Contacts of the helix formed by residues 286 - 298 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43G ARG* 2.9 32.9 + - - -
228G MET* 4.6 0.4 - - - -
260G TYR* 2.9 20.0 + - - +
281G VAL 3.5 1.2 + - - -
282G ARG* 3.1 28.8 + - + +
285G SER* 1.3 74.1 - - - +
287G PRO* 1.3 68.3 - - - +
288G ILE* 2.8 30.5 + - - +
289G MET* 2.9 22.2 + - + +
290G LEU* 3.1 24.7 + - - +
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Residues in contact with PRO 287 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39G MET* 3.9 12.4 - - - +
43G ARG* 3.5 5.4 - - - +
67G GLY 4.1 9.9 - - - +
69G GLU* 3.4 25.6 - - - +
70G ALA* 3.8 30.5 - - + +
228G MET* 3.5 28.2 - - + +
230G ILE* 4.9 3.3 - - - +
260G TYR* 3.9 5.6 - - - +
285G SER 3.3 3.5 - - - +
286G ASP* 1.3 95.2 - - - +
288G ILE* 1.3 63.7 + - + +
290G LEU* 3.7 3.5 + - + +
291G LEU* 3.4 16.1 + - - +
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Residues in contact with ILE 288 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36G TYR* 3.7 29.1 - - + +
39G MET* 3.7 37.7 - - + +
40G GLN* 3.7 23.6 - - + +
43G ARG* 3.5 50.9 - - + +
69G GLU* 4.7 1.8 - - - +
286G ASP* 2.8 13.8 + - - +
287G PRO* 1.3 71.9 - - + +
289G MET* 1.3 59.0 + - - +
291G LEU* 3.2 4.0 + - - +
292G LYS* 2.9 25.3 + - + +
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Residues in contact with MET 289 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282G ARG 4.2 9.0 - - - +
283G SER* 3.5 26.2 - - - +
284G LYS 4.8 2.5 - - - +
285G SER 4.9 0.2 - - - -
286G ASP* 2.9 22.9 + - + +
287G PRO 3.4 0.2 - - - -
288G ILE* 1.3 75.9 - - - +
290G LEU* 1.3 92.7 + - + +
292G LYS* 3.1 13.9 + - + +
293G ASP* 2.9 55.9 + - - +
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Residues in contact with LEU 290 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228G MET* 3.6 24.5 - - + +
229G ASP* 5.2 4.0 - - + -
284G LYS 4.1 5.6 - - - +
285G SER* 3.5 33.9 - - - +
286G ASP 3.1 18.5 + - - +
287G PRO 3.9 2.7 - - - +
289G MET* 1.3 105.6 - - + +
291G LEU* 1.3 59.8 + - - +
293G ASP* 4.2 3.8 - - - +
294G ARG* 3.7 28.5 + - - +
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Residues in contact with LEU 291 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27G LEU* 5.0 12.8 - - + -
32G GLY* 4.1 5.8 - - - +
35G TYR* 4.0 13.2 - - + -
36G TYR* 3.7 32.8 - - + +
39G MET* 3.3 36.6 - - + -
230G ILE* 4.0 21.1 - - + +
231G LEU* 5.5 4.9 - - + -
287G PRO 3.4 2.8 + - - +
288G ILE 3.2 3.3 + - - +
289G MET 3.1 0.6 - - - -
290G LEU* 1.3 76.0 - - - +
292G LYS* 1.3 68.5 + - - +
294G ARG* 3.4 13.2 + - + +
295G MET* 3.0 43.0 + - + +
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Residues in contact with LYS 292 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36G TYR* 4.0 22.4 - - + -
288G ILE 2.9 14.1 + - - +
289G MET* 3.2 14.8 - - + +
291G LEU* 1.3 76.6 - - - +
293G ASP* 1.3 73.5 + - - +
295G MET* 3.0 15.7 + - - +
296G VAL* 3.1 16.1 + - + +
303G VAL* 4.1 33.7 + - - +
306G LEU* 3.3 31.1 - - + +
307G LYS* 5.5 2.0 - - - +
310G ASP* 5.2 5.4 + - - -
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Residues in contact with ASP 293 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289G MET* 2.9 51.9 + - - +
290G LEU* 4.7 2.9 - - - +
291G LEU 3.3 0.2 - - - -
292G LYS* 1.3 81.7 - - - +
294G ARG* 1.3 55.3 + - - +
295G MET 3.2 0.3 + - - -
296G VAL* 3.2 4.7 + - - +
297G ASN* 2.6 54.7 + - - +
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Residues in contact with ARG 294 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7G PHE* 3.6 43.5 - - + +
8G GLU 3.5 23.4 + - - -
9G ILE* 4.4 1.4 - - - +
27G LEU* 6.5 0.2 - - + -
229G ASP* 3.1 39.5 + - - -
230G ILE* 5.4 2.2 - - - +
231G LEU* 3.1 28.4 - - - +
290G LEU* 3.7 18.1 + - - +
291G LEU* 3.4 17.9 + - + +
292G LYS 3.4 0.4 - - - -
293G ASP* 1.3 75.9 - - - +
295G MET* 1.3 59.5 + - - +
297G ASN* 4.7 4.3 - - - -
298G SER* 2.7 35.1 + - - -
300G LEU* 6.0 0.4 - - + -
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Residues in contact with MET 295 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27G LEU* 4.4 9.4 - - - -
29G ARG 4.8 2.0 - - - +
32G GLY* 2.8 42.6 - - - +
33G LEU* 3.6 26.9 - - + +
36G TYR* 4.4 2.9 - - + -
291G LEU* 3.0 25.8 - - + +
292G LYS* 3.2 9.9 - - - +
294G ARG* 1.3 79.3 - - - +
296G VAL* 1.3 61.6 + - - +
298G SER 3.5 0.3 - - - -
299G ASN 3.1 2.9 + - - -
300G LEU* 2.9 48.4 + - - +
301G ALA* 4.1 16.2 - - + -
306G LEU* 4.1 19.3 - - + -
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Residues in contact with VAL 296 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292G LYS* 3.1 13.4 + - + +
293G ASP* 3.9 6.7 - - - +
295G MET* 1.3 75.0 - - - +
297G ASN* 1.3 65.3 + - - +
298G SER 2.6 17.4 + - - -
299G ASN* 2.9 12.6 + - - +
301G ALA 4.1 6.2 - - - +
302G SER* 3.9 9.4 - - - +
303G VAL* 3.6 37.0 - - + +
306G LEU* 4.8 7.6 - - + -
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Residues in contact with ASN 297 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293G ASP* 2.6 40.8 + - - +
294G ARG* 4.3 4.0 - - - +
296G VAL* 1.3 79.9 - - - +
298G SER* 1.3 58.3 + - - +
299G ASN 3.7 0.2 - - - -
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Residues in contact with SER 298 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2G ALA* 4.4 5.4 - - - +
5G ALA* 4.0 12.9 - - - +
7G PHE* 3.1 28.5 - - - -
294G ARG 2.7 20.5 + - - -
295G MET 3.8 1.0 + - - -
296G VAL 2.6 6.3 + - - -
297G ASN* 1.3 77.0 - - - +
299G ASN* 1.3 68.6 + - - +
300G LEU* 3.2 8.5 + - - +
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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