Contacts of the strand formed by residues 159 - 164 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117B TRP* 3.8 14.1 + - + -
152B ILE 4.6 0.4 - - - -
153B SER* 3.1 7.1 - - - -
154B ARG* 2.9 40.3 + - - +
155B LYS* 5.9 0.2 - - - +
157B THR* 2.6 27.8 + - - +
158B GLY* 1.3 78.1 - - - +
160B LYS* 1.3 62.7 + - - +
161B GLN* 3.5 17.4 - - - +
275B ALA* 4.3 2.4 - - - +
359B LYS* 3.1 18.2 + - - -
363B HIS* 2.8 31.7 + - - +
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Residues in contact with LYS 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B ASN* 2.9 29.6 + - - +
151B VAL* 3.7 16.4 + - + +
152B ILE 3.6 4.7 - - - +
153B SER* 3.6 13.3 + - - +
158B GLY 4.3 0.6 + - - -
159B ASP* 1.3 75.8 - - - +
161B GLN* 1.3 63.4 + - - +
271B HIS* 3.9 48.7 + - + +
272B GLU* 4.8 8.8 + - - +
274B THR* 3.7 32.3 - - + -
275B ALA* 4.1 10.3 - - + +
281B HIS* 4.6 3.6 - - - -
363B HIS* 5.1 2.4 + - - -
1388B NZQ 2.8 36.6 + - - -
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Residues in contact with GLN 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A THR* 5.5 6.1 - - - +
117B TRP* 3.5 23.9 + - + -
120B LEU* 3.3 43.8 + - + +
121B GLN* 4.3 8.5 - - - +
151B VAL* 3.4 5.5 - - - -
152B ILE 2.9 33.4 + - - +
159B ASP* 3.5 16.8 - - - +
160B LYS* 1.3 81.2 - - - +
162B ALA* 1.3 61.2 + - - +
271B HIS* 5.1 2.0 - - - -
363B HIS* 3.8 32.9 + - + +
365B MET* 5.4 9.7 - - + +
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Residues in contact with ALA 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120B LEU* 3.8 11.2 - - - +
123B GLY* 3.9 11.8 - - - -
150B ALA 3.2 10.5 - - - +
151B VAL* 4.0 14.1 - - + +
161B GLN* 1.3 75.5 - - - +
163B PHE* 1.3 62.2 + - - +
164B HIS* 4.3 17.9 - - + +
268B MET* 5.2 9.6 - - + +
271B HIS* 4.8 9.3 - - + -
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Residues in contact with PHE 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B LYS* 4.0 7.2 - - + -
103B PHE* 3.8 30.5 - + + -
106B ALA* 4.9 0.7 - - + -
119B ILE* 3.5 23.6 - - + +
120B LEU* 3.6 19.5 - - + -
123B GLY* 3.5 19.5 - - - -
124B GLY* 3.7 2.7 - - - +
127B ILE* 3.6 26.7 - - + -
149B GLY* 3.3 0.2 - - - -
150B ALA* 2.9 59.5 + - + -
152B ILE* 4.0 14.4 - - + -
162B ALA* 1.3 75.2 - - - +
164B HIS* 1.3 75.8 + - - +
168B VAL* 4.0 19.1 - - + -
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Residues in contact with HIS 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B GLY* 2.9 20.6 + - - +
124B GLY 3.5 9.7 - - - -
125B LYS* 4.9 1.0 - - - -
148B ALA* 3.2 12.4 - - + +
149B GLY* 3.3 25.2 + - - -
150B ALA 4.9 0.9 - - - -
162B ALA* 4.3 16.1 - - + +
163B PHE* 1.3 83.3 + - - +
165B SER* 1.3 65.3 + - - +
252B LEU* 6.5 0.7 - - + -
1388B NZQ 5.5 3.6 - - - -
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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