Contacts of the helix formed by residues 112 - 123 (chain D) in PDB entry 5JHW
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 ASN 112 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98D TRP 5.4 0.2 - - - +
99D LYS* 3.8 17.3 + - - +
100D GLY 3.2 15.7 - - - +
101D PRO* 4.2 0.2 - - - -
102D VAL* 3.8 12.1 - - - +
110D TYR* 3.1 3.4 - - - +
111D ARG* 1.3 111.5 + - - +
113D GLU* 1.3 65.6 + - + +
114D CYS* 3.2 11.8 + - - +
115D ALA* 2.8 34.3 + - - +
116D LEU 3.1 16.6 + - - -
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Residues in contact with GLU 113 (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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96D ILE* 3.4 46.6 - - + +
98D TRP* 4.4 7.5 + - + +
100D GLY 4.0 4.0 + - - -
102D VAL* 4.1 12.6 - - + +
112D ASN* 1.3 74.9 - - - +
114D CYS* 1.3 57.8 + - - +
116D LEU* 3.0 6.9 + - - +
117D LEU* 2.9 49.8 + - + +
129D VAL* 2.9 35.3 - - - +
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Residues in contact with CYS 114 (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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91D PRO* 4.4 2.7 - - - +
93D CYS* 2.0 51.8 - - + -
96D ILE* 4.5 1.2 - - + +
111D ARG* 5.2 7.0 - - - +
112D ASN* 3.2 12.2 + - - +
113D GLU* 1.3 78.5 - - - +
115D ALA* 1.3 58.2 + - - +
117D LEU* 3.3 6.5 + - - +
118D LYS* 3.0 41.5 + - - +
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Residues in contact with ALA 115 (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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110D TYR* 4.3 7.8 - - + -
111D ARG* 3.5 40.1 - - + +
112D ASN* 2.8 22.8 + - - +
113D GLU 3.2 0.2 - - - -
114D CYS* 1.3 74.1 - - - +
116D LEU* 1.3 60.3 + - - +
118D LYS* 3.1 8.2 + - - +
119D ALA* 2.9 28.1 + - - +
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Residues in contact with LEU 116 (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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102D VAL* 3.9 6.7 - - + -
104D GLY* 3.6 22.7 - - - -
110D TYR* 3.6 37.0 - - + +
112D ASN 3.1 11.1 + - - +
113D GLU* 3.0 9.1 + - - +
115D ALA* 1.3 75.3 - - - +
117D LEU* 1.3 66.6 + - + +
119D ALA 3.1 1.2 + - - -
120D ARG* 2.7 32.7 + - - +
127D LEU* 3.4 20.7 - - + +
128D GLU* 3.8 26.0 - - - +
129D VAL* 3.6 23.6 - - + -
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Residues in contact with LEU 117 (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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91D PRO* 3.9 22.5 - - + +
92D ASP 4.3 11.4 - - - +
93D CYS* 4.5 3.4 - - - -
96D ILE* 3.8 28.7 - - + -
113D GLU* 2.9 32.3 + - + +
114D CYS* 3.6 10.8 - - - +
116D LEU* 1.3 86.7 - - + +
118D LYS* 1.3 56.3 + - - +
120D ARG* 3.4 21.1 - - - +
121D CYS* 3.1 25.3 + - - +
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Residues in contact with LYS 118 (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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89D CYS* 4.3 26.8 + - + +
90D ALA* 5.7 0.4 - - - +
91D PRO* 4.3 14.4 - - + +
111D ARG* 5.0 12.1 - - - +
114D CYS* 3.0 29.9 + - - +
115D ALA* 3.5 6.7 - - - +
116D LEU 3.1 0.4 - - - -
117D LEU* 1.3 74.4 - - - +
119D ALA* 1.3 61.8 + - - +
121D CYS* 3.4 3.8 + - - +
122D LYS* 3.1 45.5 + - + +
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Residues in contact with ALA 119 (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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110D TYR* 3.6 26.0 - - + +
115D ALA 2.9 13.6 + - - +
116D LEU 3.5 7.2 - - - +
118D LYS* 1.3 73.4 - - - +
120D ARG* 1.3 64.8 + - - +
122D LYS* 4.6 6.1 - - - +
123D GLU* 3.1 19.4 + - + +
124D GLN* 3.0 21.5 + - + +
127D LEU* 3.8 7.9 - - + -
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Residues in contact with ARG 120 (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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39A LYS* 4.0 5.5 - - - +
116D LEU 2.7 14.2 + - - +
117D LEU* 3.4 27.1 - - - +
119D ALA* 1.3 77.5 - - - +
121D CYS* 1.3 62.2 + - - +
124D GLN 3.1 35.5 + - - +
125D PRO* 3.1 33.3 + - + +
126D GLU 3.5 0.2 - - - -
127D LEU* 2.6 44.4 + - + +
128D GLU* 3.8 5.5 - - - +
302D FLC 2.9 47.2 + - - -
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Residues in contact with CYS 121 (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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74D GLY* 4.0 9.0 - - - +
75D LYS* 3.8 28.0 + - - -
89D CYS* 2.0 54.8 - - + -
91D PRO* 5.5 4.0 - - + -
117D LEU 3.1 13.2 + - - +
118D LYS* 3.8 1.3 - - - +
119D ALA 3.2 0.2 - - - -
120D ARG* 1.3 83.9 - - - +
122D LYS* 1.3 60.4 + - - +
125D PRO* 5.9 1.2 - - - +
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Residues in contact with LYS 122 (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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75D LYS* 6.1 0.2 - - - +
89D CYS* 3.6 19.1 - - + -
118D LYS* 3.1 29.6 + - + +
119D ALA* 4.4 2.9 - - - +
121D CYS* 1.3 78.2 - - - +
123D GLU* 1.3 87.9 + - + +
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Residues in contact with GLU 123 (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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119D ALA* 3.1 14.6 + - - +
121D CYS 3.6 0.2 - - - -
122D LYS* 1.3 113.6 + - + +
124D GLN* 1.3 74.0 + - + +
125D PRO* 3.3 11.9 - - - +
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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