Contacts of the strand formed by residues 140 - 149 (chain A) in PDB entry 1G1F
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 LEU 140 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96A TRP* 3.6 39.5 - - + +
97A GLU* 3.7 9.4 - - + +
100A TRP* 4.3 21.1 - - + -
134A ILE* 3.5 4.9 - - - +
135A PHE* 2.9 40.8 + - + -
138A THR* 3.6 25.8 - - - +
139A ASN* 1.3 80.1 - - - +
141A LYS* 1.3 58.8 + - - +
160A LEU* 4.2 15.0 - - + -
161A GLU 3.4 16.4 - - - +
162A ASN* 4.0 15.3 - - + -
163A LEU* 4.3 3.1 - - - +
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Residues in contact with LYS 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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132A GLU* 4.0 31.7 + - + +
133A MET 3.5 8.3 - - - +
134A ILE* 4.3 16.4 - - + +
140A LEU* 1.3 76.0 - - - +
142A LEU* 1.3 62.0 + - - +
143A THR* 4.3 11.9 - - - +
159A GLU* 3.6 1.9 - - - +
160A LEU* 3.5 5.4 - - - +
161A GLU* 2.8 60.9 + - + +
163A LEU* 3.9 25.3 - - + +
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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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96A TRP* 3.5 42.4 - - + +
124A TYR 3.7 11.4 - - - +
125A TRP* 4.1 2.5 - - + -
126A PRO* 3.7 23.6 - - + +
132A GLU* 3.4 3.5 - - - +
133A MET* 2.8 37.5 + - + +
135A PHE* 4.0 16.8 - - + -
141A LYS* 1.3 75.7 - - - +
143A THR* 1.3 62.3 + - - +
158A LEU* 4.0 27.1 - - + -
159A GLU 3.4 14.1 - - - +
160A LEU* 4.0 20.6 - - + -
171A ILE* 5.4 0.2 - - + -
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Residues in contact with THR 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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126A PRO* 4.0 4.3 - - - -
129A GLU* 3.8 16.6 - - + +
132A GLU* 3.6 22.4 - - + +
141A LYS* 4.3 12.6 - - - +
142A LEU* 1.3 78.0 - - - +
144A LEU* 1.3 74.8 + - - +
145A ILE* 3.5 9.3 + - + +
158A LEU* 3.4 5.1 - - - +
159A GLU* 2.9 49.4 + - - -
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Residues in contact with LEU 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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126A PRO* 3.5 29.7 - - + +
127A GLN 3.4 28.5 - - - +
129A GLU* 3.2 52.8 - - - +
132A GLU* 5.6 0.4 - - - +
143A THR* 1.3 79.4 - - - +
145A ILE* 1.3 59.3 + - - +
146A SER 3.6 27.4 - - - +
147A GLU* 4.3 16.6 - - + +
156A ARG* 4.1 17.3 - - + -
157A GLN 3.9 1.3 - - - +
158A LEU* 3.9 20.6 - - + -
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Residues in contact with ILE 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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129A GLU* 4.1 9.6 - - - +
143A THR* 4.2 12.3 - - + +
144A LEU* 1.3 78.3 - - - +
146A SER* 1.3 62.1 + - - +
157A GLN* 2.8 47.5 + - + +
158A LEU 4.2 2.2 - - - -
159A GLU* 3.8 44.9 - - + +
170A GLU* 6.5 0.2 - - + -
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Residues in contact with SER 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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129A GLU* 4.7 7.6 - - - -
144A LEU* 3.6 7.8 - - - +
145A ILE* 1.3 84.8 - - - +
147A GLU* 1.3 66.3 + - - +
156A ARG* 3.5 1.2 - - - -
157A GLN* 2.9 51.2 + - - +
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Residues in contact with GLU 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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127A GLN* 4.7 8.1 - - - +
129A GLU* 5.8 2.5 - - - +
144A LEU* 4.3 18.9 - - + +
146A SER* 1.3 79.9 - - - +
148A ASP* 1.3 61.6 + - - +
149A ILE* 3.6 30.1 + - + +
154A THR* 4.4 3.8 - - + -
155A VAL 3.4 4.7 - - - -
156A ARG* 3.3 39.3 + - + -
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Residues in contact with ASP 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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147A GLU* 1.3 71.8 - - - +
149A ILE* 1.3 63.7 + - - +
150A LYS* 3.5 34.5 + - - +
153A TYR* 4.3 1.2 + - - +
154A THR* 3.5 2.9 - - - -
155A VAL* 2.8 44.8 + - + +
197A LYS* 5.1 10.7 + - - -
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Residues in contact with ILE 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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147A GLU* 3.6 30.9 + - + +
148A ASP* 1.3 75.9 + - - +
150A LYS* 1.3 77.2 + - - +
154A THR* 3.7 27.1 - - + +
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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