Contacts of the strand formed by residues 150 - 158 (chain D) in PDB entry 6B0Z
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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156B TYR* 3.6 12.3 - - - -
157B THR 3.2 13.5 - - - -
159B SER* 3.2 11.5 + - - -
148D GLY 3.4 1.8 + - - -
149D PRO* 1.3 74.1 - - - +
151D LYS* 1.3 59.0 + - - -
171D ASN* 3.6 5.5 - - - +
172D PHE* 2.8 39.8 + - - +
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Residues in contact with LYS 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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155B THR 3.5 1.0 - - - +
156B TYR* 3.2 4.9 - - - -
157B THR* 2.8 48.8 + - + +
150D GLY* 1.3 73.2 - - - -
152D VAL* 1.3 63.6 + - - +
153D GLU* 3.5 34.2 + - + +
168D LEU* 3.6 24.7 - - + +
170D HIS 3.9 2.5 - - - -
171D ASN* 2.8 33.2 - - - +
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Residues in contact with VAL 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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154B ILE* 3.9 23.6 - - + -
155B THR 3.2 10.3 - - - +
156B TYR* 4.3 11.0 - - + -
144D PHE* 4.4 2.2 - - + -
146D VAL* 4.0 15.9 - - + -
151D LYS* 1.3 75.3 - - - +
153D GLU* 1.3 57.9 + - - +
168D LEU* 3.6 4.9 - - - +
169D VAL* 2.8 49.0 + - + -
170D HIS 2.9 18.2 + - - +
172D PHE* 3.5 27.8 - - + -
179D ALA* 4.0 10.1 - - + -
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Residues in contact with GLU 153 (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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154B ILE* 3.2 7.0 - - - +
155B THR* 2.8 48.3 + - - +
157B THR* 4.8 7.3 + - - -
164B LYS* 5.1 4.2 + - - -
151D LYS* 3.5 31.0 - - + +
152D VAL* 1.3 78.4 - - - +
154D ILE* 1.3 60.3 + - - +
155D THR* 4.3 3.1 + - - +
166D THR* 3.6 26.1 - - + +
167D TYR 3.2 13.0 - - - +
168D LEU* 4.2 8.6 - - - +
169D VAL* 4.1 1.6 - - - +
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Residues in contact with ILE 154 (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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142B THR* 4.7 4.3 - - + -
144B PHE* 3.8 29.4 - - + -
152B VAL* 4.0 14.6 - - + -
153B GLU 3.2 15.5 - - - +
154B ILE* 4.6 5.2 - - + -
169B VAL* 4.6 9.2 - - + -
179B ALA* 4.8 0.2 - - + -
180B MET* 3.6 32.8 - - - +
181B GLY* 4.0 4.0 - - - +
153D GLU* 1.3 74.3 - - - +
155D THR* 1.3 59.6 + - - +
167D TYR* 2.7 64.2 + - + +
169D VAL* 3.7 18.6 - - + +
181D GLY* 4.8 1.8 - - - -
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Residues in contact with THR 155 (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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144B PHE* 5.3 1.1 - - - -
151B LYS 3.5 1.9 - - - +
152B VAL* 3.3 5.8 - - - +
153B GLU* 2.8 47.4 + - - +
155B THR* 5.5 7.3 + - - +
153D GLU* 4.9 3.1 - - - +
154D ILE* 1.3 78.2 + - - +
156D TYR* 1.3 62.0 + - - +
157D THR* 3.7 9.9 - - - +
164D LYS* 3.5 34.9 + - + +
165D VAL 3.2 9.4 - - - +
166D THR* 3.0 23.3 + - - +
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Residues in contact with TYR 156 (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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144B PHE* 4.2 23.5 - + + -
145B VAL 5.4 1.3 - - - -
146B VAL* 3.5 19.5 - - + -
147B PRO* 3.5 28.9 - - + +
148B GLY* 2.9 29.8 + - - -
149B PRO 3.3 9.4 + - - -
150B GLY* 4.1 17.7 - - - -
151B LYS 3.4 4.0 - - - -
152B VAL* 3.8 18.4 - - + +
155D THR* 1.3 72.3 - - - +
157D THR* 1.3 64.0 + - - +
158D PRO* 3.7 27.8 - - + +
163D GLN 4.4 5.8 - - - -
164D LYS* 3.4 5.9 - - - +
165D VAL* 2.7 48.5 + - + +
167D TYR* 5.1 0.2 - - + -
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Residues in contact with THR 157 (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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150B GLY* 3.2 0.6 - - - -
151B LYS* 2.8 42.8 + - - +
153B GLU* 4.8 7.3 + - - -
155D THR* 3.7 5.7 - - - +
156D TYR* 1.3 76.1 - - - +
158D PRO* 1.3 74.7 - - + +
159D SER* 4.6 0.2 - - - -
161D GLY* 5.6 4.5 - - - -
164D LYS* 3.6 32.3 - - + -
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Residues in contact with PRO 158 (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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147B PRO* 6.2 0.2 - - + -
149B PRO 3.4 8.3 - - - +
150B GLY* 3.9 0.2 - - - -
156D TYR* 3.7 28.0 - - + +
157D THR* 1.3 95.3 - - + +
159D SER* 1.3 65.9 + - - +
160D ASP* 3.3 18.8 - - - +
161D GLY* 3.1 14.6 + - - -
162D THR* 3.9 5.2 - - - +
163D GLN* 3.1 46.9 - - + +
164D LYS* 4.1 1.1 - - - -
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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