Contacts of the strand formed by residues 104 - 119 (chain A) in PDB entry 4X8G
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 VAL 104 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A PRO* 4.7 15.7 - - + -
34A PRO* 4.8 16.8 - - + -
95A SER* 4.5 1.6 - - - -
96A TYR* 2.8 43.3 + - - +
103A PRO* 1.3 75.1 - - - +
105A LYS* 1.3 58.8 + - - +
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Residues in contact with LYS 105 (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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11A PRO* 3.8 19.1 - - - +
93A GLN* 3.9 28.0 - - + +
94A ILE 3.3 7.0 - - - +
95A SER* 4.1 7.2 - - - +
104A VAL* 1.3 73.5 - - - +
106A ALA* 1.3 60.3 + - - +
107A LEU* 4.4 3.3 + - + +
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Residues in contact with ALA 106 (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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9A VAL* 4.5 8.5 - - + -
10A THR 3.8 11.2 - - - +
11A PRO* 3.8 22.4 - - + -
93A GLN* 3.6 3.2 - - - +
94A ILE* 2.5 55.6 + - + +
96A TYR* 3.9 16.4 - - + +
105A LYS* 1.3 75.3 - - - +
107A LEU* 1.3 62.1 + - - +
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Residues in contact with LEU 107 (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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9A VAL* 3.9 10.2 - - - +
10A THR 4.7 3.1 + - - +
13A GLN 5.0 1.0 - - - +
14A PRO* 4.1 21.6 - - + +
15A THR* 3.3 19.3 + - - -
91A LYS* 5.4 9.9 - - + -
92A VAL 3.7 8.3 - - - +
93A GLN* 4.8 15.5 - - + +
94A ILE* 4.6 0.4 - - - -
105A LYS* 4.4 3.1 + - + +
106A ALA* 1.3 78.3 - - - +
108A LEU* 1.3 67.3 + - - +
109A TYR* 3.7 33.7 - - + +
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Residues in contact with LEU 108 (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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7A ILE* 4.0 13.5 - - + -
9A VAL* 3.8 20.6 - - + -
15A THR* 3.2 23.3 - - - +
17A ALA* 4.1 4.0 - - + -
27A LEU* 3.7 29.4 - - + -
78A LEU* 4.4 1.8 - - + -
91A LYS* 3.6 4.0 - - - -
92A VAL* 2.9 61.7 + - + +
94A ILE* 4.2 1.6 - - + -
107A LEU* 1.3 79.8 - - - +
109A TYR* 1.3 61.8 + - - +
110A LEU* 3.7 32.8 + - + +
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Residues in contact with TYR 109 (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 PRO* 4.3 11.4 - - + -
15A THR 2.9 11.3 + - - -
16A HIS* 3.5 38.7 - + + +
17A ALA 2.9 27.7 + - - +
88A GLY* 3.9 27.1 - - - -
90A GLN 3.7 1.8 - - - -
91A LYS* 4.2 27.3 - - + +
107A LEU* 3.7 38.4 - - + +
108A LEU* 1.3 73.9 - - - +
110A LEU* 1.3 60.6 + - - +
111A THR* 5.1 0.7 + - - -
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Residues in contact with LEU 110 (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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7A ILE* 4.2 4.0 - - + -
17A ALA* 3.4 25.6 - - + +
19A CYS* 4.0 13.7 - - - -
48A VAL* 4.1 14.4 - - + -
78A LEU* 4.0 16.6 - - + -
80A MET* 4.2 20.0 - - + -
88A GLY* 3.2 15.3 - - - -
89A ASP* 3.6 1.6 + - - +
90A GLN* 2.9 30.5 + - + +
92A VAL* 3.7 26.7 - - + -
108A LEU* 3.7 28.5 - - + +
109A TYR* 1.3 73.6 - - - +
111A THR* 1.3 62.2 + - - +
112A GLY 4.2 0.9 - - - -
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Residues in contact with THR 111 (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 ALA 3.1 12.1 + - - -
18A VAL* 3.8 11.4 - - - +
19A CYS 2.9 28.9 + - - +
80A MET* 4.5 2.2 - - - -
84A SER* 3.4 17.3 - - - -
86A SER 4.1 3.8 - - - +
87A THR* 3.7 12.2 - - + +
88A GLY* 2.8 22.7 + - - -
109A TYR 5.1 0.5 + - - -
110A LEU* 1.3 72.8 - - - +
112A GLY* 1.3 62.2 + - - +
113A VAL* 3.6 8.4 + - + -
190A PRO* 3.9 22.2 - - + -
193A PHE* 4.5 10.1 - - + -
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Residues in contact with GLY 112 (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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19A CYS 3.4 6.3 - - - -
21A LEU* 4.9 4.0 - - - -
80A MET* 3.7 21.1 - - - +
82A VAL 4.4 4.7 - - - -
83A ALA* 3.4 6.2 - - - +
84A SER* 2.5 47.0 + - - -
111A THR* 1.3 71.0 - - - +
113A VAL* 1.3 62.2 + - - +
190A PRO* 4.2 2.8 - - - +
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Residues in contact with VAL 113 (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 VAL* 4.0 9.9 - - + -
19A CYS 2.8 18.6 + - - +
20A VAL* 3.3 22.1 - - + -
21A LEU* 2.8 30.7 + - - +
111A THR* 4.3 7.0 - - + +
112A GLY* 1.3 79.3 - - - +
114A GLU* 1.3 59.4 + - - +
115A ILE* 4.3 8.1 - - + -
188A LYS 3.8 4.5 - - - -
189A THR* 3.6 23.1 - - + -
190A PRO* 4.1 4.3 - - + -
193A PHE* 3.6 35.9 - - + -
271A LEU* 4.6 1.3 - - + -
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Residues in contact with GLU 114 (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 LEU* 3.8 24.8 - - + +
83A ALA* 5.3 0.5 - - - +
113A VAL* 1.3 73.4 - - - +
115A ILE* 1.3 69.9 + - - +
116A SER* 3.9 17.5 + - - +
186A SER* 4.3 15.5 - - - +
187A THR* 3.1 23.7 - - - -
188A LYS* 3.2 37.4 + - + +
189A THR* 4.4 0.3 - - - +
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Residues in contact with ILE 115 (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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20A VAL* 4.1 17.3 - - + +
21A LEU 5.4 1.2 + - - -
113A VAL* 4.1 17.4 - - + -
114A GLU* 1.3 84.5 - - - +
116A SER* 1.3 59.4 + - - +
117A LEU 4.2 0.7 + - - -
185A LEU* 4.4 11.0 - - + -
186A SER 4.1 2.0 - - - -
187A THR* 3.7 20.2 - - + -
189A THR* 4.3 15.7 - - + -
193A PHE* 5.3 2.5 - - + -
194A PHE* 5.6 1.3 - - + -
199A LEU* 4.3 29.2 - - + -
269A ILE* 4.6 7.4 - - + -
271A LEU* 4.6 13.0 - - + -
285A PHE* 3.6 37.4 - - + -
287A ASP* 4.5 2.9 - - - +
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Residues in contact with SER 116 (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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114A GLU* 3.9 14.4 + - - -
115A ILE* 1.3 74.4 - - - +
117A LEU* 1.3 59.2 + - - +
118A CYS* 3.8 14.5 - - - -
129A PRO* 5.0 8.4 - - - +
130A THR* 5.1 5.2 - - - -
185A LEU* 3.4 6.7 - - - +
186A SER* 3.2 45.7 + - - -
287A ASP* 4.7 2.2 - - - -
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Residues in contact with LEU 117 (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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115A ILE 4.2 0.6 + - - -
116A SER* 1.3 72.3 - - - +
118A CYS* 1.3 60.3 + - - +
130A THR* 3.3 30.3 + - - +
183A MET* 4.1 24.5 - - + -
184A THR 3.6 13.5 - - - +
185A LEU* 3.9 22.0 - - + +
201A LEU* 4.5 13.9 - - + -
249A PHE* 5.3 2.7 - - + -
267A LEU 4.4 5.2 - - - +
269A ILE* 4.2 22.4 - - + +
287A ASP* 3.6 36.1 + - - +
288A SER* 4.6 0.2 - - - -
289A VAL* 4.0 28.9 - - + +
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Residues in contact with CYS 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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116A SER* 3.8 21.5 - - - -
117A LEU* 1.3 78.9 - - - +
119A ALA* 1.3 62.5 + - - +
127A VAL* 3.6 12.7 - - + +
128A LYS 3.8 2.9 - - - -
129A PRO* 3.6 33.7 - - + -
130A THR* 5.1 0.2 - - - -
183A MET* 3.3 8.5 - - - +
184A THR* 2.8 53.8 + - - +
186A SER* 5.1 5.6 - - - -
289A VAL* 4.8 1.3 - - - -
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Residues in contact with ALA 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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117A LEU 4.4 0.2 + - - -
118A CYS* 1.3 75.8 - - - +
120A ASP* 1.3 55.6 + - - +
121A ILE* 2.8 25.0 + - + +
127A VAL* 3.6 11.4 - - - +
128A LYS 2.8 22.0 + - - +
130A THR* 5.6 0.4 - - - +
148A ALA* 4.4 4.3 - - + -
182A LEU 4.0 7.0 - - - +
183A MET* 4.6 2.2 - - + -
289A VAL* 4.2 19.3 - - + +
291A PHE* 4.0 27.1 - - + -
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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