Contacts of the helix formed by residues 450 - 456 (chain D) in PDB entry 1C2O
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 450 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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202D GLU* 3.4 12.7 - - - +
228D GLN* 2.7 48.3 + - - +
229D SER* 4.1 5.3 + - - -
331D VAL* 3.7 15.9 - - + +
428D TYR* 3.9 8.0 + - - +
430D PHE* 3.6 38.8 - - + -
448D GLY* 3.5 19.1 + - - -
449D TYR* 1.3 79.4 + - - +
451D ILE* 1.4 69.7 + - - +
452D GLU 3.4 1.1 - - - -
453D PHE* 2.9 16.4 + - - +
454D ILE* 3.0 19.3 + - + +
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Residues in contact with ILE 451 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86D TRP* 4.2 12.8 - - + -
117D TRP* 3.8 13.0 - - + -
132D VAL* 4.1 8.5 - - + +
133D TYR* 3.9 20.2 - - + +
202D GLU* 3.5 44.4 - - + +
228D GLN* 5.0 2.0 - - - +
448D GLY* 2.8 23.3 - - - +
449D TYR 3.5 0.2 - - - -
450D GLU* 1.4 79.9 - - + +
452D GLU* 1.3 68.9 + - + +
453D PHE 3.0 0.5 + - - -
454D ILE* 3.1 5.3 + - + +
455D PHE* 2.9 56.7 + - + +
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Residues in contact with GLU 452 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85D MET* 4.6 7.3 - - + +
86D TRP* 6.5 0.4 - - + -
132D VAL* 4.5 23.2 - - + +
434D ALA* 4.0 11.8 - - - +
436D THR* 3.9 10.0 + - - -
437D LEU* 4.7 2.9 - - - +
448D GLY 5.1 1.3 - - - +
449D TYR* 3.6 41.7 - - + +
451D ILE* 1.3 75.5 - - - +
453D PHE* 1.3 64.7 + - + +
455D PHE* 3.9 0.7 - - - -
456D GLY 3.1 2.3 + - - -
457D LEU* 3.0 34.0 + - + +
458D PRO* 4.4 1.6 - - - -
465D TYR* 2.6 38.8 + - + +
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Residues in contact with PHE 453 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430D PHE* 3.4 24.9 - + + -
432D HIS* 3.8 14.8 - + - -
434D ALA* 3.4 36.1 - - + -
449D TYR 3.8 16.2 - - - -
450D GLU 2.9 7.6 + - - +
452D GLU* 1.3 77.9 - - + +
454D ILE* 1.3 68.6 + - - +
456D GLY* 2.7 16.8 + - - -
458D PRO* 3.7 25.6 - - + -
465D TYR* 4.0 5.6 - + - -
469D GLU* 3.6 31.9 - - + -
472D PHE* 4.2 11.4 - + - -
473D ALA* 4.1 12.2 - - + +
476D LEU* 3.5 24.2 - - + -
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Residues in contact with ILE 454 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117D TRP* 6.4 0.2 - - + -
138D LEU* 3.5 18.6 - - + +
200D PHE* 4.1 17.7 - - + -
228D GLN* 4.0 19.3 - - - +
430D PHE* 5.5 0.4 - - + -
450D GLU* 3.0 23.7 + - + +
451D ILE* 3.9 4.9 - - + +
453D PHE* 1.3 72.6 - - - +
455D PHE* 1.3 65.7 + - + +
456D GLY 3.2 0.2 + - - -
476D LEU* 3.8 18.8 - - + +
477D MET* 4.0 8.4 - - - +
480D TRP* 3.2 74.5 - - + +
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Residues in contact with PHE 455 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117D TRP* 3.5 45.1 - + - -
132D VAL 3.3 24.5 - - - +
133D TYR* 3.8 19.7 - - - -
134D ASP 3.7 17.4 - - - +
135D GLY* 4.2 0.4 - - - -
137D PHE* 3.5 20.8 - - - +
138D LEU* 3.5 22.4 + - + +
146D LEU* 3.9 24.7 - - + -
200D PHE* 3.5 24.7 - + - -
451D ILE* 2.9 30.6 + - + +
454D ILE* 1.3 76.3 - - + +
456D GLY* 1.3 60.5 + - - +
457D LEU* 3.6 12.3 - - + -
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Residues in contact with GLY 456 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137D PHE* 3.7 11.3 - - - -
452D GLU 3.1 0.8 + - - -
453D PHE 2.7 22.7 + - - -
454D ILE 3.2 0.2 - - - -
455D PHE* 1.3 73.7 - - - +
457D LEU* 1.3 65.4 + - - +
458D PRO* 3.1 5.2 - - - -
459D LEU* 3.0 40.1 + - - +
473D ALA* 4.5 0.7 - - - -
477D MET* 3.9 8.5 - - - -
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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