Contacts of the strand formed by residues 140 - 149 (chain A) in PDB entry 1M8V
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109A ILE* 5.4 3.6 - - + -
119A VAL* 4.3 20.4 - - + -
131A LEU* 4.0 14.6 - - + -
133A GLY 3.2 6.7 - - - +
134A TYR* 4.0 12.1 - - + +
138A LEU* 3.5 11.7 - - + +
139A ASN* 1.3 81.2 - - - +
141A VAL* 1.3 63.0 + - - +
142A LEU* 4.5 4.7 - - + -
160A ILE 3.8 0.9 - - - +
161A VAL* 3.6 2.1 - - - +
162A ILE* 2.9 56.4 + - + +
167A VAL* 5.2 2.2 - - + -
170A ILE* 3.9 21.8 - - + -
705G PRO* 4.8 0.7 - - - -
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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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131A LEU* 3.5 5.5 - - - +
132A ILE* 2.9 53.8 + - + -
133A GLY 2.7 12.3 + - - +
140A VAL* 1.3 76.5 - - - +
142A LEU* 1.3 63.9 + - - +
159A LYS* 4.0 9.0 - - + -
160A ILE 3.4 10.8 - - - +
161A VAL* 4.2 7.9 - - + -
703G GLU 3.0 24.5 - - - +
704G ARG 3.8 0.7 - - - -
705G PRO* 3.5 31.0 - - + -
708G VAL* 3.9 15.5 - - + -
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Residues in contact with LEU 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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117A VAL* 3.6 21.3 - - + -
119A VAL* 3.5 28.0 - - + -
127A PHE* 4.3 12.3 - - + -
128A ARG 4.9 0.4 - - - -
129A GLY* 4.5 8.3 - - - +
130A ARG 3.1 7.2 - - - +
131A LEU* 3.6 26.5 - - + +
132A ILE* 4.4 2.9 - - - -
140A VAL* 4.5 4.5 - - + -
141A VAL* 1.3 83.5 - - - +
143A ALA* 1.3 59.7 + - - +
145A ALA* 4.0 18.2 - - + +
159A LYS* 3.3 5.9 - - - +
160A ILE* 3.0 35.2 + - + +
162A ILE* 3.7 21.8 - - + -
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Residues in contact with ALA 143 (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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130A ARG* 2.7 58.6 + - - +
132A ILE* 3.7 26.5 - - + -
142A LEU* 1.3 72.5 - - - +
144A ASP* 1.3 74.5 + - - +
145A ALA 3.3 1.3 - - - -
158A GLY 3.4 7.9 - - - +
159A LYS* 4.5 3.8 - - + +
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Residues in contact with ASP 144 (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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128A ARG 3.9 0.7 - - - +
129A GLY* 3.7 9.9 - - - -
130A ARG* 3.1 28.7 + - + -
143A ALA* 1.3 73.8 - - - +
145A ALA* 1.3 61.3 + - - +
146A GLU* 4.7 5.4 - - - +
157A TYR 3.6 6.5 - - - -
158A GLY* 2.7 23.4 + - - +
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Residues in contact with ALA 145 (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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127A PHE* 5.0 4.0 - - + -
128A ARG 3.1 11.2 - - - +
129A GLY* 4.2 0.4 - - - -
142A LEU* 4.0 19.7 - - + +
144A ASP* 1.3 78.4 - - - +
146A GLU* 1.3 61.1 + - - +
156A ARG* 3.2 6.6 - - - +
157A TYR* 2.8 41.7 + - + +
160A ILE* 3.7 30.1 - - + -
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Residues in contact with GLU 146 (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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127A PHE* 3.3 7.5 - - - -
128A ARG* 2.8 67.0 + - + +
144A ASP 4.7 4.9 - - - +
145A ALA* 1.3 76.0 - - - +
147A MET* 1.3 61.1 + - - +
148A ILE* 3.4 6.4 + - + +
153A VAL* 4.0 32.0 - - + +
155A LYS 3.2 9.2 - - - +
156A ARG* 3.7 21.9 + - + +
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Residues in contact with MET 147 (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 PHE* 3.6 38.8 - - + -
126A GLU 4.0 0.4 - - - -
127A PHE* 3.5 36.2 - - + -
146A GLU* 1.3 70.8 - - - +
148A ILE* 1.3 60.2 + - - +
149A GLN* 5.3 3.8 - - + -
153A VAL* 3.6 1.3 - - - -
154A VAL* 2.8 50.5 + - + +
155A LYS* 2.6 30.8 + - + +
157A TYR* 3.4 24.8 - - + +
720G ILE* 4.7 11.4 - - + -
726G GLU* 6.0 1.8 - - - +
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Residues in contact with ILE 148 (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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118A LEU* 5.4 1.1 - - + -
125A PHE* 3.3 7.1 - - - +
126A GLU* 2.8 51.7 + - + +
127A PHE 5.3 0.4 - - - -
128A ARG* 3.3 47.8 - - + +
146A GLU* 3.4 14.6 + - + +
147A MET* 1.3 76.7 - - - +
149A GLN* 1.3 63.3 + - - +
150A ASP 5.0 0.2 - - - +
151A GLY* 3.8 31.9 - - - +
152A GLU 3.5 3.6 - - - +
153A VAL* 4.3 17.5 - - + -
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Residues in contact with GLN 149 (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 PHE* 4.5 19.3 - - + +
126A GLU* 6.0 0.2 - - - -
147A MET* 4.0 4.0 + - + -
148A ILE* 1.3 75.4 - - - +
150A ASP* 1.3 77.9 + - - +
151A GLY 2.9 3.6 - - - -
152A GLU* 2.7 47.4 + - - +
154A VAL* 3.8 32.6 - - + +
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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