Contacts of the helix formed by residues 443 - 448 (chain X) in PDB entry 2W6C
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 GLU 443 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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199X GLU* 3.2 20.4 - - - +
225X GLN* 2.9 35.0 + - - +
226X SER* 4.3 3.1 + - - -
324X ASN* 2.8 35.6 + - - +
421X TYR* 4.3 12.8 - - + +
423X PHE* 3.8 29.6 - - + -
441X GLY 3.7 3.5 + - - -
442X TYR* 1.3 76.2 + - - +
444X ILE* 1.3 69.7 + - - +
445X GLU 3.3 1.1 - - - -
446X PHE* 3.0 14.9 + - - +
447X VAL* 3.0 19.3 + - + +
469X ILE* 5.8 0.6 - - + +
473X TRP* 5.6 0.7 - - + -
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Residues in contact with ILE 444 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84X TRP* 4.3 10.8 - - + -
114X TRP* 4.2 2.9 - - + -
129X VAL* 4.0 10.3 - - + +
130X TYR* 3.6 40.4 - - + +
199X GLU* 3.7 35.7 - - + +
225X GLN* 4.2 4.0 - - - +
441X GLY* 3.5 17.0 - - - +
442X TYR 3.3 0.2 - - - -
443X GLU* 1.3 93.9 - - - +
445X GLU* 1.3 58.9 + - - +
447X VAL* 2.9 9.5 + - - +
448X PHE* 2.8 46.2 + - + +
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Residues in contact with GLU 445 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83X MET* 4.6 3.6 - - - +
84X TRP* 5.8 0.3 - - - -
129X VAL* 4.1 24.4 - - + +
427X ALA* 4.1 12.6 - - - +
429X ASN* 4.3 2.3 - - - +
430X LEU* 5.2 0.5 - - - +
441X GLY 4.7 1.3 + - - +
442X TYR* 3.4 46.5 + - - +
444X ILE* 1.3 77.9 - - - +
446X PHE* 1.3 70.3 + - + +
448X PHE* 4.8 0.4 - - - -
449X GLY 3.2 2.1 + - - -
450X LEU* 3.0 43.4 + - + -
451X PRO* 3.2 4.7 - - - +
458X TYR* 2.6 38.7 + - + +
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Residues in contact with PHE 446 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423X PHE* 3.9 18.8 - + + -
425X HIS* 4.0 21.5 - + - -
427X ALA* 4.5 9.4 - - + -
442X TYR 3.8 20.2 - - - -
443X GLU 3.0 7.1 + - - +
445X GLU* 1.3 90.3 - - + +
447X VAL* 1.3 66.6 + - - +
449X GLY 2.9 4.0 + - - -
451X PRO* 4.0 15.0 - - + -
458X TYR* 4.4 11.9 - + - -
462X GLU* 3.7 33.9 - - + -
465X LEU* 3.9 18.4 - - + -
466X SER* 2.9 38.9 + - - +
469X ILE* 4.2 18.8 - - + -
470X MET* 4.0 0.5 - - - +
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Residues in contact with VAL 447 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135X LEU* 3.8 9.6 - - + +
197X PHE* 3.9 19.3 - - + -
225X GLN* 3.9 15.5 - - - +
443X GLU* 3.0 19.6 + - + +
444X ILE* 2.9 10.1 + - - +
446X PHE* 1.3 75.9 - - - +
448X PHE* 1.3 66.6 + - + +
449X GLY 3.3 0.2 - - - -
469X ILE* 3.8 17.5 - - + -
470X MET* 3.2 20.3 - - - +
473X TRP* 3.7 49.6 - - + +
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Residues in contact with PHE 448 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114X TRP* 3.5 61.5 - + + -
129X VAL 3.3 18.4 - - - +
130X TYR* 3.4 24.5 - + - -
131X ASN 3.5 20.8 - - - +
132X GLY* 4.5 1.8 - - - -
134X TYR* 3.3 20.8 - - - +
135X LEU* 4.2 11.1 + - + -
143X LEU* 4.2 20.0 - - + -
197X PHE* 4.0 15.5 - + - -
444X ILE* 2.8 23.2 + - + +
447X VAL* 1.3 84.2 - - + +
449X GLY* 1.3 60.3 + - - +
450X LEU* 3.5 14.5 + - + +
470X MET* 4.2 3.8 - - - -
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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