Contacts of the strand formed by residues 147 - 153 (chain A) in PDB entry 1QFG
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 147 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92A ILE* 3.8 11.8 - - - +
103A ASN* 2.6 29.6 + - - +
132A MET 3.0 14.1 - - - -
134A GLY 3.2 12.4 + - - -
136A VAL* 4.7 1.1 - - - -
143A SER* 4.6 1.3 - - - -
144A SER* 3.4 10.3 + - - +
145A PRO 3.3 4.6 + - - -
146A GLY* 1.3 80.4 - - - +
148A LEU* 1.3 55.3 + - - -
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Residues in contact with LEU 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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35A THR* 4.4 13.9 - - + -
92A ILE* 3.9 8.5 - - - +
103A ASN* 3.7 13.2 - - - +
105A TYR* 3.4 31.9 - - + +
131A ILE* 3.6 3.6 - - - +
132A MET* 2.9 33.1 + - + +
136A VAL* 3.6 17.5 - - + -
140A TYR* 3.6 37.9 - - + -
143A SER* 4.7 2.7 - - - +
147A GLY* 1.3 77.7 - - - +
149A LEU* 1.3 77.1 + - - +
150A ASN* 3.7 12.8 - - + +
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Residues in contact with LEU 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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66A VAL* 4.3 14.8 - - + -
70A LEU* 4.0 24.0 - - + -
88A ASP* 5.7 0.9 - - + -
90A LEU* 4.4 19.7 - - + -
92A ILE* 5.2 0.9 - - + +
103A ASN 3.3 7.4 + - - +
104A ASN* 3.8 34.5 - - - +
105A TYR* 2.6 35.9 + - - +
129A ALA* 4.5 4.7 - - + -
130A GLU 3.6 11.9 - - - +
131A ILE* 4.1 6.1 - - + +
148A LEU* 1.3 77.2 - - - +
150A ASN* 1.3 60.5 + - - +
151A MET* 3.9 31.6 - - + -
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Residues in contact with ASN 150 (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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35A THR* 3.0 31.8 + - + +
105A TYR* 3.3 14.0 - - + +
107A ASN 3.4 5.8 + - - +
108A GLY* 3.1 34.0 + - - +
129A ALA* 3.5 1.2 - - - -
130A GLU* 2.7 42.8 + - - +
140A TYR* 5.5 2.6 + - + +
148A LEU* 3.7 13.1 - - + +
149A LEU* 1.3 73.7 - - - +
151A MET* 1.3 66.2 + - - +
152A VAL* 4.2 16.1 - - - +
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Residues in contact with MET 151 (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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66A VAL* 3.7 33.2 - - + -
88A ASP* 5.6 0.2 - - - +
104A ASN* 4.4 9.4 - - + +
105A TYR 2.9 28.6 + - - +
106A LEU* 3.3 10.7 - - + +
107A ASN 2.9 24.6 + - - -
111A LEU* 3.9 23.6 - - + -
120A VAL* 6.0 0.7 - - - -
121A ILE* 4.1 21.3 - - + +
126A LEU* 3.6 27.4 - - + -
128A ARG 3.7 4.5 - - - -
129A ALA* 4.3 0.9 - - + +
149A LEU* 3.9 20.4 - - + -
150A ASN* 1.3 76.5 - - - +
152A VAL* 1.3 62.6 + - - +
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Residues in contact with VAL 152 (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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107A ASN* 3.6 7.6 - - - +
126A LEU* 3.5 8.9 - - - +
127A GLU* 2.9 38.3 + - + +
128A ARG* 2.9 39.0 + - + +
130A GLU* 5.1 6.1 - - + +
150A ASN* 4.2 17.7 - - - +
151A MET* 1.3 81.4 - - - +
153A SER* 1.3 68.1 + - - +
155A ARG* 4.1 17.3 - - - +
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Residues in contact with SER 153 (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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106A LEU* 4.0 11.2 - - - +
107A ASN* 2.8 35.6 + - - -
125A MET 4.0 6.3 - - - -
126A LEU* 4.6 3.6 - - - -
127A GLU* 3.2 9.9 - - - +
151A MET 4.2 0.2 - - - -
152A VAL* 1.3 73.3 - - - +
154A LYS* 1.3 71.8 + - - +
155A ARG* 2.9 17.3 + - - -
232A LEU* 3.8 20.2 - - - +
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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