Contacts of the strand formed by residues 54 - 61 (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 HIS 54 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31D THR 4.1 0.7 - - - -
32D PRO* 3.4 11.0 - - + +
33D ALA* 2.9 33.4 + - + +
36D LEU* 4.5 7.4 - - + -
52D THR* 3.3 15.6 + - - +
53D ASP* 1.3 92.8 - - + +
55D MET* 1.3 63.2 + - - +
71D ILE* 4.0 5.2 - - + -
72D LYS* 3.2 23.8 - - - +
73D PRO* 4.0 1.6 - - + -
74D LEU* 4.2 6.1 - - - +
142D LEU* 3.9 18.1 - - + +
145D LEU* 3.5 30.6 - - + +
146D ASP* 2.6 33.8 + - - +
183D VAL 4.8 0.7 - - - +
185D LEU* 4.8 6.9 + - - +
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Residues in contact with MET 55 (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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81A PRO* 4.1 6.5 - - + -
54D HIS* 1.3 76.1 - - - +
56D LEU* 1.3 59.9 + - - +
57D THR* 3.8 27.8 - - + -
70D HIS 3.7 0.7 - - - +
71D ILE* 3.4 4.9 - - - -
72D LYS* 2.9 32.4 + - + +
73D PRO 3.8 13.0 - - - +
74D LEU* 3.8 6.1 - - + -
75D GLN* 3.5 38.6 - - - +
77D LEU* 4.0 20.9 - - + -
142D LEU* 3.6 8.4 - - - +
182D PHE* 4.3 8.5 - - + -
183D VAL 3.4 12.3 - - - +
184D LEU* 3.8 25.8 - - + -
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Residues in contact with LEU 56 (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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28D LEU* 3.8 25.8 - - + -
55D MET* 1.3 74.5 - - - +
57D THR* 1.3 63.1 + - - +
58D VAL* 4.2 15.7 - - + -
69D PRO* 4.2 7.6 - - + -
70D HIS 3.3 19.3 - - - +
71D ILE* 3.8 10.3 - - + +
135D LEU* 4.0 13.7 - - + -
138D CYS* 3.8 30.3 - - + +
139D ILE* 4.8 0.4 - - + +
142D LEU* 3.8 10.1 - - + +
181D LEU* 4.7 2.0 - - + -
182D PHE* 3.0 9.1 - - - +
183D VAL* 2.9 58.1 + - + +
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Residues in contact with THR 57 (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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55D MET* 3.8 24.2 - - + -
56D LEU* 1.3 79.0 - - - +
58D VAL* 1.3 63.8 + - - +
68D LYS 4.5 1.0 - - - +
69D PRO* 3.8 0.3 - - - +
70D HIS* 2.9 41.8 + - - +
72D LYS* 3.3 36.6 + - - +
77D LEU* 4.9 3.8 - - + -
180D LEU* 4.0 17.3 - - + -
181D LEU 3.3 4.9 - - - -
182D PHE* 4.1 6.3 - - + -
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Residues in contact with VAL 58 (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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23D PHE* 3.6 34.8 - - + -
56D LEU* 4.2 17.9 - - + -
57D THR* 1.3 78.1 - - - +
59D GLU* 1.3 62.7 + - - +
66D TRP* 3.7 18.1 - - + -
67D GLU 3.5 24.9 - - - +
68D LYS 4.2 1.6 - - - -
69D PRO* 3.8 22.9 - - + -
180D LEU* 3.3 6.0 - - - +
181D LEU* 2.7 47.0 + - + +
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Residues in contact with GLU 59 (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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57D THR* 4.4 0.4 - - - -
58D VAL* 1.3 74.4 - - - +
60D TRP* 1.3 61.4 + - - +
66D TRP* 3.5 5.3 - - - -
67D GLU* 2.8 55.5 + - + +
68D LYS 5.0 1.0 + - - -
167D THR* 4.5 2.4 + - - +
178D LYS* 4.3 23.3 - - - +
179D ALA 3.6 14.9 - - - +
180D LEU* 4.0 22.0 - - - +
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Residues in contact with TRP 60 (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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20D VAL 4.9 1.0 + - - -
59D GLU* 1.3 78.3 - - - +
61D SER* 1.3 76.3 + - - +
62D SER* 3.6 28.3 - - - -
65D GLY* 3.3 35.5 - - - -
66D TRP* 3.4 39.7 - + + -
67D GLU* 5.9 0.9 - - - -
128D PRO* 3.3 41.3 - - + +
175D LYS* 5.9 7.0 - - - -
176D PRO 3.5 23.3 - - - -
177D THR 3.6 14.8 - - - -
178D LYS* 3.7 11.1 - - - +
179D ALA* 3.0 40.8 + - + +
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Residues in contact with SER 61 (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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60D TRP* 1.3 84.3 - - - +
62D SER* 1.3 59.4 + - - +
63D GLU* 3.8 5.2 + - - +
64D PHE* 3.2 31.0 + - - +
65D GLY* 2.8 33.7 + - - -
67D GLU* 5.2 2.8 + - - -
177D THR 3.2 12.1 - - - -
178D LYS* 4.6 10.3 - - - -
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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