Contacts of the helix formed by residues 78 - 86 (chain A) in PDB entry 1JWG
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 GLY 78 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A ASN* 4.8 6.5 - - - -
76A SER 3.6 1.4 + - - -
77A CYS* 1.3 75.5 - - - +
79A LYS* 1.3 67.3 + - - +
80A ARG 3.3 2.4 + - - -
81A PHE* 3.5 7.1 + - - +
82A HIS* 3.1 26.3 + - - -
35B GLU* 3.0 19.0 + - - -
38B ASN* 3.8 8.3 - - - -
148B IOD 4.0 6.5 - - - -
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Residues in contact with LYS 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 GLY* 1.3 72.6 - - - +
80A ARG* 1.3 62.7 + - + +
82A HIS* 3.6 1.4 - - - +
83A ASP* 2.8 61.7 + - - +
8B GLU* 6.4 1.3 - - - -
13B ARG* 4.9 10.3 - - - +
35B GLU* 2.9 39.6 + - + +
36B GLN* 3.8 20.9 - - - +
148B IOD 3.5 5.6 - - + +
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Residues in contact with ARG 80 (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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38A ASN* 3.2 38.1 + - - +
40A ASP 2.8 25.5 + - - -
41A PHE* 3.4 33.3 + - - +
44A PRO* 3.5 20.9 - - + +
78A GLY 3.3 0.8 - - - -
79A LYS* 1.3 84.0 - - + +
81A PHE* 1.3 59.1 + - - +
83A ASP* 3.2 6.4 + - - +
84A GLU* 2.9 31.8 + - + +
38B ASN 3.6 14.3 + - - -
39B GLU* 3.6 22.4 + - - +
148B IOD 3.6 15.0 - - + +
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Residues in contact with PHE 81 (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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37A LEU* 4.1 31.0 - - + -
38A ASN* 4.6 6.6 + - - +
44A PRO* 4.1 21.4 - - + +
47A ALA* 4.1 20.2 - - + -
48A THR* 4.4 4.7 - - - -
51A LEU* 4.0 19.1 - - + -
70A LEU* 4.2 2.5 - - + -
73A CYS* 3.4 40.6 - - + -
74A MET* 3.8 19.5 - - + -
78A GLY* 3.5 7.6 + - - +
79A LYS 3.4 0.2 - - - -
80A ARG* 1.3 78.4 - - - +
82A HIS* 1.3 65.7 + + + +
84A GLU* 3.1 3.2 + - + +
85A VAL* 3.0 49.3 + - + +
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Residues in contact with HIS 82 (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 MET* 2.7 52.3 + - - +
76A SER 3.3 19.9 + - - -
77A CYS* 4.3 0.2 - - - -
78A GLY 3.1 14.2 + - - +
79A LYS 3.6 3.4 - - - +
81A PHE* 1.3 78.5 - + - +
83A ASP* 1.3 58.2 + - - +
85A VAL* 3.6 2.4 + - - +
86A GLY 3.0 20.6 + - - -
126A LEU* 3.7 32.2 - - + +
128A GLU* 6.0 0.7 - - - +
129A GLU* 3.4 24.3 - - + +
132A ILE* 5.1 0.2 - - - +
35B GLU* 2.7 39.0 + - - +
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Residues in contact with ASP 83 (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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79A LYS* 2.8 58.5 + - - +
80A ARG* 3.7 5.6 - - - +
82A HIS* 1.3 72.4 - - - +
84A GLU* 1.3 66.1 + - - +
86A GLY 3.2 9.7 + - - -
87A LYS* 3.4 23.5 + - - +
129A GLU* 2.5 34.6 - - - +
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Residues in contact with GLU 84 (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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44A PRO* 3.9 22.2 - - + +
45A PRO* 4.0 29.3 - - + +
48A THR* 4.2 20.7 + - + +
80A ARG* 2.9 17.8 + - + +
81A PHE* 3.1 9.2 + - + +
83A ASP* 1.3 76.5 - - + +
85A VAL* 1.3 63.8 + - - +
87A LYS* 2.8 52.5 + - - +
89A ARG* 5.4 6.1 + - - +
90A PHE* 3.7 9.5 - - - +
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Residues in contact with VAL 85 (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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48A THR* 3.8 12.1 - - - +
70A LEU* 3.9 9.0 - - + -
74A MET* 3.7 34.1 - - + -
81A PHE* 3.0 43.1 + - + +
82A HIS 4.0 1.1 - - - +
84A GLU* 1.3 76.2 - - - +
86A GLY* 1.3 57.7 + - - +
87A LYS 3.2 6.3 + - - +
90A PHE* 3.7 25.8 - - + -
91A LEU* 3.3 20.4 - - - +
122A TRP* 3.9 19.1 - - + -
132A ILE* 4.8 1.6 - - + -
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Residues in contact with GLY 86 (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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82A HIS 3.0 15.0 + - - -
83A ASP 3.4 9.4 - - - -
84A GLU 3.1 0.6 - - - -
85A VAL* 1.3 77.1 - - - +
87A LYS* 1.3 57.2 + - - +
91A LEU* 3.9 3.1 - - - -
129A GLU* 3.9 13.3 - - - +
131A LYS* 3.4 28.6 + - - +
132A ILE* 3.9 20.9 - - - -
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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