Contacts of the strand formed by residues 159 - 164 (chain D) in PDB entry 1OJ7
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 ASP 159 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117D TRP* 3.8 12.4 + - + -
152D ILE 4.7 0.2 - - - -
153D SER* 3.2 5.7 - - - -
154D ARG* 3.0 42.9 + - - +
157D THR* 2.5 28.0 + - - +
158D GLY* 1.3 76.1 - - - +
160D LYS* 1.3 60.3 + - - +
161D GLN* 3.4 18.4 - - - +
275D ALA* 4.3 2.3 - - - +
359D LYS* 2.7 20.7 + - - -
362D GLU* 4.0 6.6 - - - +
363D HIS* 2.6 29.6 + - - -
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Residues in contact with LYS 160 (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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68D ASN* 2.8 35.8 + - - +
69D PRO* 5.3 0.2 - - - +
151D VAL* 3.8 33.7 + - + +
152D ILE 3.6 3.8 - - - +
153D SER* 3.6 14.5 + - - +
159D ASP* 1.3 73.6 - - - +
161D GLN* 1.3 64.9 + - - +
271D HIS* 3.7 42.1 + - + +
272D GLU* 4.9 3.0 + - - +
274D THR* 3.6 32.5 - - + -
275D ALA* 3.9 17.6 - - + +
281D HIS* 4.9 9.9 - - - +
363D HIS* 4.4 8.7 + - - -
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Residues in contact with GLN 161 (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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117D TRP* 3.4 26.0 + - + +
120D LEU* 3.5 40.9 + - + +
121D GLN* 4.7 5.5 - - - +
151D VAL* 3.4 5.7 - - - -
152D ILE 2.9 34.8 + - - +
159D ASP* 3.4 14.4 - - - +
160D LYS* 1.3 79.3 - - - +
162D ALA* 1.3 60.5 + - - +
271D HIS* 5.1 2.0 - - - -
363D HIS* 3.5 36.5 + - + +
365D MET* 5.8 6.5 - - + +
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Residues in contact with ALA 162 (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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120D LEU* 3.8 10.6 - - - +
123D GLY* 3.9 12.8 - - - -
150D ALA 3.2 11.9 - - - +
151D VAL* 4.1 13.2 - - + +
161D GLN* 1.3 75.3 - - - +
163D PHE* 1.3 61.0 + - - +
164D HIS* 4.2 20.8 + - + +
268D MET* 5.6 6.1 - - + -
271D HIS* 4.8 9.5 + - + -
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Residues in contact with PHE 163 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102D LYS* 3.9 6.7 - - + -
103D PHE* 3.8 31.4 - + + -
106D ALA* 4.6 0.7 - - + -
119D ILE* 3.5 22.2 - - + +
120D LEU* 3.5 19.5 - - + -
123D GLY* 3.5 21.1 - - - -
124D GLY* 3.6 2.9 - - - +
127D ILE* 3.7 24.9 - - + -
149D GLY* 3.5 0.5 - - - -
150D ALA* 2.9 57.8 + - + +
152D ILE* 4.0 13.7 - - + -
162D ALA* 1.3 73.3 - - - +
164D HIS* 1.3 77.1 + - - +
165D SER* 4.8 0.2 - - - -
168D VAL* 4.0 21.3 - - + -
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Residues in contact with HIS 164 (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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123D GLY* 3.0 20.1 + - - +
124D GLY* 3.6 8.7 - - - +
125D LYS* 5.1 1.2 - - - +
148D ALA* 3.3 9.6 - - + +
149D GLY* 3.8 17.5 - - - -
162D ALA* 4.2 19.7 + - + +
163D PHE* 1.3 87.2 + - - +
165D SER* 1.3 63.6 + - - +
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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