Contacts of the strand formed by residues 150 - 156 (chain D) in PDB entry 5LEZ
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 150 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146D VAL* 4.2 5.6 - - - -
147D ASP 2.8 30.1 + - - -
148D GLU 3.1 2.2 + - - -
149D LYS* 1.3 79.0 - - - +
151D PRO* 1.3 78.3 - - - +
152D GLN* 3.5 8.8 + - - +
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Residues in contact with PRO 151 (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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41D GLN* 3.4 17.0 + - + -
42D THR 3.2 28.5 - - - +
43D SER* 3.6 21.3 - - - +
45D GLY* 3.6 21.3 - - - +
46D VAL* 3.9 7.6 - - + -
145D GLY 3.5 7.4 - - - +
146D VAL* 4.0 6.0 - - + -
149D LYS 4.9 1.6 - - - +
150D GLY* 1.3 83.5 - - - +
152D GLN* 1.3 68.0 + - - +
222D PRO* 4.4 13.7 - - + -
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Residues in contact with GLN 152 (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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41D GLN* 3.2 12.1 - - - +
46D VAL* 3.5 5.7 - - - +
109D VAL* 4.0 11.9 - - + +
110D GLU* 5.0 7.5 + - - +
143D PHE 3.7 1.7 - - - +
144D GLY* 3.4 2.8 - - - -
145D GLY 2.7 40.0 + - - +
147D ASP* 2.9 31.8 + - - +
149D LYS* 3.3 20.3 - - - +
150D GLY 3.5 3.6 - - - +
151D PRO* 1.3 79.2 - - - +
153D LEU* 1.3 60.7 + - - +
154D PHE* 3.5 32.9 - - + -
164D GLN* 4.8 6.6 - - + +
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Residues in contact with LEU 153 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39D GLY* 3.4 34.8 - - - +
40D ILE* 3.8 6.7 - - - +
41D GLN* 3.0 16.3 + - + +
46D VAL* 4.9 4.5 - - + -
48D LEU* 4.1 22.4 - - + -
142D LEU* 4.1 15.0 - - + -
143D PHE 3.4 20.0 - - - +
144D GLY* 4.2 2.9 - - - -
152D GLN* 1.3 74.2 - - - +
154D PHE* 1.3 66.1 + - - +
164D GLN* 3.3 8.3 - - - +
165D CYS* 2.9 49.6 + - + +
167D ALA* 4.2 5.4 - - - -
168D ARG* 4.2 7.2 - - + +
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Residues in contact with PHE 154 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109D VAL* 3.8 15.3 - - + -
110D GLU* 3.6 46.0 - - + -
113D THR* 3.7 23.6 - - + +
142D LEU* 3.3 8.3 - - - +
143D PHE* 2.9 35.0 + - + +
152D GLN* 3.5 35.0 - - + -
153D LEU* 1.3 80.2 - - - +
155D HIS* 1.3 61.6 + - - +
162D PHE* 4.0 19.7 - + - -
163D VAL* 3.3 8.3 - - - -
164D GLN* 3.4 35.7 - - + -
165D CYS* 4.6 0.9 - - - +
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Residues in contact with HIS 155 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113D THR* 5.0 0.9 - - - -
140D ALA* 4.1 7.0 - - + +
141D LEU 3.4 10.5 - - - -
142D LEU* 3.8 11.0 - - + -
154D PHE* 1.3 75.4 - - - +
156D MET* 1.3 75.4 + - - +
157D ASP* 4.2 23.0 - - + +
161D THR 5.5 0.8 + - - -
162D PHE* 3.1 24.9 - - - +
163D VAL* 3.0 15.6 + - + +
165D CYS* 4.1 18.8 - - - -
168D ARG* 3.1 35.2 + - + -
170D ILE* 3.5 33.4 - - + +
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Residues in contact with MET 156 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88D LEU* 4.3 16.6 - - + -
113D THR* 4.3 9.4 - - + +
116D VAL* 3.8 17.7 - - + +
117D SER* 3.7 38.8 - - - -
120D ALA* 5.3 6.5 - - + -
137D PHE* 6.0 1.3 - - + -
139D VAL 4.5 6.5 - - - +
140D ALA* 3.4 6.1 - - - +
141D LEU* 2.8 61.2 + - + +
143D PHE* 4.8 2.9 - - + -
155D HIS* 1.3 80.0 - - - +
157D ASP* 1.3 83.6 + - - +
158D PRO* 5.1 2.2 - - + -
160D GLY* 4.9 0.7 - - - -
161D THR 3.5 9.6 - - - +
162D PHE* 4.3 5.6 - - + -
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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