Contacts of the helix formed by residues 75 - 83 (chain D) in PDB entry 7CAL
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 TRP 75 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71D ILE 3.5 11.7 + - - +
72D TYR* 3.0 11.3 + + + +
74D ALA* 1.3 78.6 - - - +
76D ILE* 1.3 74.8 + - + +
77D CYS 3.2 4.6 + - - -
78D PRO* 3.6 1.6 - - - +
79D PHE* 3.3 51.0 - + - +
210D HIS* 3.0 36.8 + + - -
247D TYR* 3.5 22.6 + + - -
701D 3PE 3.5 44.9 - - + +
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Residues in contact with ILE 76 (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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72D TYR* 3.3 60.5 + - + +
73D SER* 4.4 2.2 - - - -
75D TRP* 1.3 94.9 - - + +
77D CYS* 1.3 64.7 + - - +
78D PRO 3.5 0.4 - - - -
79D PHE* 3.7 13.5 - - + -
80D GLN* 3.3 41.8 + - + +
91D ILE* 5.2 8.3 - - + -
95D ASP* 4.7 8.7 - - + -
171D ARG* 3.6 24.0 - - - +
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Residues in contact with CYS 77 (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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73D SER 3.3 18.8 - - - +
75D TRP 3.2 2.2 - - - +
76D ILE* 1.3 83.0 - - - +
78D PRO* 1.4 64.5 - - + +
80D GLN* 4.7 2.1 + - - +
81D PHE* 3.5 9.7 + - - +
168D SER* 3.3 27.9 + - - +
169D MET* 3.3 26.9 - - - +
171D ARG* 3.6 37.8 + - - +
172D LEU* 4.0 11.7 - - + -
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Residues in contact with PRO 78 (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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74D ALA 3.8 11.9 - - - +
75D TRP 3.6 7.0 - - - +
77D CYS* 1.4 92.4 - - + +
79D PHE* 1.3 62.0 + - - +
80D GLN 3.6 0.2 - - - -
81D PHE* 3.6 5.4 - - + +
82D ALA* 3.6 13.0 + - - +
169D MET* 3.7 10.1 - - + -
172D LEU* 4.9 5.6 - - + -
207D PHE* 5.0 1.6 - - + -
210D HIS* 3.5 25.8 - - + -
211D CYS* 4.4 15.7 - - + -
214D CYS* 3.4 22.0 - - + +
215D PHE* 4.0 24.0 - - + -
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Residues in contact with PHE 79 (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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75D TRP* 3.3 48.4 + + + +
76D ILE* 3.7 9.6 + - + -
77D CYS 3.5 0.6 - - - -
78D PRO* 1.3 79.7 - - - +
80D GLN* 1.3 64.5 + - + +
83D PHE* 3.0 62.4 + + + +
84D ILE* 3.7 12.6 + - + -
210D HIS* 4.1 5.6 - + - +
214D CYS* 4.4 4.7 - - - -
244D TRP 5.4 6.1 - - - -
245D ASN* 5.1 10.5 - - - -
247D TYR* 4.2 30.3 - + - -
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Residues in contact with GLN 80 (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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76D ILE* 3.3 28.1 + - + +
77D CYS 4.7 2.2 - - - +
79D PHE* 1.3 79.3 - - + +
81D PHE* 1.3 64.9 + - - +
82D ALA 3.2 1.5 + - - -
84D ILE* 2.9 37.9 - - + +
87D LYS* 4.9 11.1 - - + +
91D ILE* 4.0 22.5 - - + +
95D ASP* 5.3 7.0 - - - +
165D ARG* 3.3 13.4 + - - +
168D SER* 4.4 5.1 + - - -
171D ARG* 3.4 32.5 - - - +
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Residues in contact with PHE 81 (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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77D CYS 3.5 18.8 + - - +
78D PRO 3.6 8.0 - - - +
79D PHE 3.2 0.4 - - - -
80D GLN* 1.3 83.6 - - - +
82D ALA* 1.3 59.2 + - + +
162D LEU* 5.5 3.4 - - + -
165D ARG* 3.4 64.3 + - + +
166D ILE* 4.0 26.7 - - + -
169D MET* 3.6 21.5 - - + -
215D PHE* 3.8 27.8 - + - -
218D LEU* 3.5 40.1 - - + +
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Residues in contact with ALA 82 (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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78D PRO 3.6 8.9 + - - +
79D PHE 3.5 1.8 + - - -
80D GLN 3.2 0.6 - - - -
81D PHE* 1.3 81.8 - - + +
83D PHE* 1.3 78.1 + - + +
84D ILE 3.8 0.4 - - - -
85D THR* 4.1 11.4 - - - -
214D CYS 3.3 27.4 - - - +
217D TYR* 4.6 7.3 - - + -
218D LEU* 4.0 22.6 - - + +
221D ASP* 4.5 11.6 - - - +
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Residues in contact with PHE 83 (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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79D PHE* 3.0 39.5 + + + +
82D ALA* 1.3 80.5 - - + +
84D ILE* 1.3 63.0 + - + +
85D THR* 3.0 8.7 + - - -
213D GLY 4.3 0.7 - - - -
214D CYS* 3.6 30.3 - - + -
217D TYR* 3.6 49.6 - + + -
221D ASP* 5.6 1.0 - - - +
244D TRP* 4.8 30.4 + + + +
247D TYR* 3.5 39.7 - + + -
250D ALA* 4.1 9.4 - - + -
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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