Contacts of the helix formed by residues 275 - 288 (chain E) in PDB entry 1G3I
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 275 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84E THR* 5.7 3.1 - - - -
87E THR* 3.8 22.9 - - + +
261E LYS 3.5 20.2 + - - -
262E ILE* 3.7 22.0 - - + +
263E CYS 4.1 9.6 + - - +
265E LYS* 3.7 38.5 - - - +
271E ALA 4.2 8.0 + - - +
272E ASP* 2.9 38.2 + - - +
274E SER* 1.3 77.0 - - - +
276E GLU* 1.3 54.8 + - - +
277E GLY 2.4 16.8 + - - -
278E VAL* 2.7 25.3 + - - +
279E GLN 3.6 2.8 + - - -
86J ARG* 5.8 3.2 - - - +
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Residues in contact with GLU 276 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262E ILE 4.2 0.8 + - - -
263E CYS 4.8 0.4 + - - -
264E LYS* 3.0 44.9 - - + +
272E ASP* 2.9 19.2 + - - +
273E VAL* 3.8 15.4 - - - +
275E ARG* 1.3 73.2 - - - +
277E GLY* 1.3 57.3 + - - +
279E GLN* 3.7 19.6 - - - +
280E ARG* 3.8 34.0 + - - +
320E ILE* 4.0 16.4 - - + +
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Residues in contact with GLY 277 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273E VAL 3.3 14.6 + - - -
274E SER* 4.3 3.1 - - - -
275E ARG 2.4 13.1 + - - -
276E GLU* 1.3 72.8 - - - +
278E VAL* 1.3 60.5 + - - -
279E GLN 3.0 1.8 - - - -
280E ARG* 3.0 11.3 + - - +
281E ASP* 2.5 33.9 + - - +
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Residues in contact with VAL 278 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83E ALA 3.7 20.4 - - - +
86E PHE* 3.7 42.2 - - + +
87E THR* 4.2 4.0 - - - +
96E VAL* 5.2 0.4 - - + -
262E ILE* 3.6 23.6 - - + -
274E SER 3.7 15.0 + - - +
275E ARG* 2.7 20.8 + - - +
277E GLY* 1.3 71.7 - - - -
279E GLN* 1.3 66.5 + - - +
281E ASP* 3.0 13.3 + - + +
282E LEU* 2.9 25.9 + - + +
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Residues in contact with GLN 279 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262E ILE* 3.0 34.2 + - + +
263E CYS* 4.0 0.2 - - - +
264E LYS* 2.3 40.6 + - - +
275E ARG 4.2 1.8 - - - +
276E GLU* 3.7 11.8 - - - +
277E GLY 3.0 0.8 - - - -
278E VAL* 1.3 76.6 - - - +
280E ARG* 1.3 55.8 + - - +
282E LEU* 2.6 28.4 + - - +
283E LEU* 3.1 11.1 + - - +
319E LEU* 3.3 16.8 - - + +
320E ILE* 2.8 46.7 + - + +
323E LEU* 3.7 16.2 - - + +
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Residues in contact with ARG 280 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82D GLU* 3.0 42.2 - - + +
84D THR* 4.6 17.4 + - - +
258D GLU* 3.6 14.6 + - - -
261D LYS* 3.8 29.8 - - - +
276E GLU* 3.8 34.9 + - - +
277E GLY* 3.0 10.3 + - - +
279E GLN* 1.3 78.3 - - - +
281E ASP* 1.3 59.7 + - - +
283E LEU* 3.7 13.6 - - - +
284E PRO* 3.6 16.8 - - - +
320E ILE* 3.5 25.6 - - + +
322E GLU* 5.4 3.6 + - - -
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Residues in contact with ASP 281 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85D LYS* 5.0 15.9 - - - +
86E PHE* 5.7 1.6 - - + +
96E VAL* 3.4 34.0 - - + +
277E GLY* 2.5 28.9 + - - +
278E VAL* 3.2 15.7 - - + +
279E GLN 2.8 2.0 + - - -
280E ARG* 1.3 81.4 - - - +
282E LEU* 1.3 57.2 + - - -
284E PRO* 3.5 12.2 - - - +
285E LEU* 4.4 0.7 - - - +
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Residues in contact with LEU 282 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83E ALA* 5.5 1.6 - - + -
86E PHE* 5.3 3.6 - - + -
96E VAL* 3.6 23.8 - - + -
99E ILE* 4.0 14.1 - - + -
256E ILE* 3.5 39.0 - - + -
259E ILE* 4.2 17.5 - - + -
262E ILE* 4.4 13.0 - - + -
278E VAL* 2.9 16.2 + - + +
279E GLN* 2.6 16.6 + - - +
281E ASP* 1.3 71.9 - - - +
283E LEU* 1.3 67.0 + - - +
284E PRO* 3.3 1.3 - - - -
285E LEU* 2.8 32.1 + - + +
286E VAL* 3.1 11.2 + - + +
323E LEU* 5.2 7.4 - - + -
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Residues in contact with LEU 283 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82D GLU* 4.3 18.2 - - - +
279E GLN 3.1 6.1 + - - +
280E ARG* 3.7 14.1 - - - +
282E LEU* 1.3 73.3 - - - +
284E PRO* 1.3 63.7 - - + +
285E LEU 2.9 1.6 + - - -
286E VAL* 2.9 6.6 + - + -
287E GLU* 2.5 64.6 + - + +
320E ILE* 3.4 29.4 - - + -
322E GLU* 3.7 17.0 - - + +
323E LEU* 3.8 34.9 - - + +
326E ARG* 5.1 0.2 - - + -
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Residues in contact with PRO 284 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82D GLU* 5.7 6.3 - - + +
97E ASP* 5.9 0.2 - - - +
280E ARG 3.6 8.5 - - - +
281E ASP* 3.5 12.1 - - - +
282E LEU 3.3 4.5 - - - -
283E LEU* 1.3 97.8 - - + +
285E LEU* 1.3 59.3 + - + +
287E GLU* 4.2 7.2 - - + +
288E GLY 2.8 27.4 + - - +
289E SER* 2.9 29.4 + - - +
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Residues in contact with LEU 285 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96E VAL* 3.8 40.4 - - + +
97E ASP* 3.9 14.1 - - - +
99E ILE* 4.2 18.6 - - + -
100E ILE* 3.8 34.5 - - + -
281E ASP 4.4 0.4 - - - +
282E LEU* 2.8 24.9 + - + +
284E PRO* 1.3 77.3 - - + +
286E VAL* 1.3 67.3 + - - +
288E GLY* 3.0 2.3 + - - -
289E SER* 4.8 3.8 - - - +
291E VAL* 4.9 1.1 - - + -
300E THR* 2.7 34.5 + - + +
305E PHE* 3.8 16.3 - - + -
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Residues in contact with VAL 286 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52E ASN* 4.6 3.9 - - - +
256E ILE* 5.3 5.4 - - + -
282E LEU* 3.1 11.2 + - + +
283E LEU* 2.9 8.2 + - + +
285E LEU* 1.3 80.4 - - + +
287E GLU* 1.3 64.6 + - - +
288E GLY* 3.1 2.3 + - - -
300E THR 4.4 4.5 - - - +
301E ASP 4.9 2.6 - - - +
305E PHE* 3.9 38.1 - - + -
323E LEU* 4.0 23.8 - - + -
326E ARG* 3.3 57.7 + - + +
327E LEU* 5.3 5.2 - - + -
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Residues in contact with GLU 287 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68D ARG* 4.4 13.5 + - - +
80D LYS* 3.3 28.5 + - - +
394D ARG* 4.9 4.9 - - - +
453D ATP 5.2 2.1 + - - -
283E LEU* 2.5 49.3 + - + +
284E PRO* 4.2 4.4 - - + +
286E VAL* 1.3 73.1 - - - +
288E GLY* 1.3 61.5 + - - +
301E ASP* 5.1 2.8 - - - +
322E GLU* 4.3 13.2 - - - +
326E ARG* 3.7 32.4 + - + +
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Residues in contact with GLY 288 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68D ARG* 4.6 17.0 + - - -
284E PRO* 2.8 11.4 + - - +
285E LEU 3.5 1.3 - - - -
286E VAL 3.0 5.0 - - - -
287E GLU* 1.3 84.0 - - - +
289E SER* 1.3 59.5 + - - -
300E THR* 3.1 11.0 - - - -
301E ASP* 3.8 30.1 - - - +
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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