Contacts of the helix formed by residues 74 - 79 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68J ALA 4.2 6.7 - - - -
69J ALA* 2.8 31.4 + - - -
71J GLN* 2.9 22.7 + - - -
72J LEU 3.3 1.2 + - - -
73J GLY* 1.3 80.8 - - - +
75J PRO* 1.3 70.6 - - - +
76J TRP 3.7 0.3 + - - -
77J ARG* 3.3 10.6 + - - +
78J ARG* 2.9 27.5 + - - +
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Residues in contact with PRO 75 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73J GLY 4.6 0.4 - - - +
74J SER* 1.3 87.6 - - - +
76J TRP* 1.3 56.6 + - - +
78J ARG* 4.3 3.5 - - + +
79J MET* 3.0 38.0 + - + +
214J PRO* 4.3 20.0 - - + -
215J PRO* 6.5 0.4 - - + -
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Residues in contact with TRP 76 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69J ALA* 3.8 15.3 - - + +
70J PHE* 4.9 3.8 - + - -
74J SER* 3.3 1.4 + - - -
75J PRO* 1.3 80.0 - - - +
77J ARG* 1.3 62.8 + - - +
79J MET* 3.7 38.6 - - - +
84J ARG* 3.5 31.1 + - + -
87J LEU* 4.0 14.1 - - + -
88J LEU* 6.5 0.2 - - + -
183J LEU* 3.5 25.4 - - + -
186J GLY* 3.0 18.4 + - - -
187J ASN 2.8 25.3 + - - -
188J VAL* 3.7 20.4 - - + -
213J PHE* 3.9 22.4 - + - -
214J PRO* 4.0 18.2 - - + +
217J VAL* 3.6 25.8 - - + +
500K SER* 4.6 4.2 + - - -
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Residues in contact with ARG 77 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69J ALA 4.3 0.4 - - - +
70J PHE* 2.8 72.2 + - - +
71J GLN 3.2 24.0 - - - +
72J LEU* 3.8 28.6 - - - +
73J GLY 4.2 0.2 - - - +
74J SER* 3.2 12.5 + - - +
76J TRP* 1.3 80.1 - - - +
78J ARG* 1.3 60.3 + - - +
79J MET 3.7 2.8 + - - +
157J GLU* 5.2 6.3 + - - -
158J PRO* 4.7 2.4 - - - +
186J GLY 4.8 2.5 - - - -
499K ASN* 3.4 18.3 - - - +
500K SER* 2.6 75.2 + - - +
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Residues in contact with ARG 78 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73J GLY* 3.4 28.2 + - - +
74J SER 2.9 17.6 + - - +
75J PRO* 4.3 3.4 - - + +
77J ARG* 1.3 74.0 - - - +
79J MET* 1.3 67.0 + - - +
80J ASP* 3.5 2.9 + - - +
149K ASP* 4.4 15.6 + - - -
497K GLN* 3.6 41.8 - - - +
498K LYS* 3.7 31.7 + - - +
499K ASN* 4.1 2.7 - - - +
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Residues in contact with MET 79 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75J PRO* 3.0 25.8 + - + +
76J TRP* 3.7 34.6 - - + +
77J ARG 3.4 5.4 - - - +
78J ARG* 1.3 79.0 - - - +
80J ASP* 1.3 77.1 + - - +
81J ALA 3.6 1.2 + - - -
83J HIS* 3.5 35.2 - - + +
84J ARG* 4.2 17.8 + - + +
87J LEU* 3.8 11.4 - - + -
212J GLY 5.5 0.9 - - - +
214J PRO* 3.9 28.5 - - + -
498K LYS* 4.8 3.3 - - - -
500K SER* 5.5 0.9 + - - -
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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