Contacts of the strand formed by residues 159 - 164 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A TRP* 3.9 11.4 - - + -
152A ILE 4.6 0.2 - - - -
153A SER* 3.0 7.3 - - - -
154A ARG* 2.9 43.5 + - - +
157A THR* 2.6 27.6 + - - +
158A GLY* 1.3 77.7 - - - +
160A LYS* 1.3 59.3 + - - +
161A GLN* 3.7 19.3 - - - +
275A ALA* 4.4 1.1 - - - -
359A LYS* 2.9 19.7 + - - -
362A GLU* 3.9 6.4 - - - +
363A HIS* 2.6 28.7 + - - +
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Residues in contact with LYS 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A ASN* 2.9 29.3 + - - +
151A VAL* 3.7 17.8 + - + +
152A ILE 3.7 4.0 - - - +
153A SER* 3.6 15.1 + - - +
159A ASP* 1.3 73.4 - - - +
161A GLN* 1.3 64.6 + - - +
271A HIS* 3.6 42.8 + - + +
272A GLU* 4.9 2.5 + - - +
274A THR* 3.7 31.0 - - + -
275A ALA* 3.9 18.2 - - + +
281A HIS* 4.7 2.9 - - - -
363A HIS* 4.4 8.0 + - - -
1388A NZQ 2.7 36.4 + - - -
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Residues in contact with GLN 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A TRP* 3.4 26.3 + - + -
120A LEU* 3.4 36.8 + - + +
121A GLN* 4.8 6.1 - - - +
151A VAL* 3.4 5.9 - - - -
152A ILE 2.8 34.2 + - - +
159A ASP* 3.7 12.3 - - + +
160A LYS* 1.3 82.7 - - - +
162A ALA* 1.3 60.5 + - - +
271A HIS* 5.1 2.5 - - - -
363A HIS* 3.7 40.4 + - + +
365A MET* 5.8 7.6 - - + +
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Residues in contact with ALA 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A LEU* 3.6 11.6 - - - +
123A GLY* 3.9 12.1 - - - -
150A ALA 3.2 11.0 - - - +
151A VAL* 4.2 13.5 - - + +
161A GLN* 1.3 76.8 - - - +
163A PHE* 1.3 62.4 + - - +
164A HIS* 4.5 17.3 - - + -
268A MET* 5.5 7.4 - - + -
271A HIS* 4.8 9.3 - - + -
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Residues in contact with PHE 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A LYS* 4.0 8.1 - - + -
103A PHE* 3.9 30.3 - + + -
106A ALA* 4.7 1.3 - - + -
119A ILE* 3.5 24.7 - - + +
120A LEU* 3.6 19.1 - - + -
123A GLY* 3.5 20.0 - - - -
124A GLY* 3.7 2.7 - - - +
127A ILE* 3.6 24.5 - - + -
149A GLY* 3.4 2.9 - - - -
150A ALA* 2.9 58.1 + - + -
152A ILE* 4.0 12.8 - - + -
162A ALA* 1.3 74.4 - - - +
164A HIS* 1.3 74.3 + - - +
168A VAL* 4.0 21.5 - - + -
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Residues in contact with HIS 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A GLY 3.1 18.4 + - - +
124A GLY 3.6 9.9 - - - -
125A LYS* 5.1 0.5 - - - -
148A ALA* 3.3 9.4 - - + +
149A GLY* 3.6 24.6 - - - -
162A ALA* 4.5 16.6 - - + -
163A PHE* 1.3 81.2 - - - +
165A SER* 1.3 64.7 + - - +
1388A NZQ 5.6 1.4 + - - -
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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