Contacts of the strand formed by residues 135 - 142 (chain A) in PDB entry 1ASZ
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 SER 135 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96A PHE* 3.8 17.6 - - - +
97A VAL* 3.6 30.3 - - - +
131A ARG* 3.6 2.6 - - - +
132A GLN* 3.0 35.4 + - - +
134A ALA* 1.3 79.1 - - - +
136A LEU* 1.3 67.1 + - - +
183A THR* 3.2 23.8 - - - -
184A VAL* 5.9 0.4 - - - -
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Residues in contact with LEU 136 (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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96A PHE* 4.8 2.2 - - - -
116A HIS* 3.1 43.3 - - + +
129A THR* 4.0 14.1 - - + -
130A LEU 3.4 8.7 - - - +
131A ARG* 4.5 4.9 - - + -
135A SER* 1.3 83.2 - - - +
137A ILE* 1.3 65.7 + - - +
181A SER* 5.4 2.2 - - - -
182A ALA* 3.8 17.9 - - - +
183A THR* 2.7 47.7 + - + +
184A VAL* 3.3 6.8 + - - +
242A VAL* 4.4 20.6 - - + -
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Residues in contact with ILE 137 (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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96A PHE* 3.2 45.1 - - + -
99A LEU* 4.8 6.1 - - + -
129A THR* 3.2 7.7 - - - +
130A LEU* 2.7 45.1 + - + +
136A LEU* 1.3 77.7 - - - +
138A GLN* 1.3 71.5 + - - +
182A ALA* 4.0 11.6 - - - +
184A VAL* 4.4 12.3 - - + +
187A LEU 3.7 21.3 - - - +
189A ILE* 3.1 36.8 - - + -
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Residues in contact with GLN 138 (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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119A ARG* 6.1 0.2 - - - -
127A PHE* 3.1 29.6 - - - +
128A LEU 2.9 11.0 - - - +
129A THR* 4.7 4.0 - - - +
130A LEU* 4.6 2.7 - - - +
137A ILE* 1.3 86.5 - - - +
139A GLY* 1.3 58.0 + - - +
175A VAL* 4.6 1.0 - - - +
179A ILE* 3.3 40.9 - - + +
181A SER* 4.8 4.3 - - - +
182A ALA* 4.8 0.8 - - - +
187A LEU 4.9 0.2 + - - -
188A GLU* 2.9 36.4 + - + -
189A ILE* 2.8 25.3 + - - +
635R U 2.8 30.5 + - - +
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Residues in contact with GLY 139 (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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126A ALA 3.6 0.2 - - - +
127A PHE* 3.2 6.6 - - - -
128A LEU* 2.6 44.0 + - - +
130A LEU* 5.1 2.4 - - - +
138A GLN* 1.3 78.1 - - - +
140A LEU* 1.3 62.4 + - - -
141A VAL 4.2 0.6 + - - -
188A GLU* 5.0 1.1 - - - -
189A ILE* 3.0 15.7 - - - -
191A ILE* 4.4 15.7 - - - -
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Residues in contact with LEU 140 (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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125A LEU* 3.8 11.9 - - + -
126A ALA 3.0 9.4 - - - +
127A PHE* 3.4 24.7 - - + -
139A GLY* 1.3 76.2 - - - +
141A VAL* 1.3 56.4 + - - +
142A LYS* 2.7 28.2 + - + -
188A GLU* 3.1 24.7 - - - +
189A ILE 3.2 5.3 + - - -
190A HIS* 3.6 33.5 - - + +
191A ILE* 4.2 13.7 + - - +
634R G 3.3 31.4 - - + +
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Residues in contact with VAL 141 (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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124A THR 3.2 3.1 - - - +
126A ALA* 2.7 27.4 + - + +
128A LEU* 4.7 7.4 - - + -
140A LEU* 1.3 69.6 - - - +
142A LYS* 1.3 56.7 + - - +
149A ILE* 4.1 3.1 - - + -
153A MET* 3.7 26.2 - - + +
154A VAL* 3.0 49.1 - - + +
157A ALA* 3.6 23.8 - - + -
191A ILE* 4.1 32.8 - - + -
194A ILE* 4.7 3.8 - - + -
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Residues in contact with LYS 142 (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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124A THR* 2.9 12.3 - - - +
125A LEU* 3.6 23.6 - - + +
140A LEU* 2.7 19.3 + - + +
141A VAL* 1.3 71.4 - - - +
143A ALA* 1.3 75.9 + - - +
144A ASN* 4.9 3.0 - - - +
149A ILE* 3.7 18.0 - - - +
191A ILE 5.5 0.6 + - - -
633R U 3.8 34.7 + - - +
634R G 3.6 36.1 - - - +
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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