Contacts of the helix formed by residues 133 - 147 (chain H) in PDB entry 3J7Y
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 SER 133 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130H VAL* 5.3 2.1 - - - +
131H TYR* 3.0 5.4 + - - +
132H ALA* 1.3 78.0 - - - +
134H PRO* 1.3 72.9 - - - +
135H GLU* 4.1 12.5 + - - +
136H ASN* 3.0 37.8 + - - +
137H LYS* 3.4 6.2 - - - +
139X TYR* 3.6 39.5 - - - +
143X PHE* 6.4 0.7 - - - -
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Residues in contact with PRO 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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132H ALA 3.4 2.6 - - - +
133H SER* 1.3 83.1 - - - +
135H GLU* 1.3 73.9 + - + +
137H LYS* 3.6 23.8 + - + +
138H LYS* 3.8 12.1 + - - +
139X TYR* 3.7 20.0 - - + +
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Residues in contact with GLU 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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133H SER* 3.1 12.3 + - - +
134H PRO* 1.3 86.5 - - + +
136H ASN* 1.3 62.9 + - + +
137H LYS 3.3 0.2 + - - -
138H LYS* 3.6 14.4 + - - +
139H LEU* 4.2 6.6 + - - +
143X PHE* 4.2 24.1 - - - -
189X ASP 5.7 0.2 - - - +
190X LYS* 4.2 30.4 - - - +
193X GLU* 5.5 2.3 - - - +
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Residues in contact with ASN 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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97H ILE* 4.5 6.0 - - - +
130H VAL* 3.2 34.5 - - + +
131H TYR 3.4 9.9 + - - +
132H ALA 4.4 0.5 - - - -
133H SER* 3.0 32.3 + - - +
135H GLU* 1.3 76.8 - - + +
137H LYS* 1.3 63.6 + - - +
138H LYS 3.2 0.4 - - - -
139H LEU* 3.2 21.9 + - + +
140H PHE* 2.9 51.3 + - + -
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Residues in contact with LYS 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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95H GLU* 4.4 6.9 + - - -
97H ILE* 4.6 11.2 - - + -
111H LEU* 3.8 29.4 - - + +
132H ALA* 3.4 32.7 + - - +
133H SER 3.4 12.8 + - - +
134H PRO* 3.7 13.7 - - + +
135H GLU 3.2 0.2 - - - -
136H ASN* 1.3 84.4 + - - +
138H LYS* 1.3 58.9 + - + +
140H PHE* 3.2 7.8 + - - +
141H GLU* 2.9 37.6 + - + +
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Residues in contact with LYS 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 PRO 4.0 12.1 - - - +
135H GLU 3.6 8.0 + - - +
136H ASN 3.2 0.6 - - - -
137H LYS* 1.3 79.8 - - + +
139H LEU* 1.3 59.7 + - + +
141H GLU* 3.2 21.7 + - - +
142H GLU* 2.9 45.3 + - - +
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Residues in contact with LEU 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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135H GLU 4.3 4.9 - - - +
136H ASN* 3.2 26.2 + - + +
138H LYS* 1.3 82.0 - - + +
140H PHE* 1.3 61.3 + - + +
142H GLU* 3.2 22.2 + - - +
143H GLU* 2.9 31.4 + - - +
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Residues in contact with PHE 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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97H ILE* 3.3 38.8 - - + -
98H LEU 3.6 10.5 - - - -
99H THR* 4.2 18.2 - - + -
108H ARG* 3.4 26.9 - - - -
109H GLY* 3.6 20.0 - - - +
130H VAL* 5.5 2.2 - - + -
136H ASN* 2.9 38.7 + - + +
137H LYS* 3.2 10.1 + - - +
139H LEU* 1.3 81.9 - - + +
141H GLU* 1.3 56.4 + - - +
143H GLU* 3.2 14.6 + - - +
144H LYS* 2.9 38.0 + - - +
147H ARG* 4.2 5.6 + - - -
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Residues in contact with GLU 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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137H LYS* 2.9 20.8 + - + +
138H LYS* 3.2 28.7 + - - +
140H PHE* 1.3 75.5 - - - +
142H GLU* 1.3 56.7 + - + +
144H LYS* 3.2 22.1 + - + +
145H LEU* 2.9 38.3 + - + +
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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 LYS* 2.9 37.7 + - - +
139H LEU* 3.2 23.6 + - - +
141H GLU* 1.3 75.9 - - + +
143H GLU* 1.3 57.9 + - - +
145H LEU* 3.2 14.0 + - + +
146H LEU* 2.9 37.9 + - + +
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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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108H ARG* 2.7 33.1 + - - -
139H LEU* 2.9 16.6 + - - +
140H PHE* 3.2 17.5 + - - +
142H GLU* 1.3 77.2 - - - +
144H LYS* 1.3 56.7 + - - +
146H LEU* 3.2 14.6 + - + +
147H ARG* 2.9 52.7 + - + +
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Residues in contact with LYS 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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97H ILE* 6.3 0.2 - - - +
109H GLY 3.0 31.1 + - - -
110H ASP* 4.5 9.1 + - - +
111H LEU* 4.1 22.4 - - - +
140H PHE* 2.9 24.6 + - - +
141H GLU* 3.3 22.1 - - + +
143H GLU* 1.3 76.5 - - - +
145H LEU* 1.3 66.1 + - + +
147H ARG* 3.2 45.0 + - - +
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Residues in contact with LEU 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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141H GLU* 2.9 22.3 + - + +
142H GLU* 3.4 14.8 - - + +
144H LYS* 1.3 79.1 - - + +
146H LEU* 1.3 65.3 + - + +
147H ARG 3.4 4.0 + - - -
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Residues in contact with LEU 146 (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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142H GLU* 2.9 21.0 + - + +
143H GLU* 3.2 17.2 + - + +
145H LEU* 1.3 79.0 - - + +
147H ARG* 1.3 63.7 + - + +
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Residues in contact with ARG 147 (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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108H ARG* 3.1 42.0 + - - +
109H GLY* 3.9 17.4 - - - -
110H ASP* 5.1 2.0 + - - -
140H PHE* 4.2 4.0 + - - -
143H GLU* 2.9 42.4 + - + +
144H LYS* 3.2 44.4 + - - +
145H LEU 4.0 3.8 - - - -
146H LEU* 1.3 82.6 - - + +
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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