Contacts of the helix formed by residues 133 - 141 (chain S) in PDB entry 1J0B
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 LEU 133 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76S VAL* 3.6 13.8 - - + +
77S GLY 3.9 5.4 - - - +
101S VAL* 3.5 32.7 - - + +
102S LEU 3.1 19.5 - - - +
103S ARG* 3.3 32.8 - - + +
125S TYR* 3.5 23.6 - - + -
127S ALA 4.4 7.0 - - - +
130S SER 4.4 4.0 - - - +
131S PHE* 2.7 8.5 - - - -
132S GLU* 1.3 75.0 - - - +
134S MET* 1.3 59.6 + - - +
135S LYS 3.2 2.2 - - - -
136S TYR* 3.3 31.9 + - + +
137S ALA* 3.1 21.1 + - - +
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Residues in contact with MET 134 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75S THR* 6.2 0.2 - - - -
76S VAL* 4.0 21.2 - - - +
131S PHE* 3.1 18.6 + - + +
132S GLU* 4.6 2.9 - - - -
133S LEU 1.3 79.5 - - - +
135S LYS* 1.3 54.7 + - - +
137S ALA* 3.6 1.5 - - - +
138S GLU* 2.7 51.6 + - + +
153S VAL* 4.6 17.5 - - + -
154S ILE 4.8 1.6 - - - +
155S PRO* 3.3 23.8 - - + -
156S PRO* 3.2 34.1 - - + -
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Residues in contact with LYS 135 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132S GLU* 4.2 14.6 - - + +
133S LEU 3.2 1.4 - - - +
134S MET* 1.3 78.5 - - - +
136S TYR* 1.3 109.8 + - + +
138S GLU* 3.6 6.4 - - - +
139S GLU* 2.6 40.8 + - + +
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Residues in contact with TYR 136 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101S VAL* 4.5 2.2 - - + -
125S TYR* 3.5 36.3 - + + -
127S ALA* 3.0 35.2 - - + +
132S GLU 3.8 13.7 - - - -
133S LEU* 3.3 34.7 + - + +
135S LYS* 1.3 111.5 + - + +
137S ALA* 1.3 58.2 + - - +
139S GLU* 2.9 37.5 - - - +
140S ILE* 3.0 20.9 + - - +
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Residues in contact with ALA 137 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74S ILE* 4.1 18.0 - - + +
75S THR* 5.2 0.7 - - - -
76S VAL* 3.4 32.8 - - + -
101S VAL* 3.6 18.6 - - + +
133S LEU 3.1 4.8 + - - +
134S MET* 3.6 11.4 - - - +
136S TYR* 1.3 77.2 - - - +
138S GLU* 1.3 59.9 + - + +
140S ILE* 3.9 3.6 + - - +
141S ALA* 3.2 25.3 + - - +
153S VAL* 4.7 6.0 - - + +
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Residues in contact with GLU 138 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134S MET* 2.7 38.1 + - + +
135S LYS* 3.6 6.1 - - - +
137S ALA* 1.3 76.9 - - - +
139S GLU* 1.3 64.1 + - - +
141S ALA* 3.5 11.2 - - - +
142S GLU* 3.1 25.5 - - - +
153S VAL* 3.1 33.6 - - + +
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Residues in contact with GLU 139 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125S TYR* 4.7 6.1 + - - -
135S LYS* 2.6 21.2 + - + +
136S TYR* 2.9 42.8 - - - +
138S GLU* 1.3 68.9 - - - +
140S ILE* 1.3 78.4 + - - +
142S GLU* 2.6 40.6 + - - +
143S GLU* 3.3 9.6 + - - +
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Residues in contact with ILE 140 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74S ILE* 4.1 17.5 - - + -
99S ILE* 5.0 7.9 - - + -
101S VAL* 4.9 9.9 - - + -
123S ARG* 2.9 46.9 - - - +
125S TYR* 3.4 26.9 - - + +
136S TYR 3.0 20.8 + - - +
137S ALA* 3.9 3.6 - - - +
139S GLU* 1.3 84.9 - - + +
141S ALA* 1.3 56.2 + - - +
142S GLU 2.4 17.4 + - - -
143S GLU* 2.7 35.0 + - + +
144S LEU* 3.3 11.3 + - + +
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Residues in contact with ALA 141 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74S ILE* 4.3 7.2 - - + -
137S ALA 3.2 13.5 + - - +
138S GLU* 3.5 13.9 - - - +
139S GLU 3.2 0.2 - - - -
140S ILE* 1.3 80.2 - - - +
142S GLU* 1.3 50.1 + - - +
144S LEU* 3.8 7.9 - - - -
145S LYS* 2.7 45.1 + - + +
151S PRO* 3.5 14.5 - - + +
153S VAL* 4.0 22.4 - - + -
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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