Contacts of the strand formed by residues 40 - 46 (chain B) in PDB entry 3ZO7
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 40 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B MET* 3.7 25.1 - - + -
31B SER* 3.3 38.4 - - - -
34B LEU* 2.9 23.5 + - + -
35B GLN* 3.4 37.1 - - + +
38B GLY 4.3 1.3 - - - -
39B GLN* 1.3 73.8 - - - +
41B ARG* 1.3 63.8 + - - +
42B TYR 3.3 18.8 + - - -
43B LEU* 3.7 26.7 - - + +
52B ASN* 4.3 4.5 - - - -
54B SER* 2.9 31.5 + - - -
55B VAL 4.2 0.9 - - - -
56B PHE* 3.4 26.9 - + + -
71B LEU* 4.0 24.5 - - + -
90C ARG* 4.0 0.5 + - - -
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Residues in contact with ARG 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B LEU* 4.0 19.9 - - - +
38B GLY* 4.2 14.1 - - - +
39B GLN 3.5 2.4 + - - -
40B TRP* 1.3 74.3 - - - +
42B TYR* 1.3 102.9 + - + +
55B VAL* 2.9 15.4 + - - +
57B ASP* 4.0 23.3 + - + -
93B LYS* 6.1 0.8 - - - +
94B ASP* 3.5 32.3 + - - +
90C ARG* 3.1 19.5 + - - -
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Residues in contact with TYR 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B TRP* 3.3 6.4 - - - -
41B ARG* 1.3 120.4 + - + +
43B LEU* 1.3 61.7 + - - +
44B TRP* 3.7 34.8 - + + -
53B ILE 4.8 0.4 - - - -
54B SER* 3.2 9.0 - - - -
55B VAL* 3.0 45.3 + - + -
94B ASP* 3.4 14.0 + - - -
42C TYR* 3.2 38.5 + + - -
44C TRP* 3.9 19.3 - + - -
90C ARG* 3.9 13.7 - - - +
93C LYS 4.7 3.1 - - - -
94C ASP* 4.9 4.3 - - - -
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Residues in contact with LEU 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B SER* 4.7 2.2 - - - +
35B GLN* 4.0 23.6 - - - +
40B TRP* 3.7 22.7 - - + +
42B TYR* 1.3 76.2 - - - +
44B TRP* 1.3 71.8 + - - +
52B ASN* 3.6 27.6 - - + +
53B ILE 4.1 0.2 - - - -
54B SER* 3.3 19.7 - - - +
87C HIS* 3.4 38.6 + - + +
89C ALA* 4.0 13.2 - - + -
90C ARG* 3.7 30.6 - - - +
94C ASP* 4.2 1.0 - - - +
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Residues in contact with TRP 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B LEU* 5.7 0.9 - - + -
42B TYR* 3.7 38.8 - + + -
43B LEU* 1.3 83.2 + - - +
45B ARG* 1.3 59.2 + - - +
52B ASN* 3.1 9.2 - - - +
53B ILE* 3.0 61.7 + - + +
55B VAL* 4.5 12.8 - - + -
2C LEU* 3.7 15.5 - - + +
4C LEU* 5.0 6.7 - - + -
42C TYR* 4.2 11.2 - + - -
44C TRP* 4.6 3.1 - + - -
55C VAL* 3.8 30.1 - - + -
84C LEU* 3.9 28.0 - - + -
85C SER 3.8 11.9 - - - +
87C HIS* 3.8 6.7 - - - -
94C ASP* 3.1 41.8 + - + +
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Residues in contact with ARG 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B TRP* 1.3 73.6 - - - +
46B THR* 1.3 67.6 + - - +
47B THR* 3.2 4.1 + - - +
48B GLY 5.5 0.9 - - - +
49B LYS 3.5 15.2 + - - -
50B TYR* 4.6 13.1 - - - -
51B GLY* 3.0 35.6 + - - +
53B ILE* 5.0 0.4 - - - -
84C LEU* 3.9 5.7 - - - +
85C SER* 2.8 50.1 + - - +
86C HIS 3.6 15.0 - - - +
87C HIS* 3.3 30.0 + - - +
88C PRO* 3.5 31.5 - - - +
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Residues in contact with THR 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B ARG* 3.9 15.7 - - + +
7B MET 4.9 1.4 + - - +
44B TRP 3.7 0.4 + - - -
45B ARG* 1.3 73.2 - - - +
47B THR* 1.3 66.8 + - - +
48B GLY 3.2 0.2 + - - -
49B LYS* 2.8 45.5 + - + +
51B GLY* 3.3 21.5 + - - -
52B ASN 3.7 24.0 + - - +
53B ILE* 3.9 6.7 - - + +
82C GLU* 3.8 21.5 - - - +
83C PRO 5.0 1.6 - - - -
84C LEU* 5.6 0.4 - - - -
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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