Contacts of the helix formed by residues 274 - 286 (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 THR 274 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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275S ARG* 1.3 63.8 - - + +
276S GLU* 2.3 52.5 + - + +
277S GLU* 2.8 8.0 + - - +
278S ILE* 2.4 26.8 - - - +
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Residues in contact with ARG 275 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274S THR* 1.3 77.2 - - + +
276S GLU* 1.3 63.5 + - + +
278S ILE* 3.4 13.3 + - - +
279S GLN* 3.2 21.2 + - - +
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Residues in contact with GLU 276 (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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274S THR* 2.3 44.7 + - + +
275S ARG* 1.3 75.6 - - + +
277S GLU* 1.3 64.2 + - + +
279S GLN* 3.2 13.0 + - - +
280S GLU* 3.4 9.6 + - - +
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Residues in contact with GLU 277 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197S ARG* 3.5 16.9 + - - -
258S TYR* 3.3 30.3 + - - -
274S THR* 2.8 9.1 + - - +
276S GLU* 1.3 74.8 - - + +
278S ILE* 1.3 61.3 + - + +
280S GLU* 3.0 14.1 + - + +
281S VAL* 2.6 42.2 + - + +
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Residues in contact with ILE 278 (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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258S TYR* 3.0 24.9 - - + +
260S TYR* 3.8 44.0 - - + +
274S THR 2.4 37.5 - - - +
275S ARG* 3.5 11.2 - - - +
277S GLU* 1.3 75.0 - - + +
279S GLN* 1.3 57.6 + - - +
281S VAL* 3.4 5.1 - - - +
282S ARG* 3.0 37.1 + - - +
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Residues in contact with GLN 279 (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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275S ARG 3.2 7.2 + - - +
276S GLU* 3.2 11.1 + - - +
277S GLU 3.1 0.6 - - - -
278S ILE* 1.3 78.0 - - - +
280S GLU* 1.3 67.6 + - - +
282S ARG* 3.9 24.7 - - - +
283S SER* 2.7 38.7 + - - +
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Residues in contact with GLU 280 (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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276S GLU 3.4 4.9 + - - +
277S GLU* 3.0 22.1 + - + +
279S GLN* 1.3 81.0 - - - +
281S VAL* 1.3 68.0 + - + +
283S SER* 3.2 8.7 + - - -
284S LYS* 3.3 46.2 + - - +
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Residues in contact with VAL 281 (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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228S MET* 4.4 9.4 - - + -
258S TYR* 3.7 43.1 - - + -
260S TYR* 4.7 1.3 - - + -
277S GLU* 2.6 42.4 + - + +
278S ILE* 3.4 11.0 - - - +
280S GLU* 1.3 76.0 - - - +
282S ARG* 1.3 67.2 + - - +
283S SER 2.8 0.5 + - - -
284S LYS* 2.8 13.2 + - - -
285S SER* 3.0 25.5 + - - +
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Residues in contact with ARG 282 (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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43S ARG* 4.5 13.3 - - - +
47S LEU* 5.8 8.3 - - - +
66S ASP* 4.5 4.4 + - - -
260S TYR* 3.5 59.9 - - + +
261S HIS* 6.0 2.0 - - - -
278S ILE* 3.0 21.8 + - - +
279S GLN* 3.9 27.1 - - - +
281S VAL* 1.3 76.7 - - - +
283S SER* 1.3 65.5 + - - +
285S SER 3.9 0.4 - - - -
286S ASP* 3.1 30.2 + - + +
289S MET* 4.0 2.1 - - - +
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Residues in contact with SER 283 (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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279S GLN* 2.7 29.3 + - - +
280S GLU* 3.6 4.4 + - - -
281S VAL 2.8 4.8 + - - -
282S ARG* 1.3 75.0 - - - +
284S LYS* 1.3 60.7 + - - +
285S SER 2.9 6.4 + - - -
289S MET* 3.1 20.4 - - - +
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Residues in contact with LYS 284 (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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189F LYS* 6.2 2.2 - - - +
280S GLU* 3.3 34.8 + - - +
281S VAL* 2.8 12.2 + - - +
283S SER* 1.3 76.3 - - - +
285S SER* 1.3 64.4 + - - +
289S MET* 4.0 7.1 - - - +
290S LEU* 4.3 5.2 - - - +
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Residues in contact with SER 285 (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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228S MET* 3.3 32.3 - - - +
260S TYR* 4.1 1.0 + - - -
281S VAL* 3.0 24.2 + - - +
282S ARG* 3.7 3.0 - - - -
283S SER 2.9 5.3 + - - -
284S LYS* 1.3 85.0 - - - +
286S ASP* 1.3 63.4 + - - +
289S MET* 3.9 6.5 - - - -
290S LEU* 4.1 16.2 - - - -
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Residues in contact with ASP 286 (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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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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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