Contacts of the strand formed by residues 134 - 140 (chain C) in PDB entry 1SA0
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 134 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4C CYS* 4.0 6.1 - - - -
5C ILE 3.3 21.7 + - - +
132C LEU* 3.9 5.9 - - - +
133C GLN* 1.3 82.9 - - - +
135C PHE* 1.3 68.9 + - - -
136C SER 4.3 0.2 + - - -
164C LYS* 4.3 7.6 - - - -
165C SER 3.2 15.7 - - - -
252C LEU* 4.0 11.2 - - - +
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Residues in contact with PHE 135 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4C CYS* 5.9 0.2 - - - -
5C ILE* 3.2 50.0 - - + +
7C ILE* 4.2 11.2 - - + -
122C ILE* 4.8 10.5 - - + -
132C LEU* 4.1 13.7 - - + -
134C GLY* 1.3 76.2 - - - -
136C SER* 1.3 61.6 + - - +
137C VAL* 3.9 17.6 + - + +
157C LEU* 3.8 20.2 - - + -
161C TYR* 3.6 51.6 - + + -
164C LYS* 5.0 4.7 - - + -
165C SER 3.0 13.8 + - - +
166C LYS* 3.8 12.4 - - + -
167C LEU* 3.0 28.4 + - - +
252C LEU* 4.9 2.8 - - - +
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Residues in contact with SER 136 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4C CYS* 4.8 12.0 - - - -
5C ILE 2.8 10.3 + - - -
6C SER* 3.4 8.9 - - - -
7C ILE 2.9 25.5 + - - +
52C PHE* 5.1 8.1 - - - -
134C GLY 4.3 0.4 + - - -
135C PHE* 1.3 72.9 + - - +
137C VAL* 1.3 58.6 + - - +
138C PHE* 3.9 21.1 - - - -
167C LEU* 3.3 19.2 - - - +
169C PHE* 4.6 10.3 - - - -
239C THR* 5.2 5.8 - - - +
252C LEU* 5.5 4.0 - - - +
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Residues in contact with VAL 137 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C ILE* 3.4 32.5 - - + +
9C VAL* 4.2 21.1 - - + -
135C PHE* 4.3 12.3 - - + +
136C SER* 1.3 76.7 - - - +
138C PHE* 1.3 65.8 + - - +
139C HIS* 4.1 2.6 + - - +
150C THR* 4.5 15.3 - - + -
153C LEU* 4.9 5.8 - - + -
154C MET* 4.4 20.9 - - - -
157C LEU* 5.0 2.0 - - + -
166C LYS* 5.8 1.8 - - + -
167C LEU 2.9 14.4 + - - +
168C GLU* 3.3 7.8 - - + +
169C PHE* 2.8 28.0 + - - -
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Residues in contact with PHE 138 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C SER* 3.9 17.7 - - - -
7C ILE 2.9 14.7 + - - -
8C HIS* 3.3 39.0 - + + -
9C VAL* 3.0 26.7 + - - +
13C GLY* 3.4 13.8 - - - +
16C ILE* 3.7 22.0 - - + -
20C CYS* 4.4 5.6 - - - -
24C TYR* 5.1 5.6 - + - -
136C SER* 3.9 16.2 - - - -
137C VAL* 1.3 72.2 - - - +
139C HIS* 1.3 60.4 + - - +
169C PHE* 3.5 43.7 - + + +
171C ILE* 5.8 1.1 - - + -
235C VAL* 4.0 28.5 - - + -
239C THR* 5.9 1.6 - - + -
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Residues in contact with HIS 139 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C VAL* 3.8 16.2 - - + +
13C GLY* 4.2 4.8 - - - -
137C VAL* 4.2 6.8 + - + +
138C PHE* 1.3 74.7 - - - +
140C SER* 1.3 71.3 + - - +
141C PHE* 4.5 8.5 - - - -
146C GLY 3.0 21.1 - - - +
147C SER* 4.9 2.2 - - - -
150C THR* 3.4 34.1 - - + +
168C GLU* 3.7 25.9 + - + +
169C PHE 3.4 7.2 + - - +
170C SER* 2.9 35.1 + - - -
171C ILE* 3.2 26.6 + - - +
190C THR* 4.7 6.5 + - + +
194C THR* 5.3 1.8 + - - +
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Residues in contact with SER 140 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C VAL 4.6 0.2 + - - -
10C GLY 4.3 1.6 + - - -
12C ALA* 3.2 12.4 + - - +
13C GLY 4.5 0.2 - - - +
139C HIS* 1.3 91.2 - - - +
141C PHE* 1.3 64.1 + - - +
142C GLY 3.2 14.6 - - - -
146C GLY* 3.3 15.8 - - - +
171C ILE* 4.2 10.1 - - - -
601C GTP 3.2 52.5 + - - -
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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