 + - - -
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Residues in contact with MET 295 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27S LEU* 3.7 29.6 - - - -
29S ARG 4.1 5.8 - - - +
32S GLY* 3.2 33.2 - - - +
33S LEU* 3.3 12.8 - - + +
36S TYR* 5.1 2.2 - - + -
291S LEU* 2.9 32.2 + - + +
292S LYS* 3.1 6.3 + - - +
294S ARG* 1.3 76.0 - - - +
296S VAL* 1.3 60.9 + - - +
299S ASN 3.4 0.2 + - - -
300S LEU* 2.7 44.3 + - + -
301S ALA* 3.0 34.4 + - + +
306S LEU* 4.5 13.2 - - + -
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Residues in contact with VAL 296 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292S LYS* 2.8 20.4 + - + +
293S ASP* 4.9 1.8 - - - +
295S MET* 1.3 73.6 - - - +
297S ASN* 1.3 68.9 + - - +
298S SER 2.6 16.9 + - - -
299S ASN* 2.7 15.4 + - - -
301S ALA 3.3 18.6 - - - +
302S SER* 4.2 0.9 - - - -
303S VAL* 3.8 32.8 - - + +
306S LEU* 5.0 7.2 - - + -
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Residues in contact with ASN 297 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293S ASP* 3.0 33.2 + - - +
294S ARG* 3.8 2.2 - - - -
296S VAL* 1.3 88.2 - - - +
298S SER* 1.3 59.6 + - - +
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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