Contacts of the helix formed by residues 347 - 359 (chain A) in PDB entry 2G1X
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 HIS 347 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A PRO* 3.9 4.2 - - - +
40A TYR 3.7 10.1 + - - -
41A GLN* 3.5 22.4 + - - +
345A TRP* 5.1 13.3 - - + +
346A PHE* 1.3 76.8 - - - +
348A LEU* 1.3 76.6 + - + +
349A ALA* 2.9 38.8 - - + +
350A ILE* 2.8 35.1 - - + +
351A PHE* 3.6 6.1 - - - -
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Residues in contact with LEU 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A PRO* 3.0 39.9 - - + +
22A GLN* 4.4 13.7 - - + -
40A TYR* 2.9 43.7 - - + +
41A GLN* 3.6 13.5 - - - +
194A GLU* 2.7 48.3 - - - +
195A GLU* 3.8 3.8 - - - +
347A HIS* 1.3 96.6 - - + +
349A ALA* 1.3 59.2 + - - +
350A ILE 3.2 1.2 + - - -
351A PHE 3.5 1.6 + - - -
352A ASP* 2.5 16.3 + - - +
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Residues in contact with ALA 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A GLN* 3.1 15.3 + - - +
347A HIS* 2.9 18.0 - - + +
348A LEU* 1.3 76.9 - - - +
350A ILE* 1.3 64.8 + - - +
352A ASP* 3.0 26.5 + - + +
353A PHE* 3.5 7.3 + - - +
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Residues in contact with ILE 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333A ILE* 3.4 37.2 - - + -
346A PHE* 4.2 5.6 - - + -
347A HIS* 2.8 39.8 + - + +
349A ALA* 1.3 80.6 - - - +
351A PHE* 1.3 89.2 + - + +
353A PHE* 4.0 1.4 + - - +
354A PHE* 2.7 40.6 - - + -
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Residues in contact with PHE 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A PRO* 4.9 2.7 - - + -
193A GLU* 3.7 27.6 - - + +
194A GLU* 3.0 37.5 - - + +
333A ILE* 4.0 24.5 - - + -
334A SER* 5.0 0.4 - - - -
337A MET* 3.8 28.3 - - + -
338A PRO* 4.1 23.8 - - + -
346A PHE* 3.4 27.4 - + + -
347A HIS 3.6 5.6 - - - -
348A LEU 3.5 0.4 + - - -
349A ALA 3.3 0.4 - - - -
350A ILE* 1.3 110.4 - - + +
352A ASP* 1.4 64.3 + - - +
353A PHE 3.2 0.3 + - - -
354A PHE* 3.4 6.5 + - - +
355A THR* 3.0 20.1 + - - -
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Residues in contact with ASP 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A GLN* 3.3 0.6 - - - +
194A GLU* 2.7 37.1 - - - +
195A GLU* 2.7 40.4 + - - +
348A LEU 2.5 24.9 - - - +
349A ALA* 3.0 13.8 + - - +
351A PHE* 1.4 74.4 - - - +
353A PHE* 1.3 58.0 + - - +
356A TRP* 2.7 58.2 + - + +
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Residues in contact with PHE 353 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329A PRO* 5.1 2.9 - - + -
349A ALA 3.5 7.3 + - - +
350A ILE 4.6 0.7 - - - +
351A PHE 3.2 1.0 - - - -
352A ASP* 1.3 79.2 - - - +
354A PHE* 1.3 87.7 + + + +
356A TRP* 3.8 3.7 - - + +
357A LEU* 2.8 72.1 + - + +
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Residues in contact with PHE 354 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326A CYS 4.7 1.7 - - - +
329A PRO* 3.0 43.5 - - + -
330A PHE* 3.4 13.7 - - - +
332A ILE* 4.1 6.1 - - + -
333A ILE* 3.1 48.5 - - + -
350A ILE* 2.7 36.8 - - + -
351A PHE 3.4 1.5 + - - +
353A PHE* 1.3 93.3 - + + +
355A THR* 1.3 63.6 + - - +
357A LEU* 3.7 2.6 - - - +
358A GLY* 2.9 21.8 + - - -
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Residues in contact with THR 355 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A TRP* 4.9 1.1 - - - +
129A ASP* 5.6 1.8 - - - +
193A GLU* 3.4 3.5 + - - -
194A GLU* 2.7 18.7 + - - +
198A GLU* 3.1 47.6 + - + +
200A VAL* 4.7 0.2 - - + -
327A TRP* 5.8 1.4 - - - -
330A PHE* 2.8 31.9 - - + -
351A PHE 3.0 11.9 + - - -
354A PHE* 1.3 78.6 - - - +
356A TRP* 1.4 50.7 + - - +
358A GLY* 3.1 10.0 + - - -
359A TYR* 2.7 31.4 + - + -
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Residues in contact with TRP 356 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A LYS* 3.1 52.8 + - + +
52A LEU* 3.8 28.6 - - + +
53A VAL* 4.0 2.8 - - - +
56A LEU* 4.8 0.9 - - - +
110A THR* 4.3 2.2 - - + -
194A GLU* 2.7 20.6 - - - -
195A GLU* 3.9 3.1 - - - -
197A SER* 2.8 33.9 - - - -
352A ASP* 2.7 65.7 + - + +
353A PHE* 3.9 4.3 - - + +
355A THR* 1.4 73.5 - - - +
357A LEU* 1.3 61.0 + - - +
359A TYR* 2.7 64.3 + + - +
360A LEU* 3.9 1.4 + - - +
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Residues in contact with LEU 357 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325A VAL* 4.4 22.2 - - + +
326A CYS* 4.7 11.9 - - - +
329A PRO* 4.9 7.6 - - + -
353A PHE* 2.8 58.4 + - + +
354A PHE 3.7 3.6 - - - +
356A TRP* 1.3 73.4 - - - +
358A GLY* 1.3 62.8 + - - +
360A LEU* 2.9 53.2 + - + +
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Residues in contact with GLY 358 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326A CYS 4.0 12.5 + - - -
327A TRP* 4.1 16.2 - - - -
354A PHE 2.9 14.2 + - - -
355A THR 3.5 6.5 - - - -
356A TRP 3.1 0.4 - - - -
357A LEU* 1.3 76.9 - - - +
359A TYR* 1.3 50.8 + - - +
361A ASN* 2.7 49.1 + - - +
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Residues in contact with TYR 359 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A LEU* 4.6 3.4 - - + -
53A VAL* 4.2 7.9 - - + -
56A LEU* 3.1 22.2 - - + +
98A VAL* 6.0 1.0 - - - +
103A MET* 4.6 4.9 - - + +
106A SER* 4.0 9.5 - - - -
125A TRP* 2.9 46.0 - + - -
129A ASP* 5.3 7.2 - - - -
197A SER 4.7 0.2 + - - -
198A GLU* 3.3 18.7 - - - +
355A THR* 2.7 40.4 - - + -
356A TRP* 2.7 62.3 + + - +
358A GLY* 1.3 70.1 - - - +
360A LEU* 1.3 60.6 + - - +
361A ASN* 2.9 7.8 + - - -
362A SER* 3.0 23.2 + - - -
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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