Contacts of the strand formed by residues 104 - 115 (chain A) in PDB entry 1S9C
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 GLY 104 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A ALA* 3.0 2.3 - - - -
22A TYR* 2.7 54.2 + - - -
101A PRO* 5.0 3.1 - - - -
103A ALA* 1.3 76.0 - - - +
105A LYS* 1.3 64.3 + - - -
106A LEU* 5.0 1.3 - - - -
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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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19A SER* 6.4 0.7 - - - -
20A TYR 3.7 3.8 - - - -
21A ALA* 3.2 25.1 - - + -
104A GLY* 1.3 74.9 - - - -
106A LEU* 1.3 73.8 + - - +
132A SER* 3.5 12.6 + - - -
133A GLU* 5.8 0.2 - - - +
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Residues in contact with LEU 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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19A SER* 3.1 9.7 - - - -
20A TYR 2.8 35.9 + - - +
22A TYR* 3.9 18.2 - - + +
64A ILE* 3.4 48.9 - - + -
100A LEU* 5.4 2.5 - - + -
101A PRO* 5.6 4.0 - - + -
104A GLY* 5.0 0.9 - - - -
105A LYS* 1.3 85.8 - - - +
107A LYS* 1.3 61.6 + - - +
108A CYS* 4.6 1.8 - - - -
130A SER* 4.8 5.2 - - - -
131A TYR 3.4 17.0 - - - +
132A SER* 3.5 14.8 - - - +
137A ILE* 3.5 25.4 - - + -
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Residues in contact with LYS 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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17A PRO* 4.8 12.8 - - + -
18A PHE 3.8 7.4 - - - +
19A SER* 4.2 5.4 - - - -
106A LEU* 1.3 75.1 - - - +
108A CYS* 1.3 65.6 + - - +
109A GLU* 3.2 29.2 + - + +
130A SER* 3.4 0.9 - - - -
131A TYR* 2.8 47.1 + - + +
133A GLU 5.9 2.0 - - - +
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Residues in contact with CYS 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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17A PRO* 3.4 6.4 - - - +
18A PHE* 2.7 67.6 + - + +
20A TYR 4.5 4.7 - - - -
64A ILE* 3.8 26.2 - - - -
65A GLY* 4.8 0.2 - - - -
106A LEU 4.4 7.6 - - - -
107A LYS* 1.3 78.2 - - - +
109A GLU* 1.3 66.3 + - - +
128A VAL* 4.5 4.3 - - + -
129A TYR 3.4 6.1 - - - +
130A SER* 3.4 24.7 - - - +
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Residues in contact with GLU 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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15A LEU 5.5 0.7 - - - +
17A PRO* 4.3 17.0 - - + -
107A LYS* 3.2 29.8 + - - +
108A CYS* 1.3 79.4 - - - +
110A ALA* 1.3 63.3 + - - +
111A VAL* 4.9 3.2 - - + +
127A ASP 4.2 0.3 - - - +
128A VAL* 3.3 4.1 - - - -
129A TYR* 2.9 42.3 + - + +
131A TYR* 3.7 30.0 + - + +
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Residues in contact with ALA 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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14A LYS* 3.5 2.1 - - - +
15A LEU* 3.0 52.9 + - + +
16A PRO 5.1 3.2 + - - +
18A PHE* 4.9 6.1 - - + -
68A SER* 4.9 11.0 - - - -
108A CYS 4.4 0.4 + - - -
109A GLU* 1.3 73.6 - - - +
111A VAL* 1.3 74.9 + - - +
126A MET* 4.2 10.5 - - - -
127A ASP 3.6 4.3 - - - -
128A VAL* 4.1 11.2 - - + -
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Residues in contact with VAL 111 (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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12A GLY* 4.1 12.1 - - - +
13A GLN 3.6 10.3 - - - +
14A LYS* 3.5 18.4 - - + +
15A LEU* 4.2 1.7 - - - +
109A GLU* 4.9 5.8 - - + +
110A ALA* 1.3 88.6 - - - +
112A VAL* 1.3 65.9 + - - +
113A ALA* 2.7 21.5 + - + +
126A MET* 3.4 5.3 - - - +
127A ASP* 2.9 34.5 + - + +
129A TYR* 5.6 7.4 - - + -
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Residues in contact with VAL 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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10A ALA* 3.5 18.8 - - + +
11A ILE 2.2 37.8 - - - +
12A GLY* 3.2 10.0 - - - -
13A GLN* 2.9 20.0 + - + +
15A LEU* 3.7 20.0 - - + -
111A VAL* 1.3 69.3 - - - +
113A ALA* 1.3 56.8 + - - +
114A ASP 3.9 2.7 - - - +
115A VAL* 3.9 11.0 - - + -
124A ILE* 3.6 40.4 - - + -
125A ILE 3.6 3.1 - - - -
126A MET* 4.4 4.9 - - + +
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Residues in contact with ALA 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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11A ILE* 4.0 2.6 - - - +
12A GLY* 4.9 2.1 - - - -
111A VAL* 2.7 15.6 + - - +
112A VAL* 1.3 72.4 - - - +
114A ASP* 1.3 65.5 + - + +
125A ILE* 2.8 24.6 + - + +
127A ASP* 3.2 30.5 - - + +
160A LYS* 3.4 33.9 + - + +
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Residues in contact with ASP 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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11A ILE* 3.4 27.2 - - - +
112A VAL* 3.1 3.9 + - - +
113A ALA* 1.3 85.2 - - + +
115A VAL* 1.3 82.7 + - - +
116A LEU* 3.1 28.3 - - - +
125A ILE* 3.0 33.6 + - + +
158A SER* 3.6 25.6 + - - +
159A ASP* 5.4 1.2 - - - +
160A LYS* 4.6 11.0 - - + +
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Residues in contact with VAL 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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10A ALA 4.7 1.1 - - - +
11A ILE* 3.5 36.7 - - + +
112A VAL* 3.9 13.0 - - + -
114A ASP* 1.3 87.0 + - - +
116A LEU* 1.3 73.2 + - - +
122A VAL* 3.7 18.4 - - + -
123A VAL 3.1 17.7 - - - +
124A ILE* 4.4 9.9 - - + -
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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