Contacts of the strand formed by residues 119 - 125 (chain C) in PDB entry 3JZT
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 LEU 119 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56C ILE* 4.9 7.6 - - + -
61C PRO* 4.4 22.2 - - + +
62C ASP 3.7 3.6 - - - +
64C LEU* 3.6 45.1 - - + +
82C ILE* 6.1 0.7 - - + -
85C PHE* 4.2 27.8 - - + -
86C THR* 4.8 6.7 - - + -
114C ASN* 4.0 0.6 + - - -
115C VAL* 3.0 8.4 + - + +
116C LEU* 3.0 47.7 + - + -
117C GLU 3.3 1.9 - - - +
118C HIS* 1.3 77.7 - - - +
120C SER* 1.3 61.1 + - - +
121C VAL* 4.9 5.8 - - + -
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Residues in contact with SER 120 (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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62C ASP 2.8 15.7 + - - -
63C VAL* 3.2 8.6 - - - +
64C LEU 2.9 23.7 + - - -
111C LEU* 3.8 17.5 - - - +
112C PHE 3.4 10.5 - - - -
113C GLU* 3.3 6.8 - - - +
114C ASN* 2.5 27.1 + - - +
118C HIS 4.0 0.4 - - - -
119C LEU* 1.3 73.8 - - - +
121C VAL* 1.3 63.5 + - - +
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Residues in contact with VAL 121 (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 LEU* 3.3 20.9 - - + +
66C ASN* 3.9 15.7 - - + -
82C ILE* 4.1 21.3 - - + -
90C LEU* 3.5 29.2 - - + -
110C VAL 3.6 1.0 - - - +
111C LEU* 2.9 6.8 - - - +
112C PHE* 2.8 37.6 + - + +
115C VAL* 4.1 16.2 - - + +
119C LEU* 4.1 8.0 + - + -
120C SER* 1.3 72.8 - - - +
122C LEU* 1.3 61.3 + - - +
123C ASN* 3.6 15.3 + - - +
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Residues in contact with LEU 122 (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 VAL* 4.2 5.2 - - + -
64C LEU 3.0 7.6 + - - +
65C VAL* 3.8 17.7 - - + +
66C ASN 2.7 24.4 + - - -
109C ALA* 3.9 15.5 - - + +
110C VAL 3.4 32.5 - - - +
111C LEU* 3.3 17.7 - - + +
121C VAL* 1.3 74.3 - - - +
123C ASN* 1.3 60.6 + - - +
124C ALA 3.2 1.0 + - - -
144C ALA* 4.9 2.7 - - + +
145C ILE* 4.0 31.2 - - + +
148C CYS* 3.8 27.4 - - - -
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Residues in contact with ASN 123 (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* 3.2 26.8 + - - +
68C ALA* 4.7 3.1 - - + -
72C LEU* 4.2 22.9 - - + +
74C HIS* 4.0 5.5 + - - -
90C LEU* 3.7 9.5 - - - +
104C ILE* 4.5 10.0 - - + +
109C ALA* 3.0 4.1 - - - +
110C VAL* 2.8 43.5 + - - +
112C PHE* 3.6 38.1 - - - -
121C VAL* 3.6 11.5 + - - +
122C LEU* 1.3 70.9 - - - +
124C ALA* 1.3 60.4 + - - +
125C VAL* 3.9 1.5 + - + -
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Residues in contact with ALA 124 (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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65C VAL* 4.0 20.4 - - + -
66C ASN 2.4 20.2 + - - +
67C ALA* 3.4 2.8 - - - -
68C ALA* 2.6 33.4 + - - -
109C ALA* 3.5 10.3 - - + -
122C LEU* 3.2 1.7 + - + +
123C ASN* 1.3 68.4 - - - +
125C VAL* 1.3 58.6 + - - +
126C GLY 4.0 0.4 - - - -
141C VAL* 3.8 22.2 - - + -
145C ILE* 5.0 1.1 - - + -
157C ILE* 4.0 13.7 - - + -
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Residues in contact with VAL 125 (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 ALA* 3.5 12.3 - - + +
69C ASN* 3.4 38.8 - - - +
70C GLY 4.0 2.2 - - - +
72C LEU* 5.7 1.1 - - + -
104C ILE* 3.6 27.8 - - + +
106C PRO* 3.4 27.6 - - + -
107C GLY 2.9 25.5 + - - -
108C ASN 3.0 16.1 + - - +
123C ASN* 3.9 1.3 + - + +
124C ALA* 1.3 72.4 - - - +
126C GLY* 1.3 71.8 + - - +
128C ARG* 6.4 0.2 - - - +
141C VAL* 3.5 10.9 - - - +
157C ILE* 4.8 0.7 - - - -
162C PHE* 5.4 1.6 - - + -
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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