Contacts of the strand formed by residues 140 - 145 (chain B) in PDB entry 1S0O
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 140 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B VAL* 3.7 20.6 - - + -
7B ASP 3.7 11.0 - - - +
8B PHE* 3.6 24.2 - - + -
9B ASP* 3.6 5.4 - - - +
128B ILE* 5.6 0.4 - - + -
129B LYS* 2.8 51.2 + - + +
132B ILE* 4.2 22.2 - - + -
138B ILE* 3.9 17.0 + - + +
139B THR* 1.3 81.4 - - - +
141B THR* 1.3 64.4 + - - +
142B VAL* 4.3 4.5 - - + -
161B ASN* 3.9 1.7 - - - -
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Residues in contact with THR 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B PHE 3.8 0.9 - - - +
6B VAL* 3.6 4.0 - - - +
7B ASP* 2.9 36.0 + - - +
9B ASP* 2.7 22.6 + - - -
140B VAL* 1.3 72.8 - - - +
142B VAL* 1.3 63.5 + - - +
155B ALA* 3.3 37.5 - - - +
158B ALA* 3.8 7.2 - - + -
159B LYS* 3.3 24.1 - - - +
161B ASN 3.2 14.0 + - - -
162B GLY 3.3 12.6 + - - +
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Residues in contact with VAL 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B LEU* 3.8 29.8 - - + -
5B PHE 3.4 2.2 - - - -
6B VAL* 4.4 12.3 - - + -
125B GLY* 4.1 10.5 - - - +
128B ILE* 5.4 2.7 - - + -
129B LYS* 3.7 28.5 - - + +
140B VAL* 4.3 7.4 - - + -
141B THR* 1.3 80.5 - - - +
143B GLY* 1.3 61.2 + - - +
144B ILE* 3.8 14.1 - - + -
155B ALA* 4.2 4.9 - - - -
162B GLY 3.0 5.9 + - - -
163B ILE* 3.2 22.0 - - + -
164B LYS 3.0 25.8 + - - -
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Residues in contact with GLY 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B VAL 3.7 0.9 - - - +
4B LEU* 3.4 1.7 - - - -
5B PHE* 2.6 43.9 + - - +
142B VAL* 1.3 73.7 - - - +
144B ILE* 1.3 62.0 + - - +
151B ALA* 3.3 24.4 - - - +
154B ALA* 3.8 0.4 - - - -
155B ALA* 3.6 14.9 - - - +
164B LYS 3.7 2.7 - - - -
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Residues in contact with ILE 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B ILE* 4.3 4.0 - - + -
3B VAL 3.2 9.4 - - - +
4B LEU* 3.9 13.9 - - + -
118B TYR* 3.8 27.8 - - + -
121B ALA* 3.3 41.1 - - + +
122B TYR* 3.8 10.3 - - - +
125B GLY* 4.7 0.2 - - - -
142B VAL* 3.8 21.3 - - + -
143B GLY* 1.3 79.1 - - - +
145B SER* 1.3 65.5 + - - +
151B ALA* 4.4 1.1 - - - -
154B ALA* 3.9 2.8 - - - +
163B ILE* 4.6 5.4 - - + -
164B LYS 2.9 9.1 + - - +
165B VAL* 3.3 15.5 - - + +
166B ILE* 2.8 28.1 + - - +
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Residues in contact with SER 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B ILE* 3.7 2.6 - - - -
3B VAL* 2.7 36.4 + - - +
118B TYR* 3.3 14.9 - - - -
144B ILE* 1.3 78.6 - - - +
146B LYS* 1.3 64.5 + - - +
147B ASN 3.4 1.7 + - - -
150B PHE* 3.4 41.7 - - - +
151B ALA* 3.7 3.8 - - - +
166B ILE* 2.8 20.8 + - - +
171B VAL* 3.7 7.4 - - - +
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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