Contacts of the strand formed by residues 123 - 131 (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 VAL 123 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115A VAL* 3.1 7.1 - - - +
116A LEU* 2.5 57.8 + - + -
122A VAL* 1.3 77.0 - - - +
124A ILE* 1.3 69.0 + - - +
125A ILE* 4.1 15.7 - - + -
143A SER* 4.2 11.0 - - - +
144A LEU 3.5 10.1 - - - +
145A PHE* 3.7 35.7 - - + -
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Residues in contact with ILE 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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87A VAL* 5.7 1.6 - - + -
112A VAL* 3.6 35.4 - - + -
114A ASP 3.9 3.8 - - - +
115A VAL* 4.4 11.4 - - + -
122A VAL* 5.7 1.3 - - + +
123A VAL* 1.3 77.6 - - - +
125A ILE* 1.3 66.9 + - - +
126A MET* 3.9 5.1 + - + +
142A PHE 3.8 1.6 - - - +
143A SER 4.0 0.2 - - - -
144A LEU* 2.9 55.9 + - + +
145A PHE 6.0 0.7 - - - -
146A LEU* 6.3 3.1 - - + -
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Residues in contact with ILE 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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112A VAL* 3.5 3.5 - - - +
113A ALA* 2.8 37.5 + - + -
114A ASP* 3.0 21.8 + - + +
115A VAL* 4.9 0.2 - - - +
116A LEU* 4.6 18.4 - - + -
123A VAL* 4.1 13.0 - - + -
124A ILE* 1.3 76.8 - - - +
126A MET* 1.3 61.7 + - - +
141A GLN* 3.6 31.6 - - + +
142A PHE 3.7 3.4 - - - +
143A SER* 4.5 12.3 - - - +
158A SER* 5.2 3.6 - - - -
160A LYS 4.7 2.9 - - - +
161A VAL* 3.2 38.8 - - + -
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Residues in contact with MET 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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15A LEU* 3.6 27.4 - - - -
68A SER* 3.6 23.8 - - - +
69A MET* 4.2 19.1 - - + +
110A ALA* 4.2 7.0 - - + -
111A VAL 3.4 17.9 - - - +
112A VAL* 4.6 4.7 - - + +
124A ILE* 3.9 8.0 + - + +
125A ILE* 1.3 73.7 - - - +
127A ASP* 1.3 71.7 + - - +
128A VAL* 4.9 2.5 - - + -
140A ASN 3.8 0.9 - - - +
141A GLN* 3.7 1.4 - - - -
142A PHE* 3.0 61.8 + - + +
144A LEU* 5.0 12.1 - - + -
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Residues in contact with ASP 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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109A GLU 4.2 0.2 - - - +
110A ALA* 3.6 0.5 - - - -
111A VAL* 2.9 37.4 + - + +
113A ALA* 3.2 22.3 - - + +
125A ILE 4.1 0.8 - - - -
126A MET* 1.3 74.9 - - - +
128A VAL* 1.3 61.0 + - - +
129A TYR* 3.7 23.3 + - + -
139A HIS* 2.7 29.4 + - - +
140A ASN 3.3 2.0 - - - -
141A GLN* 2.8 35.8 + - - +
160A LYS* 4.2 3.8 - - - +
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Residues in contact with VAL 128 (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 PHE* 4.7 4.5 - - + -
65A GLY* 4.0 25.8 - - - +
68A SER* 5.5 0.7 - - - +
108A CYS* 4.5 9.9 - - + -
109A GLU 3.3 15.5 - - - +
110A ALA* 4.1 10.8 - - + -
126A MET* 4.1 6.3 - - + +
127A ASP* 1.3 77.8 - - - +
129A TYR* 1.3 69.0 + - - +
130A SER* 4.5 1.5 + - - +
138A CYS 4.1 0.7 - - - +
139A HIS* 3.7 1.4 - - - -
140A ASN* 2.9 40.0 + - + +
142A PHE* 3.4 36.1 - - + -
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Residues in contact with TYR 129 (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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97A TYR* 4.9 4.9 - - - -
108A CYS* 3.4 1.7 - - - -
109A GLU* 2.9 39.0 + - + +
111A VAL* 5.6 8.7 - - + -
127A ASP* 3.7 28.3 + - + +
128A VAL* 1.3 75.9 - - - +
130A SER* 1.3 61.5 + - - +
131A TYR* 3.5 33.5 - - + +
136A LEU* 3.9 18.6 - - + -
138A CYS 3.7 2.9 - - - -
139A HIS* 3.6 46.2 + + + -
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Residues in contact with SER 130 (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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64A ILE* 3.6 14.3 - - - +
65A GLY* 4.4 7.3 - - - -
106A LEU* 4.8 7.4 - - - -
107A LYS 3.4 4.7 - - - -
108A CYS* 3.4 25.9 - - - +
128A VAL* 4.5 3.3 + - - +
129A TYR* 1.3 75.9 - - - +
131A TYR* 1.3 55.3 + - - +
136A LEU* 3.5 1.6 - - - +
137A ILE* 2.8 32.8 + - - +
138A CYS* 3.0 33.2 + - - -
140A ASN* 4.8 0.7 + - - -
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Residues in contact with TYR 131 (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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106A LEU* 3.4 8.5 - - - +
107A LYS* 2.8 50.3 + - + +
109A GLU* 3.7 31.1 + - + -
129A TYR* 3.5 40.6 - - + +
130A SER* 1.3 74.2 - - - +
132A SER* 1.3 58.9 + - - +
133A GLU 3.2 13.5 + - - +
134A LYS* 4.0 10.3 - - - -
135A GLU 3.0 12.1 - - - +
136A LEU* 3.6 34.5 - - + +
137A ILE* 4.3 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