Contacts of the strand formed by residues 72 - 79 (chain A) in PDB entry 4J2X
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 GLN 72 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A GLY 4.8 1.3 - - - +
71A ASP* 1.3 69.3 - - - +
73A THR* 1.3 59.4 + - - +
105A GLY* 3.5 30.2 + - - -
106A TRP* 3.7 28.0 - - + +
109A LYS* 3.9 12.7 - - - +
173A TYR* 3.2 21.9 + - - -
365A THR* 3.5 0.2 - - - -
366A PHE* 3.0 72.6 + - + +
367A TYR* 4.6 3.8 - - - +
368A GLU* 4.3 26.7 - - - +
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Residues in contact with THR 73 (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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71A ASP* 4.7 3.5 - - - +
72A GLN* 1.3 72.5 - - - +
74A VAL* 1.3 69.0 + - - +
75A LEU* 4.4 5.8 - - + -
101A LEU* 3.5 2.9 - - - -
102A MET* 2.8 57.3 + - + -
103A GLY* 5.2 1.2 - - - -
106A TRP* 3.1 8.7 + - - -
363A GLU* 4.1 22.9 - - + +
364A TYR 3.1 5.4 - - - +
365A THR* 3.0 32.0 + - - +
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Residues in contact with VAL 74 (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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73A THR* 1.3 71.7 - - - +
75A LEU* 1.3 69.2 + - - +
76A ILE* 4.4 8.3 - - + -
99A VAL* 4.6 11.9 - - + -
100A TYR 3.6 4.5 - - - +
101A LEU* 4.0 6.7 - - + -
106A TRP* 3.6 29.2 - - + -
169A VAL* 5.2 1.6 - - + -
171A MET* 4.0 7.0 - - - -
182A PHE* 3.9 53.8 - - + -
362A ALA 3.7 1.2 - - - +
363A GLU* 3.6 3.3 - - - -
364A TYR* 2.8 35.0 + - + +
366A PHE* 4.3 2.5 - - + -
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Residues in contact with LEU 75 (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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73A THR* 4.4 3.8 - - + -
74A VAL* 1.3 74.4 - - - +
76A ILE* 1.4 62.3 + - - +
77A LEU* 4.0 16.6 - - + -
98A CYS 3.4 0.7 - - - +
99A VAL* 3.2 8.1 - - - +
100A TYR* 2.9 47.7 + - + +
102A MET* 3.7 34.3 - - + -
361A LYS* 3.8 29.6 - - + +
362A ALA 3.3 2.0 - - - +
363A GLU* 3.5 35.4 - - + -
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Residues in contact with ILE 76 (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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74A VAL* 4.4 6.7 - - + -
75A LEU* 1.4 75.3 - - - +
77A LEU* 1.4 62.6 + - - +
78A HIS* 3.5 9.7 + - - +
97A PRO* 5.2 1.6 - - + -
98A CYS 3.5 5.6 - - - +
99A VAL* 4.3 7.6 - - + -
129A ILE* 5.2 1.6 - - + -
167A LEU* 4.3 13.2 - - + -
169A VAL* 3.8 25.1 - - + -
182A PHE* 3.7 37.5 - - + +
183A LEU 3.9 17.9 - - - +
184A SER* 4.0 19.7 - - - +
361A LYS* 3.5 2.6 - - - -
362A ALA* 2.8 40.7 + - + -
364A TYR* 4.2 7.6 - - + -
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Residues in contact with LEU 77 (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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75A LEU* 4.3 19.5 - - + -
76A ILE* 1.4 70.7 - - - +
78A HIS* 1.3 60.5 + - - +
97A PRO* 3.2 4.7 - - - +
98A CYS* 2.7 40.6 + - + +
100A TYR* 3.4 35.7 - - + -
243A TRP* 3.6 19.4 - - + -
245A ALA* 5.2 11.2 - - + -
360A ASP 3.9 4.9 - - - +
361A LYS* 4.5 22.2 - - + -
501A EDO 3.8 22.0 - - - +
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Residues in contact with HIS 78 (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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76A ILE* 3.5 16.6 + - + +
77A LEU* 1.3 75.0 - - - +
79A ALA* 1.3 82.3 + - - +
80A LYS* 5.2 0.4 - - - -
95A PRO 5.5 0.4 - - - -
97A PRO* 4.3 9.9 - - + -
167A LEU* 4.0 20.4 - - + -
184A SER* 3.7 7.6 - - - -
185A LYS* 3.3 53.3 + - + +
186A ARG 4.5 2.2 + - - -
187A ILE* 3.4 20.5 - - + +
243A TRP* 3.9 11.8 - - - -
359A THR* 3.2 7.9 - - - -
360A ASP* 2.9 46.2 + - + +
362A ALA 4.8 0.2 - - - -
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Residues in contact with ALA 79 (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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78A HIS* 1.3 92.5 - - - +
80A LYS* 1.3 62.5 + - - +
81A VAL 3.3 8.1 + - - +
94A CYS 4.7 1.6 - - - +
95A PRO* 4.2 22.7 + - + +
97A PRO* 5.9 0.2 - - - +
187A ILE* 3.7 10.7 - - - +
357A ILE* 3.4 32.5 - - + -
358A SER 3.4 7.6 - - - +
359A THR* 4.0 2.7 - - - +
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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