Contacts of the strand formed by residues 144 - 150 (chain D) in PDB entry 5GJQ
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 144 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139D TRP* 3.2 22.7 - - - -
140D ASP 3.0 36.4 + - - -
141D LYS 4.8 0.2 - - - -
142D HIS 3.7 1.0 - - - -
143D TYR* 1.3 74.4 - - - +
145D PHE* 1.3 66.4 + - - -
146D GLN* 3.3 8.0 + - - -
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Residues in contact with PHE 145 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38D LEU* 3.6 28.8 - - + +
39D ALA 4.5 2.5 - - - +
40D ASN* 4.1 15.5 - - - -
41D ASP* 3.9 7.6 - - - -
42D GLY* 3.4 41.1 - - - +
43D VAL* 3.8 13.9 - - + -
138D GLY 3.5 3.1 - - - -
139D TRP* 4.0 19.1 - + + -
143D TYR 3.4 6.9 + - - +
144D GLY* 1.3 73.3 - - - -
146D GLN* 1.3 64.4 + - - +
216D LEU* 3.5 26.7 - - + -
217D THR* 4.0 2.5 - - - -
218D ARG* 3.9 28.3 - - + -
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Residues in contact with GLN 146 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38D LEU* 4.3 6.7 - - - -
43D VAL* 4.8 2.8 - - - +
107D CYS* 3.6 9.6 - - + -
108D GLU* 4.5 3.8 + - - +
136D TYR 3.7 0.4 - - - +
137D ILE* 3.4 6.2 - - - +
138D GLY 2.9 31.3 + - - +
140D ASP* 2.5 39.3 + - - +
143D TYR* 3.6 30.1 - - + +
144D GLY 3.3 10.2 + - - +
145D PHE* 1.3 81.7 - - - +
147D LEU* 1.3 61.3 + - - +
148D TYR* 2.5 45.6 + - + +
57E ARG* 4.1 3.0 + - - +
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Residues in contact with LEU 147 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36D GLY* 3.4 32.1 - - - +
37D ILE 4.4 1.3 - - - +
38D LEU* 4.6 8.6 - - + +
43D VAL* 4.7 8.5 - - + -
45D LEU* 4.7 3.6 - - + -
135D LEU* 4.5 10.5 - - + -
136D TYR 3.2 17.9 - - - +
137D ILE* 3.6 17.7 - - + -
146D GLN* 1.3 76.8 - - - +
148D TYR* 1.3 73.5 + - - +
158D GLY* 3.4 4.3 - - - -
159D TRP* 3.0 40.2 + - + +
160D LYS 4.3 2.2 - - - +
161D ALA* 3.9 20.6 - - - +
162D THR* 4.0 13.7 - - + -
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Residues in contact with TYR 148 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107D CYS* 4.1 7.0 - - + -
108D GLU* 3.6 37.7 - - + +
111D VAL* 4.1 19.1 - - + -
135D LEU* 3.4 9.4 - - - +
136D TYR* 2.9 49.2 + - + +
146D GLN* 2.5 48.3 + - + -
147D LEU* 1.3 78.9 - - - +
149D GLN* 1.3 63.5 + - - +
156D TYR* 4.1 15.0 - + - -
157D GLY 3.3 7.9 - - - +
158D GLY* 3.6 24.5 - - - -
159D TRP* 4.7 1.1 - - - +
57E ARG* 3.4 15.9 + - - -
58E THR* 4.0 12.6 - - + -
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Residues in contact with GLN 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134D LEU 3.1 13.2 - - - +
135D LEU* 3.6 12.8 - - + -
136D TYR* 4.5 1.6 - - - -
148D TYR* 1.3 78.2 - - - +
150D SER* 1.3 67.6 + - - +
151D ASP* 4.0 19.0 + - - +
155D ASN 4.1 0.2 - - - +
156D TYR* 3.1 4.2 - - - -
157D GLY 2.9 30.3 + - - -
159D TRP* 3.1 34.2 + - + +
162D THR* 3.4 18.0 + - - +
163D CYS 4.5 1.4 + - - -
164D ILE* 3.2 36.2 - - + +
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Residues in contact with SER 150 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115D CYS* 3.5 25.1 - - - -
118D LYS* 2.7 27.3 + - - -
133D SER* 3.0 9.0 + - - -
134D LEU* 3.0 35.4 + - - +
136D TYR* 3.0 23.2 + - - -
149D GLN* 1.3 78.6 - - - +
151D ASP* 1.3 64.2 + - - +
155D ASN 3.5 3.6 - - - -
156D TYR* 4.0 2.5 - - - -
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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