Contacts of the strand formed by residues 117 - 127 (chain C) in PDB entry 4ZIN
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 GLU 117 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12C MET* 4.7 0.2 - - - -
13C ARG* 3.7 40.4 - - + +
14C PHE 4.3 4.3 - - - +
15C LYS* 3.3 43.1 + - - +
113C LEU* 3.2 10.0 - - - +
114C GLN 3.0 32.8 + - - +
115C ASP* 4.0 7.9 - - + +
116C GLY* 1.3 84.2 - - - +
118C PHE* 1.3 66.2 + - - +
119C ILE* 3.8 5.6 + - + +
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Residues in contact with PHE 118 (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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8C ILE* 3.9 21.3 - - + -
12C MET* 3.7 31.2 - - + -
13C ARG 3.2 9.3 + - - -
14C PHE* 3.2 11.9 - - + -
15C LYS 2.9 26.0 + - - -
37C PRO* 4.7 2.0 - - + -
71C ALA* 3.8 14.6 - - + -
72C TYR* 3.4 34.8 - + - -
87C PHE* 3.7 47.6 - + - -
112C SER 3.3 2.2 - - - +
113C LEU* 3.9 14.6 - - + -
117C GLU* 1.3 73.9 - - - +
119C ILE* 1.3 65.2 + - - +
120C TYR* 3.7 16.2 - - + -
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Residues in contact with ILE 119 (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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15C LYS* 3.6 30.7 - - + +
110C ASP* 3.5 2.6 - - - +
111C SER* 3.4 3.8 - - - -
112C SER* 2.8 50.2 + - - +
114C GLN* 4.6 17.9 - - + +
117C GLU* 4.2 15.5 - - + +
118C PHE* 1.3 85.2 - - - +
120C TYR* 1.3 67.0 + - - +
121C LYS* 4.6 21.4 - - + +
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Residues in contact with TYR 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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14C PHE* 3.5 34.5 - + - -
15C LYS 2.8 9.7 + - - +
16C VAL* 3.3 20.5 - - + -
17C HIS 3.1 22.8 + - - -
65C PHE 4.5 5.4 - - - -
66C CH6 4.6 1.6 - - - -
69C SER* 2.6 44.8 + - - -
71C ALA* 4.3 4.9 - - + +
72C TYR* 3.5 16.3 - - - -
87C PHE* 5.5 1.8 - + - -
91C PHE* 5.6 2.0 - + - -
109C GLN* 3.3 23.3 - - - +
110C ASP 3.3 2.5 - - - -
111C SER* 3.5 20.0 - - - -
112C SER 5.3 0.2 - - - -
118C PHE* 3.7 27.4 - + + +
119C ILE* 1.3 83.8 - - - +
121C LYS* 1.3 65.5 + - - +
122C VAL* 4.9 0.4 - - + -
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Residues in contact with LYS 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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17C HIS* 3.5 13.7 - - + +
108C THR 3.8 0.5 - - - +
109C GLN* 3.2 4.9 - - - +
110C ASP* 2.9 50.3 + - + +
119C ILE* 4.6 17.9 - - + -
120C TYR* 1.3 77.9 - - - +
122C VAL* 1.3 60.6 + - - +
123C LYS* 5.8 1.1 - - - +
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Residues in contact with VAL 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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16C VAL* 3.9 25.8 - - + -
17C HIS* 2.9 8.7 + - - +
18C MET* 3.2 29.8 - - + -
19C GLU* 3.0 26.8 + - - +
64C GLN* 3.9 17.3 - - + +
65C PHE* 5.3 0.2 - - + -
93C TRP* 5.0 0.2 - - + -
107C VAL* 3.6 26.9 - - + -
108C THR 3.3 4.0 - - - +
109C GLN* 3.8 18.8 - - + +
121C LYS* 1.3 79.2 - - - +
123C LYS* 1.3 70.2 + - - +
124C LEU 5.0 0.2 - - - +
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Residues in contact with LYS 123 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19C GLU* 3.3 37.0 - - + +
107C VAL* 3.3 4.5 - - - +
108C THR* 2.9 33.5 + - - +
121C LYS 5.8 0.7 - - - -
122C VAL* 1.3 76.6 - - - +
124C LEU* 1.3 61.0 + - - +
302C SO4 2.9 33.8 + - - +
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Residues in contact with LEU 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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18C MET* 4.2 14.4 - - + -
19C GLU 3.0 9.4 + - - +
20C GLY* 3.1 4.7 - - - -
21C SER* 3.0 38.7 + - - +
22C VAL* 3.9 18.2 - - + -
27C PHE* 4.4 6.3 - - + -
60C ILE* 4.6 1.3 - - + +
61C LEU* 3.8 22.2 - - + -
64C GLN* 3.8 31.2 - - + +
105C VAL* 3.8 25.1 - - + -
106C THR 3.4 4.7 - - - +
107C VAL* 4.3 4.3 - - + -
123C LYS* 1.3 75.8 - - - +
125C ARG* 1.3 65.0 - - - +
126C GLY* 3.9 4.9 - - - +
302C SO4 3.8 4.4 + - - -
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Residues in contact with ARG 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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21C SER* 3.5 14.6 - - - +
104C VAL* 3.5 2.8 - - - +
105C VAL* 3.3 2.2 - - - -
106C THR* 2.9 49.6 + - - +
124C LEU* 1.3 78.7 - - - +
126C GLY* 1.3 60.0 + - - +
127C THR* 3.9 25.0 + - + +
302C SO4 3.7 36.8 + - - +
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Residues in contact with GLY 126 (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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21C SER* 2.8 11.9 + - - +
22C VAL* 3.3 10.2 - - - -
23C ASN 2.9 25.2 + - - -
24C GLY 4.6 0.7 + - - -
104C VAL 3.1 8.5 - - - -
105C VAL* 3.9 13.0 - - - -
124C LEU* 3.9 1.8 - - - +
125C ARG* 1.3 73.1 - - - +
127C THR* 1.3 67.2 + - - +
129C PHE* 4.1 8.1 - - - -
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Residues in contact with THR 127 (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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23C ASN* 3.6 2.9 - - - -
103C GLY* 3.6 0.3 - - - -
104C VAL* 2.9 44.5 + - - +
125C ARG* 3.9 28.2 + - + -
126C GLY* 1.3 80.8 - - - +
128C ASN* 1.3 68.5 + - - +
129C PHE* 3.2 6.3 + - - -
303C EDO 3.3 25.6 - - - -
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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