Contacts of the strand formed by residues 130 - 138 (chain A) in PDB entry 1A3K
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 MET 130 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122A LEU* 4.2 23.8 - - + -
123A PRO* 5.6 1.6 - - + +
125A GLY 4.2 5.8 - - - +
126A VAL* 3.9 31.9 - - - -
127A VAL* 3.0 23.2 + - + +
128A PRO 3.2 0.8 + - - -
129A ARG* 1.3 78.5 - - - +
131A LEU* 1.3 60.1 + - - +
132A ILE* 4.2 10.5 - - + -
202A VAL 3.8 0.5 - - - +
203A LEU* 3.7 0.9 - - - -
204A VAL* 2.9 33.1 + - + +
247A TYR* 3.7 41.5 - - + -
248A THR 3.5 9.2 - - - +
249A MET* 3.9 15.9 - - - +
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Residues in contact with LEU 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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129A ARG 3.6 0.4 + - - -
130A MET* 1.3 73.9 - - - +
132A ILE* 1.3 61.2 + - - +
133A THR* 4.1 10.5 + - - +
201A GLN* 4.0 38.8 - - + +
202A VAL 3.5 16.8 - - - +
203A LEU* 4.1 17.5 - - + -
247A TYR* 3.0 4.0 - - - -
248A THR* 2.8 52.2 + - + +
250A ILE* 3.8 31.0 - - + -
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Residues in contact with ILE 132 (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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120A LEU* 4.4 6.1 - - + -
122A LEU* 4.7 13.2 - - + -
126A VAL* 5.3 0.4 - - + -
130A MET* 4.2 20.6 - - + -
131A LEU* 1.3 76.8 - - - +
133A THR* 1.3 64.4 + - - +
134A ILE* 4.1 16.3 - - + +
149A PHE* 4.4 20.2 - - + -
200A ILE 3.7 0.7 - - - +
201A GLN* 3.2 6.2 - - - +
202A VAL* 2.9 47.4 + - + +
204A VAL* 4.3 15.7 - - + -
234A LEU* 3.9 24.0 - - + -
246A SER 3.2 11.4 - - - +
247A TYR* 3.8 14.1 - - + -
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Residues in contact with THR 133 (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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131A LEU* 4.1 12.2 + - - +
132A ILE* 1.3 76.2 + - - +
134A ILE* 1.3 67.9 + - - +
135A LEU* 4.2 8.7 - - + -
199A LYS* 4.0 30.7 - - + -
200A ILE 3.4 3.4 - - - +
201A GLN* 3.9 17.6 + - + +
244A SER* 3.9 1.9 + - - +
245A ALA* 3.4 4.0 - - - -
246A SER* 2.7 44.4 + - - -
247A TYR* 5.9 0.2 - - - -
248A THR* 5.8 1.4 - - - +
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Residues in contact with ILE 134 (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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132A ILE* 4.1 12.1 - - + -
133A THR* 1.3 79.0 - - - +
135A LEU* 1.3 64.9 + - - +
147A LEU* 3.7 38.8 - - + -
198A PHE* 4.1 17.2 - - + +
199A LYS* 3.3 5.0 - - - +
200A ILE* 2.8 52.0 + - + +
202A VAL* 5.1 2.5 - - + -
234A LEU* 4.1 17.5 - - + -
236A ILE* 4.1 16.8 - - + -
240A ILE* 5.5 0.7 - - + -
242A LEU* 3.7 26.2 - - + -
244A SER 3.3 3.8 - - - +
245A ALA* 4.5 3.6 - - - -
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Residues in contact with LEU 135 (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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133A THR* 4.2 9.6 - - + -
134A ILE* 1.3 75.8 - - - +
136A GLY* 1.3 58.4 + - - +
198A PHE* 3.6 17.3 - - - +
199A LYS* 3.6 28.0 - - + -
242A LEU* 3.7 4.2 - - - +
243A THR* 2.8 31.4 + - + -
244A SER* 2.9 36.4 + - - +
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Residues in contact with GLY 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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135A LEU* 1.3 76.6 - - - +
137A THR* 1.3 62.6 + - - -
197A PRO* 3.2 6.1 - - - +
198A PHE* 2.8 47.8 + - - +
241A ASP 3.1 14.1 - - - -
242A LEU* 4.5 0.9 - - - -
243A THR* 3.8 7.9 - - - -
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Residues in contact with THR 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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136A GLY* 1.3 77.2 + - - -
138A VAL* 1.3 70.3 + - - +
139A LYS 3.5 0.2 + - - -
195A GLY* 3.5 24.7 - - - +
196A LYS 3.7 11.2 - - - -
197A PRO* 3.8 12.8 - - + +
198A PHE* 3.5 2.9 - - - -
240A ILE* 3.3 3.8 - - - +
241A ASP* 2.9 47.1 + - - +
243A THR* 4.8 4.9 + - - -
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Residues in contact with VAL 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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137A THR* 1.3 76.4 - - - +
139A LYS* 1.3 64.8 + - - +
140A PRO* 4.3 0.2 - - - +
142A ALA* 3.3 26.0 - - + -
145A ILE* 4.2 10.3 - - + -
163A PHE* 3.5 26.2 - - + -
192A PHE* 4.3 8.7 - - + -
193A GLU 3.4 21.8 - - - +
194A SER* 3.7 7.9 - - - -
195A GLY* 2.8 25.1 + - - -
196A LYS 3.0 11.7 + - - +
198A PHE* 3.8 18.6 - - + -
239A ASP 3.9 5.6 - - - +
240A ILE* 4.3 1.8 - - - -
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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