Contacts of the strand formed by residues 54 - 61 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A THR 3.9 5.2 - - - -
32A PRO* 3.6 7.0 - - + +
33A ALA* 2.9 32.9 + - + +
36A LEU* 4.5 8.5 - - + -
52A THR* 3.4 14.9 + - - -
53A ASP* 1.3 92.2 - - + +
55A MET* 1.3 61.0 + - - +
71A ILE* 4.1 5.8 - - + -
72A LYS* 3.2 24.5 - - - +
73A PRO* 3.9 4.0 - - + -
74A LEU* 4.2 6.3 - - - +
142A LEU* 3.7 19.9 - - + +
145A LEU* 3.7 28.1 - - + +
146A ASP* 2.7 30.8 + - - +
183A VAL 4.7 1.0 - - - +
184A LEU* 5.4 0.3 - - - -
185A LEU* 4.7 5.7 + - - +
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Residues in contact with MET 55 (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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54A HIS* 1.3 75.8 - - - +
56A LEU* 1.3 59.3 + - - +
57A THR* 3.9 27.4 - - + -
70A HIS 3.6 0.9 - - - +
71A ILE* 3.3 3.8 - - - +
72A LYS* 2.7 40.8 + - + +
73A PRO 4.0 6.5 - - - +
74A LEU* 3.9 7.0 - - + -
75A GLN* 3.6 37.5 - - - +
77A LEU* 3.9 12.3 - - + -
142A LEU* 3.9 7.2 - - - -
182A PHE* 4.2 8.1 - - + -
183A VAL 3.5 11.7 - - - +
184A LEU* 3.8 25.4 - - + -
81D PRO* 3.9 15.7 - - + -
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Residues in contact with LEU 56 (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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23A PHE* 5.5 0.2 - - + -
28A LEU* 3.8 26.9 - - + -
55A MET* 1.3 74.5 - - - +
57A THR* 1.3 63.3 + - - +
58A VAL* 4.3 14.8 - - + -
69A PRO* 4.3 7.0 - - + -
70A HIS 3.2 15.7 - - - +
71A ILE* 3.8 10.8 - - + +
135A LEU* 4.1 12.6 - - + -
138A CYS* 3.8 31.4 - - + +
139A ILE 4.8 0.2 - - - +
142A LEU* 3.9 10.1 - - + +
181A LEU* 4.8 2.5 - - + -
182A PHE* 3.1 8.5 - - - +
183A VAL* 2.9 59.1 + - + +
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Residues in contact with THR 57 (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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55A MET* 3.9 24.2 - - + -
56A LEU* 1.3 79.8 - - - +
58A VAL* 1.3 65.5 + - - +
59A GLU* 6.1 1.1 - - - -
68A LYS 4.5 0.7 - - - +
69A PRO* 3.7 0.2 - - - +
70A HIS* 2.8 46.1 + - - +
72A LYS* 3.3 36.3 + - - +
77A LEU* 4.9 6.5 - - + -
180A LEU* 4.1 12.8 - - + -
181A LEU 3.5 4.7 - - - -
182A PHE* 4.1 6.5 - - + -
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Residues in contact with VAL 58 (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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23A PHE* 3.7 30.5 - - + -
56A LEU* 4.3 16.6 - - + -
57A THR* 1.3 80.3 - - - +
59A GLU* 1.3 62.0 + - - +
66A TRP* 3.8 19.5 - - + -
67A GLU 3.5 25.8 - - - +
68A LYS 4.2 1.8 - - - -
69A PRO* 3.8 23.6 - - + -
70A HIS* 6.1 0.2 - - - -
180A LEU* 3.3 7.9 - - - +
181A LEU* 2.8 43.6 + - + +
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Residues in contact with GLU 59 (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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57A THR* 6.1 1.3 - - - -
58A VAL* 1.3 73.6 - - - +
60A TRP* 1.3 62.1 + - - +
66A TRP* 3.5 7.2 - - - -
67A GLU* 2.9 47.7 + - + +
68A LYS 5.1 0.6 + - - -
167A THR* 4.9 1.4 + - - +
178A LYS* 4.4 19.2 + - - -
179A ALA 3.6 12.4 - - - +
180A LEU* 4.2 21.5 - - + +
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Residues in contact with TRP 60 (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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20A VAL 5.1 0.8 + - - -
59A GLU* 1.3 77.0 - - - +
61A SER* 1.3 70.4 + - - +
62A SER* 3.6 26.2 - - - -
65A GLY* 3.4 32.8 - - - -
66A TRP* 3.5 38.9 - + + +
128A PRO* 3.4 40.9 - - + +
175A LYS* 6.2 4.0 - - + -
176A PRO 3.4 25.4 - - - -
177A THR 3.5 13.9 - - - -
178A LYS* 3.5 9.5 + - - +
179A ALA* 3.0 42.5 + - + +
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Residues in contact with SER 61 (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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60A TRP* 1.3 85.4 - - - +
62A SER* 1.3 58.0 + - - +
63A GLU* 4.0 6.1 - - - -
64A PHE* 3.1 34.2 + - - +
65A GLY* 2.7 34.2 + - - -
67A GLU* 5.4 1.4 + - - -
177A THR 3.2 11.7 - - - -
178A LYS* 5.0 5.2 - - - -
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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