Contacts of the strand formed by residues 96 - 100 (chain D) in PDB entry 2ABJ
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 LEU 96 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94D GLU* 4.5 0.7 - - + -
95D GLY* 1.3 77.9 - - - +
97D LYS* 1.3 64.1 + - - +
108D LEU* 5.0 5.4 - - + -
109D PHE 5.1 4.5 - - - +
111D PRO* 4.0 29.4 - - + +
114D ASN* 3.7 32.1 - - + +
115D MET* 4.9 8.7 - - + -
136D LEU* 5.4 2.0 - - + -
139D ILE* 5.2 5.8 - - + -
159D TYR* 3.7 2.9 - - - -
160D ILE* 2.7 55.3 + - + +
162D PRO* 3.8 33.2 - - + -
331D THR* 4.0 7.4 - - - -
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Residues in contact with LYS 97 (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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47D PHE* 5.2 0.2 - - - -
96D LEU* 1.3 81.9 - - - +
98D ALA* 1.3 59.5 + - - +
99D PHE* 3.4 38.6 - - + -
108D LEU* 3.6 18.4 - - - +
109D PHE* 3.9 5.2 + - - +
157D SER* 3.2 25.5 + - - +
158D LEU 3.3 8.7 - - - +
159D TYR* 4.1 10.1 - - + -
160D ILE* 4.0 5.8 - - - -
188D VAL* 3.8 19.2 - - - +
189D GLY 5.1 3.2 + - - -
331D THR* 3.0 41.0 + - + +
332D ALA* 3.4 20.4 + - - +
334D VAL* 6.0 2.2 - - - +
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Residues in contact with ALA 98 (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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97D LYS* 1.3 71.9 - - - +
99D PHE* 1.3 63.4 + - - +
106D ILE* 4.1 16.2 - - + -
107D ARG 3.3 7.2 - - - +
108D LEU* 3.8 17.0 - - + -
143D VAL* 4.1 15.7 - - + -
150D VAL* 4.0 4.7 - - + +
157D SER* 3.3 6.4 - - - -
158D LEU* 2.9 43.9 + - + +
160D ILE* 4.0 4.0 - - + +
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Residues in contact with PHE 99 (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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97D LYS* 3.4 41.1 - - + -
98D ALA* 1.3 74.7 - - - +
100D ARG* 1.3 62.4 + - - +
101D GLY* 3.3 2.9 + - - -
105D LYS 3.5 0.3 - - - +
106D ILE* 3.4 1.4 - - - -
107D ARG* 2.9 42.8 + - + +
109D PHE* 3.8 15.3 - - + -
150D VAL* 3.9 3.8 - - - -
157D SER* 3.6 26.2 - - - +
371D GLN* 3.4 65.7 - - + +
372D TYR* 3.7 31.0 - + + -
380D THR* 6.1 0.2 - - + -
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Residues in contact with ARG 100 (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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99D PHE* 1.3 69.3 - - - +
101D GLY* 1.3 70.8 + - - +
104D ASN* 3.3 33.3 + - - +
105D LYS 4.0 2.9 - - - -
106D ILE* 3.7 26.7 - - + +
147D GLN* 3.3 20.9 + - - -
148D GLU* 3.7 13.1 + - - +
150D VAL* 2.4 44.3 + - + +
151D PRO 3.4 22.6 + - - +
152D TYR* 3.3 56.5 + - + +
153D SER 4.6 4.9 - - - +
154D THR* 4.7 3.8 - - - +
156D ALA 5.2 1.8 + - - -
372D TYR* 3.3 20.3 - - - -
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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