Contacts of the helix formed by residues 361 - 373 (chain C) in PDB entry 1EGE
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 361 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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269C ARG* 5.1 11.0 - - - +
273C GLU* 3.4 31.9 - - + +
351C LEU* 5.1 2.2 - - + -
359C GLU 4.6 1.3 - - - +
360C TYR* 1.3 93.9 - - + +
362C VAL* 1.3 64.0 + - + +
364C LYS* 2.7 37.3 + - + +
365C LEU* 3.2 17.4 + - + +
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Residues in contact with VAL 362 (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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273C GLU* 4.0 19.5 - - + -
344C ALA 4.4 1.0 - - - +
347C ALA* 3.6 26.9 - - + +
348C VAL* 3.5 24.4 - - + +
351C LEU* 3.5 28.3 - - + -
355C GLY* 3.4 33.4 - - - +
360C TYR* 4.5 3.6 - - + -
361C PRO* 1.3 73.7 - - + +
363C GLU* 1.3 58.7 + - - +
365C LEU* 2.9 27.5 + - + +
366C MET 3.2 10.0 + - - -
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Residues in contact with GLU 363 (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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348C VAL* 4.0 7.4 - - + -
355C GLY 3.2 16.4 - - - +
356C PHE* 4.4 2.5 - - - -
357C ASN 3.4 17.0 - - - +
358C THR* 3.5 28.3 + - - +
360C TYR 3.3 15.8 - - - +
361C PRO 3.1 0.2 + - - -
362C VAL* 1.3 82.9 - - - +
364C LYS* 1.3 74.1 + - - +
365C LEU 3.4 0.5 + - - -
366C MET* 3.7 0.9 + - - +
367C ARG* 3.2 54.7 + - - +
215D MET* 3.3 37.1 - - + +
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Residues in contact with LYS 364 (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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39C ALA* 5.1 7.9 - - - +
40C ALA* 5.4 7.2 - - - +
43C ASP* 3.6 33.2 - - + +
90C GLY 5.0 1.6 + - - -
91C CYS* 3.3 37.0 - - - +
217C GLN* 6.3 0.2 - - - +
360C TYR 4.6 0.2 - - - +
361C PRO* 2.7 24.8 + - + +
363C GLU* 1.3 88.0 - - - +
365C LEU* 1.3 67.9 + - + +
367C ARG* 3.4 21.1 + - - +
368C ASP* 2.8 42.3 + - - +
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Residues in contact with LEU 365 (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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90C GLY 5.7 1.1 - - - +
91C CYS* 6.5 0.7 - - - -
266C LEU* 3.3 30.8 - - + +
269C ARG* 4.2 35.0 - - + +
270C ALA* 4.7 13.9 - - + -
273C GLU* 4.7 2.0 - - + -
344C ALA* 3.9 8.1 - - + -
361C PRO* 3.2 33.0 + - + +
362C VAL* 2.9 23.1 + - + +
364C LYS* 1.3 89.3 - - + +
366C MET* 1.3 66.0 + - - +
367C ARG 3.0 2.0 + - - -
368C ASP* 3.3 5.9 + - - +
369C ALA* 2.9 26.3 + - - +
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Residues in contact with MET 366 (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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215C MET* 4.4 0.7 - - - +
341C ASN* 4.6 2.8 + - - +
344C ALA* 3.5 13.6 - - + +
345C THR* 3.7 31.4 - - - +
348C VAL* 4.0 13.0 - - + -
362C VAL 3.2 8.0 + - - +
363C GLU* 3.9 8.5 - - - +
364C LYS 3.5 0.2 - - - -
365C LEU* 1.3 79.1 - - - +
367C ARG* 1.3 61.8 + - - +
369C ALA* 3.7 9.2 - - - +
370C LYS 4.1 3.8 + - - -
215D MET* 4.0 19.1 - - + -
341D ASN* 4.8 4.3 - - - +
366D MET* 4.1 43.5 - - + +
367D ARG* 5.4 0.4 - - - -
370D LYS* 3.7 41.5 - - + -
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Residues in contact with ARG 367 (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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43C ASP* 2.8 38.7 + - - -
215C MET* 3.2 52.5 + - + +
216C GLY* 3.6 4.1 - - - -
218C ARG* 3.4 22.2 - - - +
358C THR* 5.1 2.2 + - - -
363C GLU* 3.2 44.9 + - - +
364C LYS* 3.4 18.6 - - - +
365C LEU 3.0 0.6 - - - -
366C MET* 1.3 76.7 - - - +
368C ASP* 1.3 69.2 + - - +
369C ALA 3.1 2.0 + - - -
370C LYS 3.6 2.6 + - - -
215D MET* 4.2 13.9 - - - +
356D PHE* 3.6 20.4 - - - -
367D ARG* 4.1 20.0 - - + +
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Residues in contact with ASP 368 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C ASP* 4.3 4.2 - - - +
92C THR* 3.3 24.4 + - - +
93C GLY 4.7 0.9 + - - -
216C GLY* 3.8 9.0 - - - -
217C GLN* 3.2 29.2 + - + +
266C LEU* 4.2 4.5 - - + -
364C LYS* 2.8 51.8 + - - +
365C LEU* 3.3 7.6 + - - +
367C ARG* 1.3 78.8 + - - +
369C ALA* 1.3 62.0 + - - +
370C LYS 3.4 0.2 - - - -
371C ILE* 3.2 24.1 - - - +
372C TYR* 4.2 3.1 - - - -
356D PHE* 4.6 0.2 - - - -
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Residues in contact with ALA 369 (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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266C LEU* 3.4 20.6 - - + +
340C ALA* 4.4 6.4 - - - +
341C ASN* 2.8 29.6 - - - +
344C ALA* 3.8 16.4 - - + -
365C LEU 2.9 18.5 + - - +
366C MET 3.7 5.8 - - - +
367C ARG 3.1 0.4 - - - -
368C ASP* 1.3 75.3 - - - +
370C LYS* 1.3 63.9 + - - +
372C TYR* 3.2 19.1 + - - +
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Residues in contact with LYS 370 (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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215C MET* 3.8 9.2 - - + -
341C ASN* 3.3 14.8 - - - +
366C MET 4.1 1.0 + - - +
367C ARG 3.6 1.8 + - - -
368C ASP 3.4 1.2 - - - -
369C ALA* 1.3 75.3 - - - +
371C ILE* 1.3 67.2 + - - +
373C GLN* 2.9 24.2 + - - +
374C ILE* 3.3 18.1 - - - +
345D THR* 3.3 44.1 + - + +
348D VAL* 3.9 20.4 - - - -
349D GLN* 2.8 31.0 + - - +
356D PHE* 3.5 18.4 - - + -
366D MET* 3.6 28.9 - - + -
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Residues in contact with ILE 371 (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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217C GLN* 3.3 28.0 - - - +
368C ASP 3.2 18.8 - - - +
370C LYS* 1.3 76.9 - - - +
372C TYR* 1.3 63.9 + - + +
373C GLN 3.0 0.2 - - - -
374C ILE* 2.8 36.9 + - + -
375C TYR* 3.2 35.1 + - + -
399C FAD 3.4 48.5 - - + -
356D PHE* 3.3 23.6 - - + -
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Residues in contact with TYR 372 (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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92C THR* 3.9 22.9 - - + +
95C GLN* 4.0 8.8 + - - -
96C THR* 4.5 0.3 + - - -
217C GLN* 4.0 17.9 + - - -
259C VAL* 2.9 36.7 - - + -
260C ALA* 5.5 0.2 - - - -
262C GLY* 3.0 19.5 + - - -
263C ALA* 3.1 35.2 - - + -
266C LEU* 4.8 3.8 - - + -
333C LYS* 2.7 28.3 + - + +
337C GLY* 4.1 16.9 - - - +
340C ALA* 5.2 1.3 - - + -
368C ASP 4.2 3.4 - - - -
369C ALA* 3.2 19.8 + - - +
370C LYS 3.0 1.8 + - - -
371C ILE* 1.3 82.5 - - + +
373C GLN* 1.3 59.0 + - - +
374C ILE 3.3 1.3 - - - -
375C TYR* 3.3 25.2 + - - -
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Residues in contact with GLN 373 (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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333C LYS* 4.2 4.3 - - - +
337C GLY* 3.9 10.3 - - - +
338C ASP* 3.0 32.4 - - - +
341C ASN* 3.6 29.5 + - - +
370C LYS* 2.9 32.1 + - - +
372C TYR* 1.3 78.5 - - - +
374C ILE* 1.3 60.0 + - - +
378C THR* 3.6 7.5 - - - +
379C SER* 3.5 18.4 + - - +
345D THR* 4.6 5.3 - - - +
349D GLN* 2.8 34.4 + - - +
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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