Contacts of the helix formed by residues 86 - 94 (chain D) in PDB entry 1CX2
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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83D LYS* 5.4 6.5 - - - +
84D PRO 3.7 1.3 - - - +
85D THR* 1.4 92.3 - - + +
87D ASN* 1.3 55.0 + - - +
89D VAL* 3.4 13.1 - - + +
90D HIS* 2.8 25.2 + - - +
471D SER 5.4 5.6 - - - +
472D LEU* 4.3 13.2 - - + -
513D ARG* 3.0 29.4 + - - +
520D GLU* 3.8 23.8 - - + +
524D GLU* 3.6 22.7 - - - +
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Residues in contact with ASN 87 (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 THR* 2.9 26.6 - - + +
86D PRO* 1.3 80.6 - - - +
88D THR* 1.3 55.8 + - + +
89D VAL 2.9 4.5 - - - -
90D HIS* 3.4 7.5 - - - +
91D TYR* 2.7 36.7 + - - +
513D ARG* 3.7 22.9 + - - +
520D GLU* 4.2 18.2 + - - +
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Residues in contact with THR 88 (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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84D PRO* 3.1 14.2 - - - +
85D THR* 2.7 53.2 + - + +
87D ASN* 1.3 73.9 - - + +
89D VAL* 1.3 56.6 + - - +
91D TYR* 4.1 6.7 - - - +
92D ILE* 3.1 31.7 + - - +
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Residues in contact with VAL 89 (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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84D PRO* 3.3 33.4 - - + +
85D THR 2.7 17.0 + - - +
86D PRO* 3.4 11.4 - - + +
88D THR* 1.3 78.6 - - - +
90D HIS* 1.3 66.9 + - - +
91D TYR 3.3 0.3 + - - -
92D ILE* 3.4 10.3 + - + +
93D LEU* 3.2 33.8 + - + +
120D ARG* 4.7 16.6 - - - +
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Residues in contact with HIS 90 (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 PRO 2.8 19.9 + - - +
87D ASN* 3.4 9.4 - - - +
89D VAL* 1.3 77.2 - - - +
91D TYR* 1.3 62.1 + - - +
93D LEU* 3.1 9.6 + - - +
94D THR* 2.7 65.5 + - + -
353D SER 4.0 8.8 + - - -
354D GLY 4.5 0.4 - - - -
355D TYR* 4.1 10.2 - + - -
513D ARG* 3.1 39.8 - - + +
514D PRO* 5.8 8.6 - - + +
701D S58 2.9 37.2 + + - -
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Residues in contact with TYR 91 (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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87D ASN 2.7 19.3 + - - +
88D THR* 4.2 8.5 - - - +
90D HIS* 1.3 71.2 - - - +
92D ILE* 1.3 71.7 + - + +
94D THR* 2.9 4.1 + - - -
95D HIS* 2.8 73.4 + + - -
96D PHE* 3.9 22.8 - + - -
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Residues in contact with ILE 92 (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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84D PRO* 6.1 2.7 - - + -
88D THR 3.1 22.7 - - - +
89D VAL* 3.7 9.2 - - + +
90D HIS 3.4 0.2 - - - -
91D TYR* 1.3 82.2 - - + +
93D LEU* 1.3 62.5 - - - +
95D HIS 3.0 11.1 + - - +
96D PHE* 3.3 26.8 - - + -
100D TRP* 3.0 30.9 + - + -
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Residues in contact with LEU 93 (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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89D VAL* 3.2 24.2 + - + +
90D HIS* 3.3 10.8 - - - +
92D ILE* 1.3 81.0 - - - +
94D THR* 1.3 57.3 + - - +
100D TRP* 3.6 30.4 + - + -
112D ILE* 5.5 2.5 - - + -
116D VAL* 5.4 9.6 - - + -
120D ARG* 5.4 5.4 - - - +
355D TYR* 3.0 71.0 - - + +
356D HIS* 3.7 6.2 - - - +
357D PHE* 4.1 19.7 - - + -
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Residues in contact with THR 94 (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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90D HIS* 2.7 45.9 + - + -
91D TYR* 3.9 2.5 - - - -
93D LEU* 1.3 72.5 - - - +
95D HIS* 1.3 65.4 + - - +
354D GLY* 2.9 25.2 + - - +
355D TYR* 3.4 5.0 - - - +
356D HIS* 2.7 26.1 + - - -
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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