Contacts of the strand formed by residues 104 - 115 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20D TYR 3.9 0.2 - - - +
21D ALA* 3.1 2.9 - - - +
22D TYR* 2.9 46.4 + - - -
101D PRO* 5.0 3.4 - - - -
103D ALA* 1.3 77.3 - - - +
105D LYS* 1.3 65.2 + - - -
106D LEU* 5.0 1.3 - - - -
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Residues in contact with LYS 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D SER* 6.3 1.1 - - - -
20D TYR 3.4 3.6 - - - +
21D ALA* 3.4 24.2 - - + -
104D GLY* 1.3 73.0 - - - -
106D LEU* 1.3 74.4 + - - +
132D SER* 3.9 13.6 - - - +
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Residues in contact with LEU 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D SER* 3.2 8.9 - - - -
20D TYR 2.7 38.1 + - - +
22D TYR* 4.1 15.0 - - + +
64D ILE* 3.5 43.7 - - + -
100D LEU* 5.4 0.7 - - + -
101D PRO* 5.5 4.7 - - + -
104D GLY 5.0 0.9 - - - -
105D LYS* 1.3 85.8 - - - +
107D LYS* 1.3 62.2 + - - +
108D CYS* 4.7 1.3 - - - -
130D SER* 4.5 13.0 - - - -
131D TYR* 3.0 25.1 - - - +
132D SER* 3.6 3.6 - - - -
137D ILE* 3.3 38.6 - - + -
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Residues in contact with LYS 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D PRO* 4.9 11.2 - - + -
18D PHE 3.8 7.2 - - - +
19D SER* 4.5 4.3 - - - +
106D LEU* 1.3 73.8 - - - +
108D CYS* 1.3 67.2 + - - +
109D GLU* 3.2 31.8 + - + +
130D SER* 3.3 1.2 - - - -
131D TYR* 2.8 47.0 + - + +
132D SER 4.7 4.4 + - - +
133D GLU 5.4 6.1 - - - +
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Residues in contact with CYS 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D PRO* 3.4 5.4 - - - +
18D PHE* 2.8 71.3 + - + +
20D TYR* 4.7 3.8 - - - -
64D ILE* 4.0 15.3 - - - -
65D GLY* 4.7 0.4 - - - -
106D LEU 4.5 7.6 - - - -
107D LYS* 1.3 77.8 - - - +
109D GLU* 1.3 69.1 + - - +
110D ALA 4.3 0.2 - - - -
128D VAL* 4.2 4.9 - - + -
129D TYR 3.0 6.7 - - - +
130D SER* 3.3 25.4 - - - -
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Residues in contact with GLU 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D LEU 5.3 1.1 - - - +
17D PRO* 4.4 10.8 - - + -
107D LYS* 3.2 34.7 + - + +
108D CYS* 1.3 80.5 - - - +
110D ALA* 1.3 61.1 + - - +
111D VAL* 4.8 3.8 - - + +
127D ASP 3.8 0.2 - - - +
128D VAL* 3.2 4.5 - - - -
129D TYR* 2.8 42.8 + - + +
131D TYR* 3.7 29.4 + - + +
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Residues in contact with ALA 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D LYS* 3.7 1.9 - - - +
15D LEU* 2.8 58.9 + - + +
16D PRO 5.3 2.3 + - - +
18D PHE* 4.9 7.6 - - + -
68D SER* 4.8 11.0 - - - +
108D CYS 4.3 0.2 - - - -
109D GLU* 1.3 72.7 - - - +
111D VAL* 1.3 67.2 + - - +
126D MET* 4.6 8.1 - - + -
127D ASP 3.2 8.5 - - - +
128D VAL* 4.1 11.0 - - + +
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Residues in contact with VAL 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D GLY* 3.9 20.9 - - - +
13D GLN 3.8 5.6 - - - +
14D LYS* 4.5 17.3 - - + -
15D LEU* 5.4 0.2 - - - -
109D GLU* 4.8 8.1 - - + +
110D ALA* 1.3 80.9 - - - +
112D VAL* 1.3 67.0 + - - +
113D ALA* 3.1 12.4 + - - +
126D MET* 3.3 6.9 - - - +
127D ASP* 2.7 43.5 + - + +
129D TYR* 4.9 11.2 - - + -
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Residues in contact with VAL 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D ALA 3.6 20.2 - - - +
11D ILE 3.6 0.9 - - - -
12D GLY* 3.3 18.9 + - - +
13D GLN* 3.1 20.1 + - + +
15D LEU* 4.4 8.3 - - + -
77D ILE* 3.2 44.0 - - + -
111D VAL* 1.3 78.1 - - - +
113D ALA* 1.3 66.2 + - - +
114D ASP 2.8 21.0 + - - +
115D VAL* 4.2 4.0 - - + -
124D ILE* 4.1 15.5 - - + -
125D ILE 3.8 4.0 - - - +
126D MET* 4.4 2.9 - - + +
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Residues in contact with ALA 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D ILE* 4.4 6.2 - - - +
12D GLY* 5.2 1.2 - - - -
111D VAL* 3.1 14.7 + - - -
112D VAL* 1.3 72.6 - - - +
114D ASP* 1.3 65.4 + - - +
125D ILE* 3.1 21.3 + - + +
127D ASP* 3.0 30.3 - - + +
160D LYS* 3.2 43.4 + - + +
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Residues in contact with ASP 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D ILE* 3.8 12.8 - - - +
112D VAL* 2.8 9.7 + - - +
113D ALA* 1.3 81.2 - - + +
115D VAL* 1.3 82.8 + - - +
116D LEU* 3.1 14.0 - - + +
123D VAL 4.5 0.2 - - - -
125D ILE* 3.2 33.8 + - + +
155D LYS* 2.9 32.9 + - - -
158D SER* 3.0 30.6 + - - +
160D LYS* 4.6 7.1 - - + +
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Residues in contact with VAL 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D ALA 4.4 9.2 - - - +
11D ILE* 3.8 21.5 - - + +
77D ILE* 6.0 2.0 - - + -
112D VAL* 4.2 14.6 - - + -
114D ASP* 1.3 88.6 + - - +
116D LEU* 1.3 74.9 + - - +
122D VAL* 3.9 21.3 - - + -
123D VAL 3.4 4.7 - - - -
124D ILE* 4.3 18.4 - - + -
155D LYS* 4.4 4.9 + - - +
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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