Contacts of the helix formed by residues 129 - 142 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44D THR* 3.5 5.9 - - - +
125D LYS 4.7 1.6 + - - -
126D GLU* 3.5 17.7 + - - -
127D HIS 3.1 1.0 - - - -
128D LEU* 1.3 82.8 - - - +
130D GLU* 1.3 69.8 + - + +
131D GLU* 3.7 18.2 - - + +
132D GLY 4.1 2.7 - - - -
133D LEU* 3.0 25.1 + - - +
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Residues in contact with GLU 130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44D THR* 3.8 12.3 - - + +
129D THR* 1.3 77.7 - - + +
131D GLU* 1.3 56.9 + - - +
133D LEU* 3.6 4.9 - - - +
134D ASN* 2.8 42.3 + - - +
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Residues in contact with GLU 131 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129D THR* 3.2 12.4 - - + +
130D GLU* 1.3 77.1 - - - +
132D GLY* 1.3 61.0 + - - +
134D ASN* 3.3 7.8 + - - +
135D GLN* 3.0 32.3 + - + +
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Residues in contact with GLY 132 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121D LEU* 4.5 4.5 - - - +
126D GLU* 3.2 31.3 + - - -
127D HIS* 4.3 2.0 - - - -
129D THR* 3.5 4.9 + - - -
130D GLU 3.4 0.2 - - - -
131D GLU* 1.3 76.8 - - - +
133D LEU* 1.3 60.5 + - - +
135D GLN* 3.2 10.5 + - - +
136D ILE* 2.9 35.8 + - - +
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Residues in contact with LEU 133 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36D VAL* 4.6 1.6 - - + -
44D THR* 3.7 31.0 - - + +
46D TRP* 3.9 27.1 - - + +
48D VAL* 3.5 28.3 - - + -
126D GLU 4.1 1.2 + - - -
127D HIS* 4.0 12.2 + - - +
129D THR 3.0 18.4 + - - +
130D GLU* 3.6 6.3 - - - +
132D GLY* 1.3 76.5 - - - +
134D ASN* 1.3 64.3 + - - +
136D ILE* 3.1 7.5 + - + +
137D LEU* 2.9 46.9 + - + +
155D PHE* 4.1 14.1 - - + -
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Residues in contact with ASN 134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130D GLU* 2.8 30.7 + - - +
131D GLU* 3.3 7.8 + - - +
133D LEU* 1.3 76.3 - - - +
135D GLN* 1.3 62.5 + - - +
137D LEU* 3.2 9.9 + - - +
138D THR* 3.0 26.0 + - + +
155D PHE* 3.8 29.4 - - - +
158D THR* 5.0 4.4 + - - +
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Residues in contact with GLN 135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121D LEU* 4.0 29.8 - - + +
126D GLU* 5.3 1.0 - - - +
131D GLU* 3.0 21.1 + - + +
132D GLY* 3.6 8.2 - - - +
133D LEU 3.2 0.2 - - - -
134D ASN* 1.3 73.4 - - - +
136D ILE* 1.3 66.6 + - - +
138D THR* 2.3 36.8 + - + +
139D LEU* 3.0 13.2 + - + +
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Residues in contact with ILE 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34D LEU* 4.5 17.0 - - + +
36D VAL* 4.9 5.8 - - + -
48D VAL* 3.7 33.7 - - + -
118D ALA* 4.6 5.4 - - + +
121D LEU* 3.9 20.9 - - + -
122D ILE* 3.9 13.2 - - + -
127D HIS* 3.5 32.8 - - + -
132D GLY 2.9 17.6 + - - +
133D LEU* 3.1 9.8 + - + +
135D GLN* 1.3 75.5 - - - +
137D LEU* 1.3 61.2 + - + +
139D LEU* 2.9 12.2 + - - +
140D LYS* 2.8 26.1 + - + +
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Residues in contact with LEU 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36D VAL* 4.3 22.2 - - + -
133D LEU* 2.9 50.5 + - + +
134D ASN* 3.2 11.9 + - - +
136D ILE* 1.3 75.3 - - + +
138D THR* 1.3 59.9 + - - +
140D LYS* 4.2 4.9 - - - -
141D ALA* 2.9 31.2 + - - +
147D LEU* 3.8 20.6 - - + +
151D LEU* 5.0 7.4 - - + +
155D PHE* 3.3 50.5 - - + -
158D THR* 4.3 11.9 - - + +
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Residues in contact with THR 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134D ASN* 3.0 18.2 + - + +
135D GLN* 2.3 36.2 + - + +
137D LEU* 1.3 76.1 - - - +
139D LEU* 1.3 62.4 + - - +
141D ALA* 3.7 3.3 + - - +
142D SER 3.9 1.0 + - - -
158D THR* 4.4 11.0 - - + -
159D ILE 3.4 26.7 - - - +
160D PRO* 3.6 5.5 - - - +
161D ALA* 2.7 34.9 + - - +
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Residues in contact with LEU 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34D LEU* 4.7 6.5 - - + -
114D LEU* 3.7 36.9 - - + +
117D LYS* 3.8 18.4 - - + -
118D ALA* 3.4 38.6 - - + +
121D LEU* 3.9 18.2 - - + -
135D GLN* 3.0 16.1 + - + +
136D ILE* 2.9 9.2 + - - +
138D THR* 1.3 81.2 + - - +
140D LYS* 1.3 64.5 + - - +
142D SER* 3.2 10.9 + - - -
143D LEU* 3.2 12.7 + - - +
161D ALA* 3.9 14.1 - - + -
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Residues in contact with LYS 140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34D LEU* 2.5 47.8 + - + +
36D VAL* 3.9 23.6 - - + +
136D ILE* 2.8 20.0 + - + +
137D LEU* 3.4 4.0 + - + +
139D LEU* 1.3 70.4 - - - +
141D ALA* 1.3 64.8 + - - +
143D LEU* 3.0 30.8 + - + +
146D GLY* 3.3 16.2 + - - +
147D LEU* 3.6 17.3 - - + +
148D SER 5.6 0.7 - - - +
151D LEU* 3.7 25.1 - - + -
19G G 4.8 12.1 + - - -
20G A 3.7 19.2 + - - -
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Residues in contact with ALA 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137D LEU 2.9 17.8 + - - +
138D THR* 3.7 4.3 - - - +
139D LEU 3.2 0.4 - - - -
140D LYS* 1.3 77.2 - - - +
142D SER* 1.3 58.2 + - - +
146D GLY* 3.2 15.2 - - - -
147D LEU* 3.5 26.8 + - + +
158D THR* 4.8 2.7 - - + -
160D PRO* 3.7 32.3 - - + +
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Residues in contact with SER 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114D LEU* 3.5 17.9 - - - -
138D THR 4.4 1.8 - - - -
139D LEU 3.2 5.1 + - - -
140D LYS 3.1 0.4 - - - -
141D ALA* 1.3 76.2 - - - +
143D LEU* 1.3 60.4 + - - +
144D ASN 3.7 4.0 + - - +
160D PRO* 3.4 15.8 - - - +
161D ALA 2.6 31.1 + - - -
163D 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