Contacts of the strand formed by residues 117 - 127 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13B ARG* 3.5 41.8 - - + +
14B PHE 4.5 1.4 - - - +
15B LYS* 3.3 37.9 - - - +
113B LEU* 3.4 7.5 - - - +
114B GLN* 2.8 34.3 + - - +
115B ASP 3.7 10.3 - - - +
116B GLY* 1.3 85.0 - - - +
118B PHE* 1.3 64.7 + - - +
119B ILE* 4.0 4.7 - - + +
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Residues in contact with PHE 118 (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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8B ILE* 3.4 40.6 - - + -
12B MET* 3.8 20.0 - - + -
13B ARG 3.0 11.4 + - - -
14B PHE* 3.1 12.2 - - + -
15B LYS 2.9 26.0 + - - -
37B PRO* 4.6 2.7 - - + -
71B ALA* 3.6 16.4 - - + -
72B TYR* 3.4 41.5 - + - -
87B PHE* 3.5 38.1 - + - -
112B SER 3.3 2.5 - - - -
113B LEU* 3.8 8.0 - - + +
117B GLU* 1.3 72.4 - - - +
119B ILE* 1.3 63.1 + - - +
120B TYR* 3.9 15.9 - + + -
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Residues in contact with ILE 119 (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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15B LYS* 3.6 31.6 - - + +
110B ASP* 3.7 1.6 - - - +
111B SER* 3.4 4.2 - - - -
112B SER* 2.8 48.9 + - - +
114B GLN* 3.4 45.3 - - + +
117B GLU* 4.0 5.6 - - + +
118B PHE* 1.3 82.7 - - - +
120B TYR* 1.3 64.1 + - - +
121B LYS* 3.7 32.9 - - + +
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Residues in contact with TYR 120 (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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14B PHE* 3.6 37.5 - + + -
15B LYS 2.9 7.1 + - - +
16B VAL* 3.4 21.1 - - + -
17B HIS 3.0 24.8 + - - -
65B PHE* 5.0 5.2 - - - -
66B CH6 4.8 2.7 - - - -
69B SER* 4.0 28.2 - - - -
71B ALA* 4.1 6.1 - - - +
72B TYR* 3.5 27.4 - - - -
91B PHE* 5.1 4.5 - + - -
109B GLN* 3.4 12.6 - - - +
110B ASP 3.5 2.7 - - - -
111B SER* 3.3 30.7 - - - -
118B PHE* 3.9 25.1 - + + -
119B ILE* 1.3 80.8 - - - +
121B LYS* 1.3 66.4 + - - +
122B VAL* 4.2 2.2 - - + -
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Residues in contact with LYS 121 (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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17B HIS* 3.5 30.3 + - + +
108B THR 4.0 0.3 - - - +
109B GLN* 3.3 4.2 - - - +
110B ASP* 2.9 50.5 + - + +
112B SER* 6.0 0.2 - - - +
119B ILE* 3.7 25.2 - - + +
120B TYR* 1.3 76.6 + - - +
122B VAL* 1.3 61.7 + - - +
123B LYS* 5.2 13.2 + - - +
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Residues in contact with VAL 122 (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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16B VAL* 4.2 17.7 - - + -
17B HIS* 2.9 15.9 + - - +
18B MET* 3.4 30.1 - - + -
19B GLU* 3.0 25.8 + - - +
64B GLN* 3.9 17.9 - - + +
65B PHE* 5.0 0.4 - - + -
107B VAL* 3.6 26.5 - - + -
108B THR 3.4 4.5 - - - +
109B GLN* 3.9 18.2 - - + +
120B TYR* 4.9 0.2 - - + -
121B LYS* 1.3 78.1 - - - +
123B LYS* 1.4 71.8 + - - +
124B LEU 4.8 0.2 - - - +
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Residues in contact with LYS 123 (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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19B GLU* 3.4 34.1 - - + +
107B VAL* 3.2 4.0 - - - +
108B THR* 2.9 51.0 + - - +
110B ASP* 6.2 1.6 - - - +
121B LYS* 5.2 14.8 + - - +
122B VAL* 1.4 77.9 - - - +
124B LEU* 1.3 60.1 + - - +
301B SO4 2.9 14.1 + - - +
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Residues in contact with LEU 124 (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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18B MET* 4.2 11.2 - - + -
19B GLU 3.1 10.3 + - - +
20B GLY* 3.1 5.1 - - - -
21B SER* 3.1 36.3 + - - +
22B VAL* 3.8 18.4 - - + -
27B PHE* 4.3 5.6 - - + -
60B ILE* 4.4 3.4 - - + +
61B LEU* 3.9 22.4 - - + -
64B GLN* 3.7 31.6 - - + +
105B VAL* 3.8 24.9 - - + -
106B THR 3.4 3.1 - - - +
107B VAL* 4.0 5.2 - - + -
123B LYS* 1.3 76.3 - - - +
125B ARG* 1.3 62.9 + - - +
126B GLY* 3.9 4.7 - - - +
301B SO4 3.2 4.0 - - - -
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Residues in contact with ARG 125 (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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21B SER* 3.5 13.2 - - - +
104B VAL* 3.7 3.8 - - - +
105B VAL* 3.3 1.9 - - - -
106B THR* 2.8 69.3 + - - +
124B LEU* 1.3 78.0 - - - +
126B GLY* 1.3 62.0 + - - +
127B THR* 3.8 28.0 + - + +
301B SO4 3.1 24.7 + - - +
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Residues in contact with GLY 126 (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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21B SER* 2.9 13.2 + - - +
22B VAL* 3.3 9.0 - - - -
23B ASN 2.9 25.8 + - - -
24B GLY 4.7 1.0 + - - -
104B VAL 3.2 9.0 - - - -
105B VAL* 3.9 12.8 - - - -
124B LEU* 3.9 3.8 - - - +
125B ARG* 1.3 72.1 - - - +
127B THR* 1.3 67.0 + - - +
129B PHE* 4.1 7.4 - - - -
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Residues in contact with THR 127 (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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23B ASN* 3.6 6.5 - - - +
103B GLY* 3.5 0.9 - - - -
104B VAL* 2.9 46.1 + - - +
125B ARG* 3.8 33.0 + - + +
126B GLY* 1.3 80.3 - - - +
128B ASN* 1.3 69.0 + - - +
129B PHE* 3.2 6.8 + - - -
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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