Contacts of the helix formed by residues 126 - 137 (chain H) in PDB entry 5JKL
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 ASP 126 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11H ASN* 3.2 15.5 + - - +
12H TYR* 3.6 13.3 - - - -
13H HIS 4.8 0.7 + - - +
16H SER* 4.6 4.1 + - - +
76H ARG* 3.1 33.8 + - - -
121H ALA* 3.0 18.4 + - + +
122H THR* 5.1 0.2 - - - +
124H LYS* 4.4 8.3 - - + +
125H ASN* 1.3 72.6 - - - +
127H PRO* 1.4 64.0 - - - +
128H HIS* 3.5 4.2 + - - +
129H LEU* 3.0 32.7 + - + +
130H CYS* 3.0 25.9 + - - -
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Residues in contact with PRO 127 (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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11H ASN* 4.0 8.1 - - - +
125H ASN 3.2 15.3 - - - +
126H ASP* 1.4 80.9 - - - +
128H HIS* 1.3 61.8 + - - +
130H CYS* 3.6 9.5 - - + +
131H ASP* 2.9 30.3 + - - +
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Residues in contact with HIS 128 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72H LEU* 3.7 28.4 - - + +
75H GLN* 5.4 5.3 - - + -
76H ARG* 3.1 40.5 + - - +
126H ASP* 3.3 2.3 + - - +
127H PRO* 1.3 81.7 - - - +
129H LEU* 1.3 57.4 + - - +
131H ASP* 3.3 11.3 + - + +
132H PHE* 2.9 30.3 + + + +
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Residues in contact with LEU 129 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12H TYR* 4.4 7.6 - - + -
16H SER* 3.9 27.6 - - - +
20H ILE* 3.9 29.6 - - + -
72H LEU* 4.2 18.4 - - + -
76H ARG* 4.1 3.4 - - - +
117H LEU* 4.8 8.5 - - + -
121H ALA* 3.7 21.5 - - + +
126H ASP* 3.0 27.8 + - - +
128H HIS* 1.3 76.7 + - - +
130H CYS* 1.3 65.5 + - - +
132H PHE* 3.1 13.3 + - + +
133H ILE* 2.9 35.4 + - + +
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Residues in contact with CYS 130 (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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118H HIS* 3.4 25.7 - - + +
121H ALA* 3.7 17.5 - - - +
122H THR* 3.6 30.7 - - - -
126H ASP 3.0 20.7 + - - +
127H PRO* 3.6 11.2 - - + +
128H HIS 3.4 0.2 - - - -
129H LEU* 1.3 77.0 - - - +
131H ASP* 1.3 57.9 + - - +
133H ILE* 3.3 0.8 + - - -
134H GLU* 3.0 39.0 + - - +
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Residues in contact with ASP 131 (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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127H PRO 2.9 17.7 + - - +
128H HIS* 3.6 11.9 - - + +
129H LEU 3.2 0.2 - - - -
130H CYS* 1.3 72.5 - - - +
132H PHE* 1.3 60.5 + - - +
134H GLU* 3.8 9.8 - - - +
135H THR* 2.8 55.3 + - - +
136H HIS* 6.0 0.3 + - - -
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Residues in contact with PHE 132 (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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20H ILE* 5.0 0.4 - - + -
68H LYS* 3.9 25.6 - - + -
69H LEU* 3.6 19.5 - - + -
72H LEU* 3.8 45.5 - - + -
75H GLN* 5.4 2.7 - - - -
128H HIS* 2.9 19.0 + + + +
129H LEU* 3.1 15.7 + - + +
131H ASP* 1.3 80.3 + - - +
133H ILE* 1.3 75.0 + - + +
136H HIS* 3.0 47.8 + + - +
137H TYR* 3.5 29.8 - + - -
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Residues in contact with ILE 133 (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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20H ILE* 5.5 0.7 - - + -
69H LEU* 6.3 0.7 - - + -
114H LEU* 4.1 22.9 - - + +
117H LEU* 3.7 36.1 - - + +
118H HIS* 3.9 27.8 - - + +
121H ALA* 4.8 0.7 - - + -
129H LEU* 2.9 34.7 + - + +
130H CYS 3.8 2.9 - - - +
132H PHE* 1.3 88.5 - - + +
134H GLU* 1.3 58.6 + - - +
137H TYR* 2.9 29.4 + - + -
138H LEU* 2.9 35.1 + - + -
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Residues in contact with GLU 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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118H HIS* 2.7 34.7 + - + +
130H CYS* 3.0 23.6 + - - +
131H ASP* 3.8 7.0 + - - +
133H ILE* 1.3 79.8 - - - +
135H THR* 1.3 65.3 + - - +
138H LEU* 3.9 27.3 + - + +
139H ASN* 4.2 10.6 + - - +
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Residues in contact with THR 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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131H ASP* 2.8 40.7 + - - +
134H GLU* 1.3 77.4 - - - +
136H HIS* 1.3 87.2 + - + +
139H ASN* 5.8 3.1 + - - +
140H GLU* 5.6 2.1 - - - +
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Residues in contact with HIS 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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65H HIS* 5.5 3.6 + - - -
68H LYS* 3.8 32.8 + - + +
132H PHE* 3.0 41.4 + + - +
135H THR* 1.3 99.8 + - + +
137H TYR* 1.3 82.8 + - + +
140H GLU* 3.4 21.8 - - - +
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Residues in contact with TYR 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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27H GLU* 4.2 8.1 - - - -
65H HIS* 2.6 54.4 + + + -
68H LYS* 3.4 19.1 - - + +
69H LEU* 3.4 22.7 + - + +
114H LEU* 3.8 36.6 - - + -
132H PHE* 3.5 36.1 - + - -
133H ILE* 2.9 14.8 + - + +
135H THR 3.7 0.4 - - - -
136H HIS* 1.3 97.3 - - + +
138H LEU* 1.3 66.6 + - - +
139H ASN 3.5 1.8 - - - -
140H GLU* 3.4 5.6 + - + +
141H GLN* 3.0 29.9 + - - +
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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