Contacts of the strand formed by residues 63 - 71 (chain C) in PDB entry 3ZJX
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 TYR 63 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61C ASP 3.9 7.9 - - - +
62C PHE* 1.3 77.6 - - - +
64C ILE* 1.3 84.1 + - - +
65C ASN* 3.3 27.8 + - - -
66C ASN 5.6 0.4 - - - -
125C ILE* 4.2 3.1 - - + +
126C GLN 6.1 1.3 - - - -
197C GLN 3.7 0.7 - - - +
198C VAL* 3.2 6.2 - - - +
199C SER* 3.0 41.8 + - - +
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Residues in contact with ILE 64 (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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20C VAL* 5.8 0.2 - - + -
63C TYR* 1.3 87.3 - - - +
65C ASN* 1.3 61.7 + - - +
67C PRO* 3.7 24.5 - - + +
121C VAL* 4.2 10.1 - - + -
125C ILE* 3.6 41.1 - - + +
126C GLN 4.7 1.6 + - - +
127C ALA* 3.7 29.6 - - + +
148C PHE* 4.3 7.0 - - + -
196C GLY* 4.2 14.6 - - - -
197C GLN 3.8 3.4 - - - +
198C VAL* 4.1 7.6 - - + -
238C ILE* 3.7 33.2 - - + -
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Residues in contact with ASN 65 (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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63C TYR* 3.3 23.6 + - - -
64C ILE* 1.3 70.3 - - - +
66C ASN* 1.3 82.1 + - - +
67C PRO 3.4 0.3 - - - -
196C GLY* 3.6 1.4 - - - -
197C GLN* 2.7 53.9 + - + +
199C SER* 3.1 32.7 + - - +
235C THR* 4.0 9.2 - - + +
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Residues in contact with ASN 66 (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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63C TYR* 5.6 0.6 - - - -
65C ASN* 1.3 80.5 - - - +
67C PRO* 1.3 74.7 - - - +
68C LYS* 3.3 15.1 + - + +
195C VAL 3.8 4.7 - - - +
196C GLY* 4.0 3.1 - - - -
197C GLN* 3.7 19.9 + - - +
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Residues in contact with PRO 67 (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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64C ILE* 3.7 21.5 - - + +
65C ASN 3.4 1.9 - - - +
66C ASN* 1.3 91.2 - - - +
68C LYS* 1.3 60.8 + - - +
127C ALA* 4.3 7.2 - - + -
128C THR 3.5 22.9 - - - +
129C ALA* 3.7 7.9 - - - +
148C PHE* 3.6 22.9 - - + -
195C VAL 3.4 8.5 - - - +
196C GLY* 4.5 1.6 - - - -
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Residues in contact with LYS 68 (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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66C ASN* 3.8 11.0 - - + +
67C PRO* 1.3 75.9 - - - +
69C VAL* 1.3 64.1 + - - +
70C GLU* 4.2 18.2 - - + +
129C ALA* 3.8 10.8 - - - -
148C PHE* 3.9 2.2 - - - -
194C LEU* 3.7 3.3 - - - -
195C VAL* 2.9 51.6 + - + +
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Residues in contact with VAL 69 (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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68C LYS* 1.3 78.7 - - - +
70C GLU* 1.3 69.1 + - - +
71C LEU 5.6 0.2 - - - +
129C ALA* 4.0 6.1 - - + +
130C LYS 3.3 25.9 + - - +
131C PHE* 3.6 23.1 - - + -
132C THR 5.2 0.7 - - - +
146C TYR* 3.9 19.5 - - + -
192C VAL* 3.6 35.9 - - + -
193C LYS 3.6 2.0 - - - -
194C LEU* 3.9 7.9 - - + -
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Residues in contact with GLU 70 (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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68C LYS* 4.2 14.7 - - + +
69C VAL* 1.3 79.9 - - - +
71C LEU* 1.3 64.6 + - - +
192C VAL* 3.1 7.3 - - - -
193C LYS* 2.7 59.5 + - + +
195C VAL* 3.7 28.2 - - + +
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Residues in contact with LEU 71 (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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69C VAL* 5.6 0.6 - - + +
70C GLU* 1.3 76.6 - - - +
72C ASP* 1.3 60.0 + - - +
73C GLY 3.8 12.4 + - - +
74C GLU* 5.1 7.9 - - - +
75C PRO* 4.6 13.2 - - + -
131C PHE* 3.9 27.8 - - + -
134C PRO* 4.0 24.5 - - + -
135C PHE* 6.0 1.3 - - + -
191C ASN 3.9 3.6 - - - +
192C VAL* 4.4 0.7 - - + +
193C LYS* 4.7 2.3 - - - +
244C TYR* 4.0 21.5 - - + +
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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