Contacts of the helix formed by residues 129 - 142 (chain H) in PDB entry 6BCH
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 THR 129 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44H THR* 3.6 5.8 - - - +
125H LYS 4.8 1.4 + - - -
126H GLU* 3.5 17.6 + - - -
127H HIS 3.1 0.8 - - - +
128H LEU* 1.3 82.8 + - - +
130H GLU* 1.3 70.6 + - + +
131H GLU* 3.7 18.8 - - + +
132H GLY 4.1 2.5 - - - -
133H LEU* 3.0 24.8 + - - +
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Residues in contact with GLU 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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44H THR* 3.8 12.8 - - + +
129H THR* 1.3 76.9 - - + +
131H GLU* 1.3 57.3 + - - +
133H LEU* 3.5 5.0 + - - +
134H ASN* 2.8 42.1 + - - +
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Residues in contact with GLU 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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129H THR* 3.7 12.4 - - + +
130H GLU* 1.3 77.0 - - - +
132H GLY* 1.3 60.6 + - - +
134H ASN* 3.3 8.0 + - - +
135H GLN* 3.0 32.8 + - - +
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Residues in contact with GLY 132 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121H LEU* 4.5 4.2 - - - +
126H GLU* 3.2 31.7 + - - -
127H HIS* 4.3 2.0 - - - -
129H THR* 3.5 4.8 + - - -
130H GLU 3.4 0.2 - - - -
131H GLU* 1.3 80.4 - - - +
133H LEU* 1.3 57.1 + - - +
135H GLN* 3.2 10.1 + - - +
136H ILE* 2.9 36.5 + - - +
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Residues in contact with LEU 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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36H VAL* 4.7 1.6 - - + -
44H THR* 3.7 29.8 - - + +
46H TRP* 4.0 20.9 - - + +
48H VAL* 3.6 28.3 - - + -
126H GLU 4.2 1.0 + - - -
127H HIS* 4.1 11.1 + - - +
129H THR 3.0 18.2 + - - +
130H GLU* 3.6 6.3 - - - +
132H GLY* 1.3 76.5 - - - +
134H ASN* 1.3 63.9 + - - +
136H ILE* 3.1 7.1 + - + +
137H LEU* 2.9 46.5 + - + +
155H PHE* 4.0 20.6 - - + -
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Residues in contact with ASN 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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130H GLU* 2.8 30.4 + - - +
131H GLU* 3.3 7.3 + - - +
133H LEU* 1.3 75.2 - - - +
135H GLN* 1.3 63.1 + - - +
137H LEU* 3.2 8.2 + - - +
138H THR* 3.0 26.6 + - + +
155H PHE* 3.8 27.7 - - - +
158H THR* 4.8 13.3 - - + +
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Residues in contact with GLN 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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121H LEU* 4.0 29.2 - - + +
126H GLU* 5.3 1.4 - - - +
131H GLU* 3.0 21.1 + - + +
132H GLY* 3.7 8.0 - - - +
133H LEU 3.2 0.4 - - - -
134H ASN* 1.3 73.4 - - - +
136H ILE* 1.3 66.4 + - - +
138H THR* 2.3 36.5 + - + +
139H LEU* 3.0 12.9 + - + +
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Residues in contact with ILE 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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34H LEU* 4.4 16.8 - - + +
36H VAL* 5.0 5.8 - - + -
48H VAL* 3.7 34.1 - - + -
118H ALA* 4.6 5.4 - - + +
121H LEU* 3.9 21.1 - - + -
122H ILE* 3.9 13.0 - - + -
127H HIS* 3.5 32.5 - - + -
132H GLY 2.9 17.0 + - - +
133H LEU* 3.1 9.8 + - + +
135H GLN* 1.3 75.6 - - - +
137H LEU* 1.3 60.4 + - + +
139H LEU* 2.9 12.0 + - - +
140H LYS* 2.8 26.3 + - + +
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Residues in contact with LEU 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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36H VAL* 4.4 22.0 - - + -
133H LEU* 2.9 50.3 + - + +
134H ASN* 3.2 10.3 + - - +
136H ILE* 1.3 76.0 - - + +
138H THR* 1.3 59.7 + - - +
140H LYS* 4.3 5.2 - - - -
141H ALA* 2.9 31.2 + - - +
147H LEU* 3.8 20.1 - - + +
151H LEU* 5.0 7.6 - - + +
155H PHE* 3.3 50.5 - - + -
158H THR* 4.4 14.6 - - + -
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Residues in contact with THR 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 ASN* 3.0 18.2 + - + +
135H GLN* 2.3 35.8 + - + +
137H LEU* 1.3 76.3 - - - +
139H LEU* 1.3 62.5 + - - +
141H ALA* 3.7 4.0 + - - +
142H SER 3.9 1.6 + - - -
158H THR* 5.4 5.8 - - + -
159H ILE 3.4 31.0 - - - +
160H PRO* 3.6 7.2 - - - +
161H ALA* 2.7 34.8 + - - +
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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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34H LEU* 4.7 6.5 - - + -
114H LEU* 3.8 30.2 - - + +
117H LYS* 3.8 17.9 - - + -
118H ALA* 3.5 38.4 - - + +
121H LEU* 3.9 18.2 - - + -
135H GLN* 3.0 19.2 + - + +
136H ILE* 2.9 8.8 + - - +
138H THR* 1.3 77.7 + - - +
140H LYS* 1.3 63.6 + - - +
142H SER* 3.2 13.0 + - - -
143H LEU* 3.3 12.8 + - - +
161H ALA* 3.8 20.9 - - + -
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Residues in contact with LYS 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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34H LEU* 2.5 47.7 + - + +
36H VAL* 3.9 23.1 - - + +
136H ILE* 2.8 18.7 + - + +
137H LEU* 3.4 4.5 + - + +
139H LEU* 1.3 71.0 - - - +
141H ALA* 1.3 64.8 + - - +
143H LEU* 3.0 31.0 + - + +
146H GLY* 3.3 16.3 + - - +
147H LEU* 3.6 17.3 - - + +
148H SER 5.5 0.9 - - - +
151H LEU* 3.7 24.2 - - + -
19K G 4.8 11.7 + - - -
20K A 3.7 19.4 + - - -
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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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137H LEU 2.9 18.6 + - - +
138H THR* 3.7 4.5 - - - +
139H LEU 3.2 0.6 - - - -
140H LYS* 1.3 77.0 - - - +
142H SER* 1.3 57.7 + - - +
146H GLY* 3.3 14.9 - - - -
147H LEU* 3.5 27.0 + - + +
158H THR* 5.8 2.2 - - - +
159H ILE 5.4 0.2 - - - -
160H PRO* 3.7 33.0 - - + +
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Residues in contact with SER 142 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114H LEU* 3.5 19.3 - - - -
138H THR 4.4 1.3 - - - -
139H LEU 3.2 5.3 + - - -
140H LYS 3.1 0.6 - - - -
141H ALA* 1.3 76.3 - - - +
143H LEU* 1.3 59.7 + - - +
144H ASN 3.8 3.9 + - - +
160H PRO* 3.4 15.4 - - - +
161H ALA 2.6 30.1 + - - -
163H ARG* 2.9 40.0 + - - +
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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