Contacts of the helix formed by residues 133 - 145 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76H VAL* 3.9 7.4 - - + -
77H GLY 3.6 13.2 - - - +
101H VAL* 2.8 40.9 - - + +
102H LEU 3.3 24.5 - - - +
103H ARG* 3.0 43.5 - - + +
125H TYR* 4.7 5.2 - - + +
127H ALA* 4.4 10.5 - - + -
128H LYS 3.8 4.3 - - - +
131H PHE* 2.8 4.4 - - - -
132H GLU* 1.3 77.9 - - - +
134H MET* 1.3 67.2 + - - +
135H LYS 3.1 1.3 - - - -
136H TYR* 2.8 35.0 + - + +
137H ALA* 3.2 3.5 + - - +
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Residues in contact with MET 134 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75H THR* 5.3 0.4 - - - -
76H VAL* 3.5 22.0 - - + +
131H PHE 3.6 9.4 + - - +
132H GLU* 4.2 4.5 - - - -
133H LEU* 1.3 77.1 - - - +
135H LYS* 1.3 64.7 + - - +
137H ALA* 2.9 12.5 + - + +
138H GLU* 2.7 42.6 + - + +
153H VAL* 3.0 36.8 - - + -
154H ILE 4.3 12.1 - - - +
155H PRO* 4.2 6.1 - - + -
156H PRO* 3.9 25.1 - - + -
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Residues in contact with LYS 135 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128H LYS* 4.3 7.6 - - - +
132H GLU 3.4 16.3 + - - +
133H LEU 3.1 0.8 + - - -
134H MET* 1.3 77.4 - - - +
136H TYR* 1.3 102.2 + - + +
138H GLU* 2.9 15.5 - - - +
139H GLU* 2.8 47.4 + - - +
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Residues in contact with TYR 136 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101H VAL* 4.0 8.7 - - + -
125H TYR* 3.0 59.5 - + + -
126H ASP 5.4 1.2 + - - -
127H ALA* 4.0 9.0 - - + +
128H LYS* 3.6 25.8 + - - -
133H LEU* 2.8 27.5 + - - +
135H LYS* 1.3 107.9 + - + +
137H ALA* 1.3 55.0 + - - +
139H GLU* 3.2 23.3 + - - +
140H ILE* 2.9 36.9 + - - +
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Residues in contact with ALA 137 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74H ILE* 3.3 31.6 - - + +
75H THR 3.9 13.2 - - - +
101H VAL* 3.8 12.0 - - + +
133H LEU 3.2 4.1 + - - +
134H MET* 2.9 24.1 + - + +
136H TYR* 1.3 75.5 - - - +
138H GLU* 1.3 67.6 + - - +
140H ILE* 3.9 4.9 - - - +
141H ALA* 3.1 23.7 + - - +
153H VAL* 4.4 1.3 - - - +
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Residues in contact with GLU 138 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134H MET* 2.7 49.4 + - + +
135H LYS* 2.9 20.6 - - - +
137H ALA* 1.3 74.9 - - - +
139H GLU* 1.3 64.1 + - + +
141H ALA* 3.3 7.6 + - - +
142H GLU* 2.9 22.7 + - - +
153H VAL* 3.7 11.1 - - - +
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Residues in contact with GLU 139 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125H TYR* 5.5 1.4 + - - -
135H LYS* 2.8 46.8 + - + +
136H TYR* 3.2 25.2 + - - +
138H GLU* 1.3 75.9 - - + +
140H ILE* 1.3 51.8 + - + +
142H GLU* 2.5 31.8 + - - +
143H GLU* 2.7 19.2 + - - +
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Residues in contact with ILE 140 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72H VAL* 6.2 0.2 - - + -
74H ILE* 4.5 12.3 - - + -
99H ILE* 4.4 16.4 - - + -
101H VAL* 3.6 26.2 - - + -
123H ARG* 3.2 44.4 - - - +
125H TYR* 4.0 13.7 - - - +
136H TYR 2.9 21.9 + - - +
137H ALA* 3.9 6.7 - - - +
139H GLU* 1.3 76.8 - - + +
141H ALA* 1.3 63.6 + - - +
143H GLU* 4.0 6.1 - - - +
144H LEU* 3.0 31.6 + - + +
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Residues in contact with ALA 141 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74H ILE* 3.9 2.9 - - + +
137H ALA 3.1 17.4 + - - +
138H GLU* 3.3 6.3 - - - +
140H ILE* 1.3 78.1 - - - +
142H GLU* 1.3 52.3 + - - +
144H LEU* 4.9 0.4 - - - -
145H LYS* 2.7 45.3 + - + +
151H PRO* 3.3 32.7 - - + +
153H VAL* 3.8 16.2 - - + -
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Residues in contact with GLU 142 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138H GLU 2.9 12.9 + - - +
139H GLU* 2.5 23.3 + - - +
141H ALA* 1.3 70.9 - - - +
143H GLU* 1.3 58.5 + - - -
145H LYS* 3.1 36.1 + - - +
146H ARG* 2.9 49.1 + - - +
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Residues in contact with GLU 143 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139H GLU 2.7 12.6 + - - +
140H ILE* 3.3 8.3 + - - +
142H GLU* 1.3 70.7 - - - +
144H LEU* 1.3 69.2 + - - +
145H LYS 3.0 1.3 - - - -
146H ARG* 2.8 59.3 + - - +
147H GLU* 3.7 19.6 - - - +
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Residues in contact with LEU 144 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72H VAL* 3.4 38.1 - - + -
74H ILE* 6.4 0.2 - - + -
99H ILE* 5.7 5.2 - - + -
140H ILE* 3.0 20.5 + - + +
141H ALA* 4.2 3.1 - - - +
143H GLU* 1.3 73.2 - - - +
145H LYS* 1.3 54.5 + - - +
146H ARG 2.6 17.6 + - - -
147H GLU* 2.7 50.8 + - - +
149H ARG* 3.3 58.5 + - + +
151H PRO* 5.5 1.1 - - + -
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Residues in contact with LYS 145 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262C GLU* 4.7 16.2 + - - +
288C TYR* 5.2 6.3 + - - -
141H ALA* 2.7 24.3 + - + +
142H GLU* 3.1 42.4 + - - +
144H LEU* 1.3 74.9 - - - +
146H ARG* 1.3 56.0 + - - +
147H GLU 3.5 2.4 + - - -
148H GLY* 4.2 6.2 + - - -
149H ARG 3.3 12.9 + - - +
150H LYS* 5.6 0.2 - - - -
151H PRO* 4.2 16.8 - - + -
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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