Contacts of the helix formed by residues 69 - 75 (chain a) in PDB entry 5W97
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 MET 69 (chain a).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23a GLY 3.8 11.2 - - - +
27a GLY* 3.6 20.4 - - - +
64a VAL 2.8 5.3 + - - +
65a MET* 3.2 45.1 + - + +
68a PHE* 1.3 79.3 - - - +
70a VAL* 1.3 87.7 + - + +
71a MET 3.6 0.2 - - - -
72a PRO* 3.4 1.4 - - - +
73a ILE* 3.1 44.4 + - + +
386a VAL* 4.3 10.1 - - + -
389a ILE* 4.2 8.1 - - - -
601a HEA 3.9 39.9 - - + -
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Residues in contact with VAL 70 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65a MET 2.7 21.8 + - - +
69a MET* 1.3 85.0 - - + +
71a MET* 1.3 68.3 + - - +
73a ILE* 3.2 1.4 + - - +
74a MET* 3.0 48.5 + - + +
246a LEU* 3.6 30.3 - - + +
385a ALA* 4.4 13.2 - - + -
386a VAL* 5.4 1.1 - - + -
389a ILE* 4.3 10.3 - - + -
601a HEA 3.4 25.8 - - + -
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Residues in contact with MET 71 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66a ILE 3.2 16.4 + - - +
67a PHE* 4.1 24.0 - - + +
70a VAL* 1.3 79.2 - - - +
72a PRO* 1.3 71.4 - - + +
74a MET* 5.1 0.7 - - - -
75a ILE* 3.1 48.9 + - + +
76a GLY 3.5 0.2 + - - -
157a SER* 3.4 26.2 - - - +
195a LEU* 3.8 23.3 - - + -
199a LEU* 5.5 2.5 - - + -
242a GLU* 3.1 27.6 - - - +
245a ILE* 4.3 3.6 - - + -
246a LEU* 3.6 15.0 - - + -
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Residues in contact with PRO 72 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19a TYR* 3.4 34.4 - - + +
22a PHE* 4.4 9.4 - - + -
23a GLY* 5.0 0.9 - - - -
67a PHE 3.2 25.6 - - - +
68a PHE* 3.3 22.0 - - - +
69a MET 3.4 10.8 - - - +
71a MET* 1.3 89.6 - - + +
73a ILE* 1.3 55.9 + - - +
76a GLY* 3.1 6.4 + - - +
77a GLY 2.8 24.6 + - - -
105a LEU* 4.2 17.5 - - + -
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Residues in contact with ILE 73 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19a TYR 4.7 2.5 - - - +
20a LEU* 3.8 18.5 - - + +
23a GLY* 3.8 32.1 - - - -
24a ALA 4.5 0.4 - - - +
69a MET* 3.1 42.3 + - - +
70a VAL 3.2 3.2 + - - +
71a MET 3.2 0.6 - - - -
72a PRO* 1.3 77.2 - - - +
74a MET* 1.3 58.2 + - - +
77a GLY* 3.1 6.1 + - - +
78a PHE* 3.0 53.3 + - + -
389a ILE* 3.7 20.4 - - + -
601a HEA 4.0 24.0 - - + -
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Residues in contact with MET 74 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70a VAL* 3.0 23.0 + - - +
71a MET* 4.5 0.9 - - - +
73a ILE* 1.3 78.8 - - - +
75a ILE* 1.3 60.9 + - + +
78a PHE* 3.3 13.4 - - - +
79a GLY* 3.1 21.5 + - - -
184a PHE* 4.1 7.1 - - - -
188a VAL* 5.4 0.3 - - - +
245a ILE 5.2 0.4 - - - +
246a LEU* 3.3 27.4 - - - +
249a PRO* 4.1 17.7 - - + +
250a GLY* 3.7 31.9 - - - -
253a MET* 3.7 17.3 - - + -
385a ALA* 3.4 33.4 - - + +
388a ALA* 4.4 0.4 - - + -
389a ILE* 3.8 17.0 - - + -
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Residues in contact with ILE 75 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71a MET* 3.1 38.7 + - + +
74a MET* 1.3 75.6 - - + +
76a GLY* 1.3 69.1 + - - +
79a GLY* 3.1 22.6 - - - -
160a GLY* 6.1 1.3 - - - -
164a PHE* 3.3 36.2 - - + -
188a VAL* 5.3 9.0 - - + -
191a THR* 4.1 28.3 - - + -
195a LEU* 4.3 14.6 - - + -
245a ILE* 4.2 16.2 - - + +
249a PRO* 4.3 10.1 - - + -
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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