Contacts of the strand formed by residues 57 - 63 (chain A) in PDB entry 5JSJ
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 ARG 57 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A GLY 5.4 0.2 - - - +
56A CYS* 1.3 74.3 - - - +
58A ILE* 1.3 67.6 + - - +
73A LYS* 3.6 23.8 - - - +
74A GLY 3.2 16.7 - - - +
75A THR* 3.2 24.8 + - - +
92A ASP* 2.7 44.4 + - - -
113A VAL* 3.8 5.9 - - - +
114A LEU* 2.9 39.6 + - + +
116A ASP* 3.5 40.5 + - + +
118A VAL* 3.7 24.5 - - + -
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Residues in contact with ILE 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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53A ILE* 4.9 8.7 - - + -
56A CYS 4.5 1.8 - - - +
57A ARG* 1.3 81.8 - - - +
59A GLN* 1.3 62.2 + - - +
60A HIS* 4.1 21.1 - - + -
73A LYS* 3.3 4.3 - - - -
74A GLY 2.9 42.0 + - - +
76A VAL* 3.9 23.1 - - + -
89A ILE* 4.2 12.3 - - + -
91A TYR* 5.4 0.9 - - + -
102A LEU* 3.8 28.3 - - + -
111A LEU* 4.3 10.3 - - + -
112A GLU 3.3 12.8 - - - +
113A VAL* 4.4 15.0 - - + -
114A LEU* 3.7 10.9 - - - +
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Residues in contact with GLN 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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58A ILE* 1.3 74.8 - - - +
60A HIS* 1.3 63.3 + - - +
71A GLN* 3.3 22.2 + - - +
72A TRP 3.1 17.5 - - - +
73A LYS* 4.0 21.6 - - + +
110A ALA 3.7 1.4 - - - +
111A LEU* 3.6 1.8 - - - +
112A GLU* 2.8 63.1 + - + +
114A LEU* 3.6 25.8 - - + +
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Residues in contact with HIS 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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58A ILE* 4.1 23.1 - - + -
59A GLN* 1.3 76.9 - - - +
61A GLY* 1.3 81.1 + - - +
62A TRP* 4.1 10.3 - + + -
70A THR 3.8 0.2 - - - +
71A GLN* 3.7 8.1 - - - +
72A TRP* 3.1 31.2 + - + +
91A TYR* 2.8 37.6 + + - -
100A LEU* 4.5 2.5 - - + -
102A LEU* 4.1 8.7 - - + +
108A VAL* 4.1 12.2 - - + +
109A SER 3.6 11.4 - - - +
110A ALA 3.9 4.7 - - - -
111A LEU* 3.8 14.6 - - + -
301A 6PD 3.7 23.6 - + - -
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Residues in contact with GLY 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 HIS* 1.3 86.8 + - - +
62A TRP* 1.3 61.0 + - - -
69A VAL* 3.8 8.3 - - - -
70A THR 3.2 8.5 - - - -
71A GLN* 4.0 8.9 + - - -
107A ARG 4.2 0.2 - - - -
108A VAL* 3.5 2.6 - - - -
109A SER* 2.7 46.0 + - - -
110A ALA* 4.6 3.2 - - - +
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Residues in contact with TRP 62 (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 HIS* 4.1 4.9 - + + -
61A GLY* 1.3 73.9 - - - -
63A LYS* 1.3 60.3 + - - +
64A GLU* 3.1 42.1 + - + +
68A PRO 3.6 1.4 - - - +
69A VAL* 3.2 6.7 - - - +
70A THR* 2.8 38.2 + - - -
72A TRP* 3.7 28.5 - + + +
100A LEU* 3.7 20.0 - - + -
105A ASP* 3.7 6.1 - - - -
107A ARG* 3.3 73.6 - - + -
108A VAL* 3.6 28.5 - - + -
251A PHE* 4.2 8.3 - + - -
301A 6PD 3.3 30.7 - + - -
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Residues in contact with LYS 63 (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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62A TRP* 1.3 77.4 - - - +
64A GLU* 1.3 60.9 + - - +
65A GLY 3.7 18.4 + - - +
66A ASN* 4.3 15.3 + - - +
67A GLY 3.0 25.4 + - - +
68A PRO* 4.1 7.2 - - - +
69A VAL* 4.4 18.6 - - + +
107A ARG* 3.2 40.8 + - + +
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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