Contacts of the helix formed by residues 74 - 79 (chain G) in PDB entry 1ZUM
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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68G ALA 4.3 6.1 - - - -
69G ALA* 2.8 31.5 + - - -
71G GLN* 2.9 22.6 + - - -
72G LEU 3.3 0.8 + - - -
73G GLY* 1.3 81.4 - - - +
75G PRO* 1.3 76.6 - - - +
76G TRP 3.6 0.2 + - - -
77G ARG* 3.2 13.5 + - - +
78G ARG* 3.0 22.5 + - - +
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Residues in contact with PRO 75 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69G ALA* 5.5 0.4 - - - +
73G GLY 4.6 0.7 - - - +
74G SER* 1.3 89.4 - - - +
76G TRP* 1.3 57.2 + - - +
78G ARG* 4.2 3.5 - - + +
79G MET* 3.0 38.0 + - + +
214G PRO* 4.3 18.6 - - + -
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Residues in contact with TRP 76 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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500F SER* 4.6 3.6 + - - -
69G ALA* 3.7 15.5 - - + +
70G PHE* 5.0 0.2 - + - -
74G SER* 3.3 1.0 + - - -
75G PRO* 1.3 81.7 - - - +
77G ARG* 1.3 67.2 + - - +
79G MET* 3.7 36.7 + - - +
84G ARG* 3.8 26.0 + - + -
87G LEU* 4.0 4.0 - - + -
88G LEU* 6.4 0.2 - - + -
183G LEU* 3.5 26.9 - - + -
186G GLY* 3.0 21.3 + - - -
187G ASN 2.8 23.4 + - - -
188G VAL* 3.8 19.3 - - + -
213G PHE* 3.7 35.7 - + - -
214G PRO* 3.8 22.9 - - + +
217G VAL* 3.5 27.1 - - + +
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Residues in contact with ARG 77 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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498F LYS* 5.9 0.5 - - - -
499F ASN* 3.3 21.5 - - - +
500F SER* 2.9 72.9 + - - +
69G ALA 5.0 0.2 - - - -
70G PHE* 2.6 89.9 + - - +
71G GLN 3.3 6.3 - - - +
72G LEU* 3.7 31.8 - - - +
74G SER* 3.2 19.0 + - - +
76G TRP* 1.3 80.4 - - - +
78G ARG* 1.3 59.6 + - - +
79G MET 3.4 2.8 + - - +
157G GLU* 5.8 2.0 + - - +
158G PRO* 5.0 1.2 - - - +
186G GLY 4.8 2.7 - - - -
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Residues in contact with ARG 78 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149F ASP* 4.1 18.0 + - - -
497F GLN* 3.6 40.5 - - - +
498F LYS* 3.8 26.0 + - - +
499F ASN* 4.0 6.5 - - - +
73G GLY* 3.3 28.2 + - - +
74G SER 3.0 18.5 + - - +
75G PRO* 4.2 4.0 - - + +
77G ARG* 1.3 75.4 - - - +
79G MET* 1.3 64.5 + - - +
80G ASP* 3.5 3.8 + - - +
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Residues in contact with MET 79 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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498F LYS* 4.8 3.1 - - - -
500F SER* 5.6 0.7 - - - -
75G PRO* 3.0 21.0 + - + +
76G TRP* 3.7 26.4 - - + +
77G ARG 3.4 4.8 - - - +
78G ARG* 1.3 79.0 - - - +
80G ASP* 1.3 75.9 + - - +
81G ALA 3.5 1.7 + - - -
83G HIS* 3.6 25.1 - - + -
84G ARG* 4.0 20.8 + - + -
87G LEU* 3.4 34.8 - - + -
212G GLY 5.6 0.9 - - - +
214G PRO* 4.0 22.0 - - + -
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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