Contacts of the helix formed by residues 277 - 292 (chain C) in PDB entry 1I43
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 PRO 277 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130C GLU* 3.8 16.6 - - + +
248C LEU* 5.1 1.8 - - + -
253C ASP* 3.0 22.9 - - + +
254C LEU* 4.5 0.4 - - + -
276C GLY* 1.3 85.4 - - - +
278C LEU* 1.3 60.7 + - - +
279C LYS* 4.6 6.5 - - + +
280C LEU* 3.2 31.3 + - + +
281C VAL* 2.9 27.4 + - - +
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Residues in contact with LEU 278 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130C GLU* 2.9 42.3 + - + +
131C SER* 4.5 11.0 - - - -
277C PRO* 1.3 69.0 - - - +
279C LYS* 1.3 67.7 + - - +
280C LEU 2.8 2.1 + - - -
281C VAL* 3.7 8.1 - - + -
282C SER* 2.8 38.6 + - - +
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Residues in contact with LYS 279 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130C GLU* 4.5 1.2 + - - -
277C PRO* 3.4 5.4 - - + -
278C LEU* 1.3 78.8 - - - +
280C LEU* 1.3 69.3 + - + +
282C SER* 3.3 13.7 + - - -
283C GLU* 3.7 14.7 - - - +
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Residues in contact with LEU 280 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149C LEU* 4.1 20.4 - - + +
232C LEU* 4.0 20.6 - - + -
253C ASP* 4.0 18.2 - - + +
254C LEU* 3.8 37.2 - - + -
277C PRO* 3.2 22.9 + - + +
278C LEU 2.8 4.4 + - - -
279C LYS* 1.3 87.2 - - + +
281C VAL* 1.3 67.3 + - - +
282C SER 3.1 1.6 - - - -
283C GLU* 2.9 24.6 + - + +
284C ILE* 3.5 8.9 + - - +
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Residues in contact with VAL 281 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131C SER* 3.2 40.6 - - - +
132C THR 4.5 0.2 - - - -
133C LEU* 4.0 21.2 - - + +
254C LEU* 4.4 3.5 - - + +
274C ILE* 3.8 30.7 - - + +
276C GLY* 4.5 6.1 - - - +
277C PRO 2.9 22.7 + - - +
278C LEU* 3.5 7.0 - - + +
280C LEU* 1.3 74.0 - - - +
282C SER* 1.3 62.3 + - - +
284C ILE* 3.2 13.2 + - + +
285C ARG* 3.0 28.2 + - - +
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Residues in contact with SER 282 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278C LEU* 2.8 36.1 + - - +
279C LYS* 3.3 10.4 + - - -
281C VAL* 1.3 76.7 - - - +
283C GLU* 1.3 70.9 + - - +
285C ARG* 3.2 12.1 + - - +
286C ASN* 3.1 28.1 + - - +
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Residues in contact with GLU 283 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148C ALA* 4.3 17.5 - - - +
149C LEU* 4.6 15.2 - - + +
279C LYS 3.7 14.1 - - - +
280C LEU* 2.9 13.7 + - + +
282C SER* 1.3 82.2 + - - +
284C ILE* 1.3 63.4 + - - +
286C ASN* 3.5 25.5 + - - +
287C LEU* 3.6 4.3 + - - +
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Residues in contact with ILE 284 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133C LEU* 3.7 19.3 - - + -
135C MET* 4.0 5.2 - - + -
144C VAL* 3.8 20.0 - - + -
145C MET* 3.9 36.6 - - + -
148C ALA* 4.1 8.7 - - + -
149C LEU* 4.2 19.7 - - + -
254C LEU* 4.4 5.2 - - + -
274C ILE* 4.0 23.3 - - + -
280C LEU 4.0 6.7 - - - +
281C VAL* 3.4 17.5 - - + +
282C SER 3.1 0.4 - - - -
283C GLU* 1.3 73.8 - - - +
285C ARG* 1.3 66.5 + - - +
286C ASN 3.0 2.5 + - - -
287C LEU* 3.0 5.7 + - - +
288C HIS* 2.8 19.1 + - - +
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Residues in contact with ARG 285 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111C TYR 5.4 3.4 + - - -
117C VAL* 5.9 1.4 - - - +
120C GLU* 3.0 30.5 + - - -
131C SER* 3.5 17.4 + - - -
132C THR 3.4 22.0 + - - -
133C LEU* 3.6 26.2 - - + +
281C VAL* 3.0 16.9 + - - +
282C SER* 3.4 14.3 - - - +
284C ILE* 1.3 76.1 - - - +
286C ASN* 1.3 59.6 + - - +
288C HIS* 3.1 9.9 - - - +
289C HIS* 2.9 57.5 + - + +
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Residues in contact with ASN 286 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282C SER* 3.1 15.6 + - - +
283C GLU* 3.5 22.3 + - - +
284C ILE 3.0 0.8 + - - -
285C ARG* 1.3 79.9 - - - +
287C LEU* 1.3 66.6 + - - +
289C HIS* 3.1 25.6 + - - +
290C ILE* 3.5 12.6 + - - +
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Residues in contact with LEU 287 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A ILE* 3.8 33.4 - - + -
144C VAL* 3.7 12.3 - - + +
147C LEU* 3.7 19.1 - - + +
148C ALA* 3.6 41.1 - - + +
283C GLU 3.6 2.9 + - - +
284C ILE 3.0 8.0 + - - +
286C ASN* 1.3 78.7 - - - +
288C HIS* 1.3 57.0 + - - +
290C ILE* 3.0 16.0 + - + +
291C LEU* 2.9 49.8 + - + +
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Residues in contact with HIS 288 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110C ARG 4.9 5.0 + - - -
133C LEU* 3.9 27.6 - - + +
134C LEU 3.8 11.1 + - - -
135C MET* 3.5 27.0 - - + +
140C CYS* 5.0 1.6 - - - -
144C VAL* 4.1 7.4 - - - +
284C ILE 2.8 13.1 + - - +
285C ARG* 3.1 12.6 - - - +
287C LEU* 1.3 72.9 - - - +
289C HIS* 1.3 71.5 + + - +
290C ILE 2.9 5.1 + - - -
291C LEU* 4.5 3.1 - - - +
292C GLY* 2.9 29.6 + - - -
293C GLY* 3.3 42.1 + - - -
294C ALA* 3.7 9.6 - - - +
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Residues in contact with HIS 289 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A LYS* 4.6 6.4 - - - +
110C ARG* 3.1 51.9 + - - +
111C TYR* 3.5 45.6 + + + -
285C ARG* 2.9 48.2 + - + +
286C ASN* 3.1 16.9 + - - +
288C HIS* 1.3 83.4 - + - +
290C ILE* 1.3 60.5 + - + +
292C GLY 4.3 0.9 - - - -
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Residues in contact with ILE 290 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A MET* 3.3 30.6 - - + +
143A THR* 3.9 1.6 + - - +
165A LYS* 4.5 26.0 - - + +
168A ILE* 4.0 27.1 - - + -
169A PHE* 4.0 37.9 - - + +
172A THR* 5.4 2.7 - - - +
173A ILE* 5.5 3.1 - - + -
286C ASN 3.9 12.8 - - - +
287C LEU* 3.0 19.0 + - + +
288C HIS 2.9 0.8 - - - -
289C HIS* 1.3 81.7 - - + +
291C LEU* 1.3 69.6 + - + +
292C GLY 3.0 2.4 + - - -
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Residues in contact with LEU 291 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A CYS* 2.9 31.1 - - - +
143A THR* 3.4 35.2 - - + +
147A LEU* 5.1 4.0 - - + -
169A PHE* 3.8 18.6 - - + -
173A ILE* 5.9 0.7 - - + -
291A LEU* 6.3 2.7 - - + -
140C CYS* 6.3 0.7 - - - -
143C THR* 5.3 2.5 - - + -
144C VAL* 3.8 28.9 - - + -
147C LEU* 4.4 16.8 - - + -
287C LEU* 2.9 44.6 + - + +
288C HIS* 4.3 3.6 - - - +
290C ILE* 1.3 75.3 - - - +
292C GLY* 1.3 60.8 + - - +
293C GLY 4.9 2.2 - - - +
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Residues in contact with GLY 292 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A ALA* 3.7 5.4 - - - +
137A SER* 2.7 29.2 + - - -
139A MET* 4.3 1.1 - - - -
140A CYS* 3.2 12.4 - - - +
110C ARG* 3.8 19.3 - - - -
288C HIS* 2.9 14.5 + - - -
290C ILE 3.0 3.4 - - - -
291C LEU* 1.3 77.7 - - - +
293C GLY* 1.3 55.8 + - - -
294C ALA 3.2 8.7 + - - -
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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