Contacts of the helix formed by residues 129 - 142 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44A THR* 3.5 6.4 - - - +
125A LYS 4.7 1.4 + - - -
126A GLU* 3.5 18.6 + - - +
127A HIS 3.1 1.3 - - - +
128A LEU* 1.3 82.2 + - - +
130A GLU* 1.3 69.4 + - + +
131A GLU* 3.7 18.4 - - + +
132A GLY 4.1 2.2 - - - -
133A LEU* 3.0 24.8 + - - +
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Residues in contact with GLU 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A THR* 3.8 11.5 - - + +
129A THR* 1.3 76.6 - - + +
131A GLU* 1.3 57.8 + - - +
133A LEU* 3.5 5.7 + - - +
134A ASN* 2.8 42.0 + - - +
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Residues in contact with GLU 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A THR* 3.2 13.3 - - + +
130A GLU* 1.3 77.3 - - - +
132A GLY* 1.3 60.4 + - - +
134A ASN* 3.3 7.3 + - - +
135A GLN* 3.0 33.3 + - + +
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Residues in contact with GLY 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A LEU* 4.5 4.1 - - - +
126A GLU* 3.2 31.8 + - - -
127A HIS* 4.3 2.5 - - - -
129A THR* 3.5 4.8 + - - -
130A GLU 3.4 0.2 - - - -
131A GLU* 1.3 80.8 - - - +
133A LEU* 1.3 56.4 + - - +
135A GLN* 3.2 10.6 + - - +
136A ILE* 2.9 35.9 + - - +
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Residues in contact with LEU 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A VAL* 4.6 1.6 - - + -
44A THR* 3.6 30.1 - - + +
46A TRP* 3.9 27.8 - - + +
48A VAL* 3.5 28.0 - - + -
126A GLU 4.2 0.8 + - - -
127A HIS 4.1 11.8 + - - +
129A THR 3.0 20.7 + - - +
130A GLU* 3.6 5.4 - - - +
132A GLY* 1.3 75.2 - - - +
134A ASN* 1.3 63.3 + - - +
136A ILE* 3.1 7.8 + - + +
137A LEU* 2.9 46.9 + - + +
155A PHE* 4.0 14.8 - - + -
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Residues in contact with ASN 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A GLU* 2.8 31.1 + - - +
131A GLU* 3.3 6.6 + - - +
133A LEU* 1.3 75.8 - - - +
135A GLN* 1.3 62.3 + - - +
137A LEU* 3.2 9.7 + - - +
138A THR* 3.0 26.3 + - + +
155A PHE* 3.8 30.6 - - - +
158A THR* 5.0 5.5 + - - +
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Residues in contact with GLN 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A LEU* 4.0 30.7 - - + +
126A GLU* 5.3 1.6 - - - +
131A GLU* 3.0 22.1 + - + +
132A GLY* 3.6 8.4 - - - +
134A ASN* 1.3 72.7 - - - +
136A ILE* 1.3 66.5 + - - +
138A THR* 2.3 36.9 + - - +
139A LEU* 3.0 12.8 + - + +
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Residues in contact with ILE 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A LEU* 4.4 17.5 - - + -
36A VAL* 4.9 5.6 - - + -
48A VAL* 3.7 34.1 - - + -
118A ALA* 4.7 5.8 - - + +
121A LEU* 3.9 20.0 - - + -
122A ILE* 3.9 13.2 - - + -
127A HIS* 3.5 33.2 - - + -
132A GLY 2.9 17.4 + - - +
133A LEU* 3.3 9.0 - - - +
135A GLN* 1.3 76.5 - - - +
137A LEU* 1.3 60.3 + - + +
139A LEU* 2.9 11.6 + - - +
140A LYS* 2.8 25.0 + - + +
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Residues in contact with LEU 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A VAL* 4.3 22.0 - - + -
133A LEU* 2.9 50.7 + - + +
134A ASN* 3.2 11.4 + - - +
136A ILE* 1.3 75.2 - - + +
138A THR* 1.3 59.4 + - - +
140A LYS* 4.3 5.4 - - - -
141A ALA* 2.9 31.5 + - - +
147A LEU* 3.7 22.1 - - + +
151A LEU* 5.0 6.5 - - + +
155A PHE* 3.3 50.5 - - + -
158A THR* 4.3 11.9 - - + +
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Residues in contact with THR 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A ASN* 3.0 16.7 + - + +
135A GLN* 2.3 37.1 + - + +
137A LEU* 1.3 76.9 - - - +
139A LEU* 1.3 63.1 + - - +
141A ALA* 3.7 3.1 + - - +
142A SER 3.9 1.4 + - - -
158A THR* 4.3 9.4 - - + +
159A ILE 3.4 28.0 - - - +
160A PRO* 3.6 7.0 - - - +
161A ALA* 2.7 34.9 + - - +
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Residues in contact with LEU 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A LEU* 4.7 5.8 - - + -
114A LEU* 3.7 32.3 - - + +
117A LYS* 3.8 18.2 - - + -
118A ALA* 3.5 38.6 - - + +
121A LEU* 3.9 18.2 - - + -
135A GLN* 3.0 13.4 + - + +
136A ILE* 2.9 8.6 + - - +
138A THR* 1.3 82.3 + - - +
140A LYS* 1.3 64.6 + - - +
142A SER* 3.2 10.6 + - - -
143A LEU* 3.2 12.8 + - - +
161A ALA* 3.8 20.0 - - + -
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Residues in contact with LYS 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A LEU* 2.7 47.2 + - + +
36A VAL* 4.0 22.4 - - + +
136A ILE* 2.8 18.9 + - + +
137A LEU* 3.9 4.3 - - + +
139A LEU* 1.3 70.3 - - - +
141A ALA* 1.3 66.6 + - - +
143A LEU* 2.9 31.5 + - + +
146A GLY* 3.3 18.7 + - - +
147A LEU* 3.6 18.6 - - + +
148A SER 5.4 0.4 - - - +
151A LEU* 3.7 23.8 - - + -
19X G 4.6 13.3 + - - -
20X A 3.7 19.1 + - - -
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Residues in contact with ALA 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A LEU 2.9 18.6 + - - +
138A THR* 3.8 4.5 - - - +
139A LEU 3.2 0.4 - - - -
140A LYS* 1.3 77.3 - - - +
142A SER* 1.3 57.8 + - - +
146A GLY* 3.3 14.7 - - - -
147A LEU* 3.7 27.9 + - + +
158A THR* 4.9 2.5 - - + -
160A PRO* 3.6 34.2 - - + +
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Residues in contact with SER 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A LEU* 3.5 20.0 - - - -
138A THR 4.5 0.9 - - - -
139A LEU 3.2 4.2 + - - -
140A LYS 3.1 0.2 - - - -
141A ALA* 1.3 76.0 - - - +
143A LEU* 1.3 59.6 - - - +
144A ASN 3.8 3.7 + - - +
160A PRO* 3.4 15.8 - - - +
161A ALA 2.6 30.3 + - - -
163A 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