Contacts of the strand formed by residues 123 - 131 (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 VAL 123 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115D VAL* 3.4 5.6 - - - -
116D LEU* 2.5 47.5 + - + +
122D VAL* 1.3 75.5 - - - +
124D ILE* 1.3 61.9 + - - +
125D ILE* 3.4 35.4 + - + +
143D SER* 4.1 8.7 - - - +
144D LEU 3.4 11.0 - - - +
145D PHE* 4.1 17.5 - - + -
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Residues in contact with ILE 124 (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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77D ILE* 4.5 16.6 - - + -
78D PRO 6.2 4.0 - - - -
84D PHE* 6.2 1.8 - - + -
87D VAL* 4.6 20.2 - - + -
112D VAL* 4.1 23.1 - - + -
114D ASP 4.2 2.2 - - - -
115D VAL* 4.3 11.9 - - + -
122D VAL* 4.8 13.2 - - + +
123D VAL* 1.3 70.7 - - - +
125D ILE* 1.3 61.4 + - - +
126D MET* 5.2 2.7 - - + -
144D LEU* 2.8 60.8 + - + +
146D LEU* 4.8 12.3 - - + -
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Residues in contact with ILE 125 (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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112D VAL* 3.5 2.7 - - - -
113D ALA* 3.1 34.2 + - + -
114D ASP* 3.2 23.8 + - + +
116D LEU* 5.1 9.2 - - + -
123D VAL* 3.4 29.8 + - + +
124D ILE* 1.3 71.5 - - - +
126D MET* 1.3 59.0 + - - +
141D GLN* 3.7 32.8 - - + +
142D PHE 3.7 3.8 - - - +
143D SER* 4.4 13.5 - - - +
158D SER* 5.2 0.7 - - - +
160D LYS 4.6 3.8 - - - +
161D VAL* 3.1 44.2 - - + -
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Residues in contact with MET 126 (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* 3.8 25.1 - - + -
68D SER* 4.4 12.1 - - - +
69D MET* 4.1 26.5 - - + -
77D ILE* 4.8 8.3 - - - -
110D ALA* 4.6 4.0 - - + -
111D VAL 3.3 22.2 - - - +
112D VAL* 4.6 4.5 - - + -
124D ILE* 3.7 6.9 + - + +
125D ILE* 1.3 74.5 - - - +
127D ASP* 1.3 66.4 + - - +
128D VAL* 5.2 4.0 - - + -
140D ASN 3.7 0.5 - - - +
141D GLN* 3.5 2.0 - - - -
142D PHE* 3.0 68.2 + - + +
144D LEU* 4.5 13.9 - - + -
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Residues in contact with ASP 127 (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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109D GLU 3.8 0.8 - - - +
110D ALA* 3.2 4.0 - - - +
111D VAL* 2.7 43.8 + - + +
113D ALA* 3.0 25.0 - - + +
125D ILE 4.3 0.4 + - - -
126D MET* 1.3 73.5 - - - +
128D VAL* 1.3 62.1 + - - +
129D TYR* 3.7 25.6 + - + -
139D HIS* 2.7 26.9 + - - +
140D ASN 3.3 1.8 - - - -
141D GLN* 2.9 31.2 + - - +
160D LYS* 4.5 2.1 - - - +
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Residues in contact with VAL 128 (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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18D PHE* 4.3 5.2 - - + -
65D GLY* 3.8 27.6 - - - +
68D SER* 5.5 0.9 - - - +
108D CYS* 4.2 18.4 - - + -
109D GLU 3.2 9.6 - - - +
110D ALA* 4.2 9.6 - - + -
126D MET* 4.6 4.5 - - + +
127D ASP* 1.3 77.6 - - - +
129D TYR* 1.3 64.5 + - - +
130D SER* 4.1 1.2 + - - +
138D CYS 4.0 0.7 - - - +
139D HIS* 3.7 1.4 - - - -
140D ASN* 2.9 40.0 + - + +
142D PHE* 3.3 37.2 - - + -
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Residues in contact with TYR 129 (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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97D TYR* 5.1 3.1 - - - -
107D LYS 3.5 1.4 - - - +
108D CYS* 3.0 4.9 - - - -
109D GLU* 2.8 41.7 + - + +
111D VAL* 4.9 12.3 - - + -
127D ASP* 3.7 26.8 + - + +
128D VAL* 1.3 74.3 - - - +
130D SER* 1.3 62.5 + - - +
131D TYR* 3.5 27.1 - - + +
136D LEU* 3.8 23.1 - - + -
138D CYS 3.6 2.9 - - - -
139D HIS* 3.6 43.9 + + + -
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Residues in contact with SER 130 (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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64D ILE* 3.5 13.6 - - - +
65D GLY* 4.4 6.9 + - - -
106D LEU* 4.5 8.7 - - - -
107D LYS 3.3 4.7 - - - -
108D CYS* 3.3 23.8 - - - +
128D VAL* 4.5 2.4 + - - +
129D TYR* 1.3 75.4 - - - +
131D TYR* 1.3 55.1 + - - +
136D LEU* 3.6 1.7 - - - +
137D ILE* 2.7 32.8 + - - +
138D CYS* 3.0 37.3 + - - -
140D ASN* 4.7 0.3 + - - -
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Residues in contact with TYR 131 (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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106D LEU* 3.0 13.8 - - - -
107D LYS* 2.8 50.8 + - + +
109D GLU* 3.7 31.2 + - - -
129D TYR* 3.5 38.7 - - + +
130D SER* 1.3 73.4 - - - +
132D SER* 1.3 61.7 + - - +
133D GLU 4.0 14.1 - - - +
134D LYS* 4.5 8.5 - - - -
135D GLU 3.2 11.0 - - - +
136D LEU* 3.4 38.9 - - + +
137D ILE* 4.2 0.4 - - - +
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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