Contacts of the helix formed by residues 86 - 94 (chain B) in PDB entry 1CQE
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 86 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B ARG* 5.5 8.1 - - - +
84B PRO 4.3 1.8 - - - +
85B SER* 1.3 89.7 - - - +
87B SER* 1.3 56.1 + - - +
89B ILE* 3.5 8.1 + - + +
90B HIS* 2.9 29.5 + - - +
471B GLY 5.5 2.7 - - - +
472B MET* 4.4 12.3 - - + -
513B HIS* 4.6 3.3 + - + -
520B GLU* 3.4 35.2 - - + +
524B GLU* 3.9 30.8 - - + +
2802B BOG 6.4 1.3 - - - -
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Residues in contact with SER 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B SER* 3.9 10.7 + - - -
86B PRO* 1.3 74.5 - - - +
88B PHE* 1.3 64.6 + - - +
90B HIS* 3.4 2.9 + - - +
91B PHE* 3.1 22.3 + - - +
513B HIS* 4.2 19.5 + - - -
520B GLU* 3.2 18.7 + - - -
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Residues in contact with PHE 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B PRO* 3.4 26.0 - - + -
85B SER* 2.9 26.5 + - - +
87B SER* 1.3 72.9 - - - +
89B ILE* 1.3 70.3 + - + +
91B PHE* 3.2 25.2 - + + +
92B LEU* 3.2 51.0 - - + +
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Residues in contact with ILE 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B PRO* 3.2 37.9 - - + +
85B SER 3.0 15.0 + - - +
86B PRO* 3.7 9.4 - - + +
88B PHE* 1.3 80.6 - - + +
90B HIS* 1.3 64.2 + - - +
91B PHE 3.0 1.4 + - - -
92B LEU* 3.1 13.9 + - + +
93B LEU* 3.0 38.1 + - + +
2802B BOG 4.0 44.0 - - + -
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Residues in contact with HIS 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B PRO 2.9 19.1 + - - +
87B SER 3.6 5.4 - - - +
89B ILE* 1.3 76.2 - - - +
91B PHE* 1.3 60.3 + - - +
93B LEU* 3.6 9.0 + - - +
94B THR* 3.0 44.4 + - + +
192B GLN* 5.9 0.7 - - - -
353B SER 4.3 16.6 - - - -
355B TYR* 4.3 10.7 + + - -
513B HIS* 3.4 44.0 + + + +
514B PRO* 5.3 4.2 + - + -
516B SER* 3.5 21.4 + - - -
523B ILE* 3.9 18.1 - - + +
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Residues in contact with PHE 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B SER 3.1 12.2 + - - +
88B PHE* 3.2 17.7 - + + +
89B ILE 3.0 0.4 + - - -
90B HIS* 1.3 76.9 - - - +
92B LEU* 1.3 84.1 + - + +
94B THR* 3.1 17.3 + - - -
95B HIS* 2.9 58.8 + + + -
2803B BOG 4.6 16.8 - - + -
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Residues in contact with LEU 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88B PHE* 3.2 59.5 - - + +
89B ILE* 3.1 11.2 + - + +
91B PHE* 1.3 94.8 - - + +
93B LEU* 1.3 59.1 + - - +
95B HIS* 3.1 10.7 - - - +
100B TRP* 2.8 25.2 + - + -
2802B BOG 4.1 24.2 - - + -
2803B BOG 4.4 28.8 - - + +
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Residues in contact with LEU 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B ILE* 3.0 36.2 + - + +
90B HIS* 3.9 6.3 - - - +
91B PHE 3.1 0.2 - - - -
92B LEU* 1.3 76.2 - - - +
94B THR* 1.3 55.5 + - - +
95B HIS 3.5 0.7 - - - -
100B TRP* 3.7 27.7 + - + +
112B LEU* 6.2 0.2 - - + -
116B VAL* 6.3 0.4 - - + -
355B TYR* 3.5 45.2 - - + +
356B PHE* 2.7 36.4 + - - +
357B LEU* 4.0 23.9 + - + -
2802B BOG 4.4 25.1 - - + -
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Residues in contact with THR 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B HIS* 3.0 44.2 + - + +
91B PHE* 3.1 8.0 + - - -
93B LEU* 1.3 79.9 - - - +
95B HIS* 1.3 80.7 + - - +
353B SER 4.6 0.9 - - - +
354B GLY 3.7 25.8 - - - +
355B TYR* 4.4 4.0 - - + -
356B PHE* 3.0 23.8 - - - -
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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