Contacts of the strand formed by residues 52 - 59 (chain C) in PDB entry 1Z9N
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 GLY 52 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49C SER* 2.7 40.5 + - - -
50C ALA 3.7 0.6 - - - -
51C TYR* 1.3 79.1 - - - +
53C LEU* 1.3 68.0 + - - -
133C LEU* 3.5 3.8 - - - +
134C ALA 3.7 5.6 - - - -
135C PRO* 4.4 2.9 - - - -
137C LEU 3.1 15.0 - - - -
138C LYS* 4.9 5.8 - - - -
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Residues in contact with LEU 53 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C ILE* 4.1 13.9 - - + -
47C THR 3.3 7.2 - - - +
48C GLU* 3.6 31.4 - - + -
52C GLY* 1.3 72.7 - - - -
54C VAL* 1.3 59.9 + - - +
55C PHE* 3.9 14.7 - - + -
132C VAL 3.9 0.5 - - - +
133C LEU* 3.5 2.3 - - - -
134C ALA 2.9 32.9 + - - -
137C LEU* 3.0 39.4 + - + +
138C LYS 3.8 12.6 - - - +
139C LYS 3.8 19.5 - - - +
140C LEU* 4.0 5.8 - - + +
143C VAL* 3.8 22.2 - - + -
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Residues in contact with VAL 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C GLU 3.4 1.9 - - - +
46C ILE* 3.3 6.6 - - - +
47C THR* 2.8 46.0 + - - +
48C GLU 5.2 0.2 - - - -
49C SER* 3.9 17.3 - - - -
53C LEU* 1.3 76.7 - - - +
55C PHE* 1.3 62.8 + - - +
56C THR* 3.6 19.2 + - - +
131C PRO* 4.1 3.4 - - + -
132C VAL 3.4 6.5 - - - +
133C LEU* 3.9 8.7 - - + -
108D TRP* 3.5 52.5 - - + +
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Residues in contact with PHE 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44C VAL* 4.1 9.2 - - + -
45C GLU 3.6 3.6 - - - -
46C ILE* 3.7 37.2 - - + -
53C LEU* 3.9 20.4 - - + -
54C VAL* 1.3 73.5 - - - +
56C THR* 1.3 60.1 - - - +
57C PRO* 3.4 4.9 - - - +
69C PHE* 4.0 9.9 - - + -
71C ILE* 4.0 23.3 - - + -
117C LEU* 3.9 26.9 - - + -
131C PRO* 3.1 3.8 - - - +
132C VAL* 2.8 50.7 + - + +
134C ALA* 3.9 24.7 - - + -
137C LEU* 4.3 4.9 - - + -
143C VAL* 4.9 0.9 - - + -
148C LEU* 4.1 16.2 - - + -
176C ILE* 5.3 0.4 - - + -
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Residues in contact with THR 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44C VAL* 3.6 1.7 - - - +
45C GLU* 2.8 46.3 + - - +
47C THR* 4.9 3.7 + - - +
54C VAL* 3.6 17.7 + - - +
55C PHE* 1.3 73.8 - - - +
57C PRO* 1.3 74.1 - - + +
58C LYS* 4.2 16.7 - - - +
129C THR 5.1 4.0 - - - +
131C PRO* 3.8 13.2 - - + +
106D TYR* 5.9 2.0 - - - +
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Residues in contact with PRO 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C THR 3.9 4.5 - - - +
44C VAL* 4.1 8.7 - - + -
55C PHE* 3.4 8.5 - - + +
56C THR* 1.3 88.8 - - + +
58C LYS* 1.3 64.6 - - - +
59C LEU* 4.1 11.7 - - + -
69C PHE* 6.0 1.1 - - + -
120C LEU* 3.8 28.0 - - + -
128C ALA* 3.3 20.1 - - + +
129C THR* 3.4 15.6 - - - +
130C THR* 3.4 42.4 - - - +
131C PRO* 3.8 0.4 - - + -
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Residues in contact with LYS 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C LYS* 5.0 1.4 - - - +
42C GLY* 3.5 6.1 - - - -
43C THR* 2.8 40.7 + - - +
45C GLU* 2.9 44.1 + - + +
56C THR* 4.2 15.0 - - + +
57C PRO* 1.3 78.2 - - - +
59C LEU* 1.3 58.2 + - - +
60C HIS* 4.9 1.7 - - - -
128C ALA 3.7 1.8 - - - -
129C THR* 5.1 5.2 - - + -
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Residues in contact with LEU 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C VAL* 3.9 18.8 - - + -
41C VAL* 3.1 18.4 - - + +
42C GLY 3.8 2.9 - - - -
43C THR 3.4 31.6 - - - +
44C VAL* 4.0 11.7 - - + -
57C PRO* 4.1 7.4 - - + -
58C LYS* 1.3 78.9 - - - +
60C HIS* 1.3 63.7 + - - +
62C LEU* 3.9 18.8 - - + -
120C LEU* 4.0 13.0 - - + -
126C GLY 4.4 0.2 - - - -
127C SER* 3.3 6.9 - - - -
128C ALA* 3.0 33.9 + - + +
129C THR* 4.9 1.6 - - - +
150C ILE* 3.8 27.8 - - + -
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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