Contacts of the strand formed by residues 145 - 153 (chain D) in PDB entry 1S9V
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 PHE 145 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10D VAL* 4.8 10.5 - - + -
12D LEU* 4.1 24.5 - - + -
21D GLN* 5.2 0.4 - - - -
111D ASN 3.3 7.8 + - - -
112D ILE* 2.6 50.0 + - + +
113D PHE* 4.0 8.5 - + - -
115D PRO* 4.0 19.7 - - + -
137D PHE* 3.7 37.5 - - + -
138D LEU 3.4 18.6 - - - +
139D SER* 4.1 10.5 - - - -
140D LYS* 4.0 6.0 - - - +
143D HIS 3.8 9.4 - - - -
144D SER* 1.3 79.1 - - - +
146D PHE* 1.3 61.1 + - - +
10E GLN* 3.2 39.0 - - + -
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Residues in contact with PHE 146 (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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28D GLY* 4.3 14.1 - - - -
108D LEU* 3.8 16.2 - - + -
109D VAL 3.1 12.1 - - - +
110D ASP* 3.4 23.8 - - - +
112D ILE* 3.9 2.5 - - - -
137D PHE* 3.7 1.9 - - - -
138D LEU* 2.9 74.7 + - + +
139D SER 3.7 12.3 - - - -
140D LYS* 3.7 16.2 - - + -
145D PHE* 1.3 74.4 - - - +
147D LYS* 1.3 64.5 + - - +
148D ILE* 4.0 22.7 - - + -
149E ARG* 4.4 15.7 - - - -
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Residues in contact with LYS 147 (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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21D GLN* 5.2 0.2 + - - -
107D CYS 3.6 1.7 - - - +
108D LEU* 3.8 0.2 - - - +
109D VAL* 2.9 34.4 + - - +
112D ILE* 3.7 12.3 - - + +
117D VAL* 4.2 7.0 - - + -
119D ILE* 3.7 20.9 - - + -
134D GLU* 2.9 32.3 + - - +
135D THR* 2.9 33.0 + - - +
136D SER* 3.7 11.6 - - - +
137D PHE* 3.5 41.2 - - + +
146D PHE* 1.3 78.4 - - - +
148D ILE* 1.3 71.6 + - - +
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Residues in contact with ILE 148 (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 ILE* 3.3 32.1 - - + -
107D CYS 3.5 3.4 - - - +
108D LEU* 4.0 19.3 - - + -
134D GLU* 3.1 5.3 - - - +
135D THR* 2.9 41.0 + - + +
138D LEU* 5.5 0.9 - - + -
146D PHE* 4.0 21.3 - - + -
147D LYS* 1.3 79.0 - - - +
149D SER* 1.3 60.7 + - - +
150D TYR* 3.4 24.8 - - + +
149E ARG* 4.3 10.1 - - + +
150E ASN 3.6 4.7 - - - +
151E GLY* 3.6 29.8 - - - +
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Residues in contact with SER 149 (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 ILE* 3.5 4.0 - - - -
107D CYS* 2.8 38.4 + - - -
119D ILE* 3.7 32.4 + - - +
121D TRP* 2.9 29.8 + - - -
132D VAL* 4.2 4.9 - - - +
133D SER 3.5 9.0 + - - -
134D GLU* 4.0 10.2 + - - +
147D LYS 4.2 0.2 + - - -
148D ILE* 1.3 74.8 - - - +
150D TYR* 1.3 63.5 + - - +
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Residues in contact with TYR 150 (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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94D LYS* 6.2 0.9 - - + -
104D ILE* 4.0 17.5 - - + -
105D LEU 3.4 2.2 - - - -
106D ILE* 3.9 22.4 - - + -
121D TRP* 3.6 3.2 + - - -
131D GLY 4.2 1.3 - - - +
132D VAL* 3.2 11.6 - - - +
133D SER* 2.7 56.4 + - - +
134D GLU* 4.3 1.3 - - - -
135D THR* 3.7 21.3 - - + +
148D ILE* 3.4 20.7 - - + +
149D SER* 1.3 75.0 + - - +
151D LEU* 1.3 61.3 + - - +
152D THR* 6.1 1.6 - - + -
150E ASN 2.7 29.5 + - - -
151E GLY* 3.2 22.6 + - - -
152E ASP* 4.5 15.5 - - + -
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Residues in contact with LEU 151 (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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104D ILE* 3.4 3.9 - - - +
105D LEU* 2.9 44.1 + - + +
121D TRP* 3.6 44.4 - - + +
128D VAL* 3.6 32.8 - - + -
130D GLU 4.4 1.3 - - - +
131D GLY 3.4 3.4 - - - +
132D VAL* 3.9 11.4 - - + -
150D TYR* 1.3 75.7 - - - +
152D THR* 1.3 80.8 + - - +
153D LEU* 3.7 2.9 + - + +
161D TYR* 3.8 31.4 - - + -
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Residues in contact with THR 152 (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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103D ASN 3.6 6.7 - - - +
104D ILE* 4.3 19.5 - - + -
130D GLU 5.4 0.3 - - - +
131D GLY* 2.9 34.7 + - - +
150D TYR* 6.1 1.3 - - + -
151D LEU* 1.3 87.0 - - - +
153D LEU* 1.3 63.3 + - - +
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Residues in contact with LEU 153 (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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102D PRO* 3.6 4.0 - - - +
103D ASN* 2.9 58.0 + - + +
104D ILE 3.7 2.9 - - - +
105D LEU* 3.9 23.3 - - + +
151D LEU* 3.8 9.6 - - + +
152D THR* 1.3 77.5 - - - +
154D LEU* 1.3 63.5 + - - +
155D PRO* 3.6 27.0 - - + +
161D TYR* 3.6 39.9 - - + +
178D TRP* 4.6 10.1 - - + -
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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