Contacts of the helix formed by residues 74 - 79 (chain E) in PDB entry 3SZ9
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 SER 74 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68E ALA 4.2 6.5 - - - -
69E ALA* 2.7 32.3 + - - -
71E GLN* 3.0 22.1 + - - +
72E LEU 3.3 1.2 + - - -
73E GLY* 1.3 79.8 - - - +
75E PRO* 1.3 77.1 - - - +
76E TRP 3.6 0.7 + - - -
77E ARG* 3.2 14.1 + - - +
78E ARG* 3.0 22.6 + - - +
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Residues in contact with PRO 75 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73E GLY 4.5 0.7 - - - +
74E SER* 1.3 89.0 - - - +
76E TRP* 1.3 56.1 + - - +
78E ARG* 4.0 2.8 - - + +
79E MET* 3.0 36.2 + - + +
214E PRO* 4.4 19.1 - - + -
215E PRO* 6.5 0.4 - - + -
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Residues in contact with TRP 76 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69E ALA* 3.7 13.9 - - + +
70E PHE* 5.1 2.9 - + - -
74E SER* 3.3 1.8 + - - -
75E PRO* 1.3 79.9 - - - +
77E ARG* 1.3 62.3 + - - +
78E ARG 3.6 0.2 + - - -
79E MET* 3.7 38.0 + - - +
84E ARG* 3.7 27.1 + - + -
87E LEU* 3.9 4.7 - - + -
183E LEU* 3.6 25.1 - - + -
186E GLY* 3.2 20.0 + - - -
187E ASN 2.8 23.1 + - - -
188E VAL* 3.6 22.0 - - + -
213E PHE* 3.8 33.4 - + - -
214E PRO* 3.8 22.4 - - + +
217E VAL* 3.4 29.3 - - + +
500H SER* 4.7 3.6 + - - -
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Residues in contact with ARG 77 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70E PHE* 2.8 80.8 + - - +
71E GLN 3.2 13.0 - - - +
72E LEU* 3.7 30.0 - - - +
74E SER* 3.2 13.5 + - - +
76E TRP* 1.3 79.6 - - - +
78E ARG* 1.3 59.9 + - - +
79E MET 4.2 2.4 - - - +
157E GLU* 5.3 2.8 + - - -
158E PRO* 4.5 3.4 - - - +
186E GLY 4.7 2.7 - - - -
6801E GAI 4.9 9.3 + - - -
444F GLN* 5.8 2.0 + - - +
498H LYS* 5.1 0.2 - - - +
499H ASN* 3.3 18.4 - - - +
500H SER* 2.7 76.6 + - - +
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Residues in contact with ARG 78 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73E GLY* 3.4 20.2 + - - +
74E SER 3.0 14.9 + - - +
75E PRO* 4.4 3.1 - - + +
77E ARG* 1.3 74.3 - - - +
79E MET* 1.3 70.2 + - - +
80E ASP* 3.3 2.8 + - - +
149H ASP* 4.4 17.1 + - - +
497H GLN* 3.6 35.0 - - - +
498H LYS* 3.5 29.4 + - - +
499H ASN* 3.7 15.0 - - - +
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Residues in contact with MET 79 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75E PRO* 3.0 21.5 + - + +
76E TRP* 3.7 37.0 - - + +
77E ARG 3.4 5.8 - - - +
78E ARG* 1.3 79.9 - - - +
80E ASP* 1.3 75.3 + - - +
81E ALA 3.6 1.2 + - - -
83E HIS* 3.4 32.1 - - + +
84E ARG* 4.0 19.7 + - + +
87E LEU* 3.6 21.1 - - + -
212E GLY 5.6 0.9 - - - +
214E PRO* 3.9 15.7 - - + -
498H LYS* 4.4 4.3 - - - +
500H SER* 5.5 0.5 - - - -
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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