Contacts of the strand formed by residues 117 - 127 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A MET* 4.7 0.2 - - - -
13A ARG* 3.6 37.7 - - + +
14A PHE 4.5 0.9 + - - +
15A LYS* 2.9 38.8 + - - +
32A GLU* 5.3 1.6 - - - +
113A LEU* 3.4 7.2 - - - +
114A GLN 2.8 38.5 + - - +
115A ASP* 4.1 7.7 - - - +
116A GLY* 1.3 84.7 - - - +
118A PHE* 1.3 69.1 + - - +
119A ILE* 3.6 8.2 + - + +
144B GLU* 4.5 4.2 - - - +
166B LYS* 6.3 0.2 - - - -
170B GLY* 5.7 0.7 - - - -
171B GLY 4.9 5.5 + - - -
172B HIS* 4.3 18.0 - - - -
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Residues in contact with PHE 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A ILE* 3.3 39.9 - - + -
12A MET* 3.8 24.2 - - + -
13A ARG 3.0 10.9 + - - -
14A PHE* 3.1 13.3 - - + +
15A LYS 2.9 26.7 + - - -
37A PRO* 4.8 2.2 - - + -
71A ALA* 3.7 17.3 - - + -
72A TYR* 3.5 35.2 - + - -
87A PHE* 3.5 39.5 - + - -
112A SER 3.3 3.1 - - - -
113A LEU* 4.0 6.7 - - + -
117A GLU* 1.3 74.0 - - - +
119A ILE* 1.3 62.1 + - - +
120A TYR* 3.7 16.4 - + + -
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Residues in contact with ILE 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A LYS* 3.6 21.3 - - + +
110A ASP* 3.5 1.7 - - - +
111A SER* 3.5 4.2 - - - -
112A SER* 2.8 44.1 + - - +
114A GLN* 3.8 28.7 - - + +
117A GLU* 3.8 10.3 - - + +
118A PHE* 1.3 86.0 - - - +
120A TYR* 1.3 63.7 + - - +
121A LYS* 3.5 31.8 - - + +
168B LYS 4.8 1.8 - - - +
169B ASP* 3.8 9.0 - - + +
170B GLY* 3.5 30.3 - - - +
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Residues in contact with TYR 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A PHE* 3.5 31.2 - + + -
15A LYS 2.9 10.2 + - - +
16A VAL* 3.3 14.5 - - + -
17A HIS 3.0 23.4 + - - -
65A PHE 3.7 12.6 - - - -
66A CH6 4.5 0.9 - - - -
69A SER* 2.7 42.6 + - - -
71A ALA* 4.7 4.5 - - + +
72A TYR* 3.5 15.9 - - - -
87A PHE* 5.6 1.1 - + - -
91A PHE* 5.7 2.2 - + - -
109A GLN* 3.5 21.8 - - - +
110A ASP 3.3 3.4 - - - -
111A SER* 3.5 20.2 - - - -
118A PHE* 3.7 25.9 - + + +
119A ILE* 1.3 79.2 - - - +
121A LYS* 1.3 66.9 + - - +
122A VAL* 4.9 0.7 - - + -
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Residues in contact with LYS 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A HIS* 3.5 28.9 - - + +
108A THR 4.0 0.2 - - - +
109A GLN* 3.3 3.6 - - - +
110A ASP* 2.9 44.7 + - + +
119A ILE* 3.5 26.4 - - + +
120A TYR* 1.3 80.6 + - - +
122A VAL* 1.3 61.4 + - - +
123A LYS* 5.9 0.7 - - - -
168B LYS 4.3 5.1 + - - -
169B ASP* 2.8 31.1 + - - -
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Residues in contact with VAL 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A VAL* 3.9 18.4 - - + -
17A HIS* 2.8 16.2 + - - +
18A MET* 3.3 30.9 - - + -
19A GLU* 2.9 26.0 + - - +
64A GLN* 3.9 19.3 - - + +
93A TRP* 4.9 0.2 - - + -
107A VAL* 3.5 28.3 - - + -
108A THR 3.4 5.2 - - - +
109A GLN* 3.8 17.7 - - + +
120A TYR* 4.9 0.2 - - + -
121A LYS* 1.3 78.8 - - - +
123A LYS* 1.3 67.4 + - - +
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Residues in contact with LYS 123 (chain A).
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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19A GLU* 3.3 32.5 - - - +
107A VAL* 3.3 4.5 - - - +
108A THR* 2.9 34.7 + - - +
121A LYS 5.9 0.7 - - - -
122A VAL* 1.3 77.4 - - - +
124A LEU* 1.3 60.3 + - - +
301A SO4 2.7 33.3 + - - +
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Residues in contact with LEU 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A MET* 4.1 12.6 - - + -
19A GLU 3.0 9.6 + - - +
20A GLY* 3.2 5.7 - - - -
21A SER* 3.1 25.2 + - - +
22A VAL* 3.9 22.0 - - + -
27A PHE* 4.4 4.0 - - + -
60A ILE* 4.5 2.2 - - + +
61A LEU* 3.9 23.6 - - + -
64A GLN* 3.7 31.6 - - + +
105A VAL* 3.8 24.5 - - + -
106A THR 3.5 3.4 - - - +
107A VAL* 4.0 5.6 - - + -
123A LYS* 1.3 75.2 - - - +
125A ARG* 1.3 62.4 + - - +
126A GLY* 3.8 13.5 - - - +
301A SO4 2.9 4.9 + - - -
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Residues in contact with ARG 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A SER* 3.5 15.5 - - - +
104A VAL* 3.7 5.1 - - - +
105A VAL* 3.3 1.6 - - - -
106A THR* 2.9 72.5 + - - +
124A LEU* 1.3 74.7 - - - +
126A GLY* 1.3 59.9 + - - +
127A THR* 3.8 26.5 + - + +
301A SO4 2.6 26.5 + - - +
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Residues in contact with GLY 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A SER* 2.7 16.1 + - - +
22A VAL* 3.3 10.9 - - - -
23A ASN* 2.8 25.0 + - - -
24A GLY 4.6 0.7 + - - -
104A VAL 3.2 8.5 - - - -
105A VAL* 4.0 13.2 - - - -
124A LEU* 3.8 2.4 - - - +
125A ARG* 1.3 72.1 - - - +
127A THR* 1.3 67.6 + - - +
129A PHE* 4.2 7.6 - - - -
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Residues in contact with THR 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A ASN* 3.6 8.1 - - - +
103A GLY* 3.5 0.3 - - - -
104A VAL* 2.8 50.8 + - - +
125A ARG* 3.8 31.9 + - + +
126A GLY* 1.3 79.5 - - - +
128A ASN* 1.3 67.5 + - - +
129A PHE* 3.2 6.7 + - - -
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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