Contacts of the helix formed by residues 129 - 142 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44L THR* 3.6 5.8 - - - +
125L LYS 4.8 1.4 + - - -
126L GLU* 3.5 18.3 + - - -
127L HIS 3.1 0.8 - - - +
128L LEU* 1.3 81.8 + - - +
130L GLU* 1.3 68.6 + - + +
131L GLU* 3.7 18.6 - - + +
132L GLY 4.1 2.2 - - - -
133L LEU* 3.0 25.5 + - - +
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Residues in contact with GLU 130 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44L THR* 3.8 11.9 - - + +
129L THR* 1.3 76.6 - - + +
131L GLU* 1.3 57.9 + - - +
133L LEU* 3.5 5.7 + - - +
134L ASN* 2.8 41.2 + - - +
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Residues in contact with GLU 131 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129L THR* 3.2 13.1 - - + +
130L GLU* 1.3 76.9 - - - +
132L GLY* 1.3 60.5 + - - +
134L ASN* 3.3 7.3 + - - +
135L GLN* 3.0 33.4 + - + +
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Residues in contact with GLY 132 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121L LEU* 4.5 4.8 - - - +
126L GLU* 3.2 30.7 + - - -
127L HIS* 4.3 2.2 - - - -
129L THR* 3.6 4.6 + - - -
130L GLU 3.4 0.2 - - - -
131L GLU* 1.3 77.7 - - - +
133L LEU* 1.3 59.3 + - - +
135L GLN* 3.2 10.5 + - - +
136L ILE* 2.9 36.3 + - - +
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Residues in contact with LEU 133 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36L VAL* 4.6 1.8 - - + -
44L THR* 3.7 29.6 - - + +
46L TRP* 4.0 21.5 - - + +
48L VAL* 3.6 27.6 - - + -
126L GLU 4.2 1.0 + - - -
127L HIS* 4.1 12.0 + - - +
129L THR 3.0 19.7 + - - +
130L GLU* 3.6 6.5 - - - +
132L GLY* 1.3 75.8 - - - +
134L ASN* 1.3 63.8 + - - +
136L ILE* 3.1 6.4 + - - +
137L LEU* 2.9 47.3 + - + +
155L PHE* 4.0 21.1 - - + -
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Residues in contact with ASN 134 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130L GLU* 2.8 30.3 + - - +
131L GLU* 3.3 6.8 + - - +
133L LEU* 1.3 77.5 - - - +
135L GLN* 1.3 62.7 + - - +
137L LEU* 3.2 8.1 + - - +
138L THR* 3.0 26.5 + - + +
155L PHE* 3.8 27.4 - - - +
158L THR* 4.8 13.5 - - + +
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Residues in contact with GLN 135 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121L LEU* 4.0 29.3 - - + +
126L GLU* 5.4 1.2 - - - +
131L GLU* 3.0 21.6 + - + +
132L GLY* 3.6 8.4 - - - +
134L ASN* 1.3 72.1 - - - +
136L ILE* 1.3 67.3 + - - +
138L THR* 2.3 37.0 + - - +
139L LEU* 3.0 13.4 + - + +
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Residues in contact with ILE 136 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34L LEU* 4.4 17.7 - - + -
36L VAL* 4.9 5.2 - - + -
48L VAL* 3.7 33.9 - - + -
118L ALA* 4.6 6.1 - - + +
121L LEU* 3.9 20.2 - - + -
122L ILE* 3.9 13.2 - - + -
127L HIS* 3.5 32.8 - - + -
132L GLY 2.9 16.8 + - - +
133L LEU* 3.3 9.0 - - - +
135L GLN* 1.3 76.7 - - - +
137L LEU* 1.3 60.3 + - + +
139L LEU* 2.9 11.9 + - - +
140L LYS* 2.8 25.4 + - + +
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Residues in contact with LEU 137 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36L VAL* 4.3 22.4 - - + -
133L LEU* 2.9 50.0 + - + +
134L ASN* 3.5 9.9 - - - +
135L GLN 3.2 0.2 - - - -
136L ILE* 1.3 75.0 - - + +
138L THR* 1.3 58.9 + - - +
140L LYS* 4.3 5.4 - - - -
141L ALA* 2.9 31.4 + - - +
147L LEU* 3.8 23.2 - - + +
151L LEU* 5.0 6.7 - - + +
155L PHE* 3.3 50.9 - - + -
158L THR* 4.4 12.1 - - + -
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Residues in contact with THR 138 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134L ASN* 3.0 16.7 + - + +
135L GLN* 2.3 35.9 + - + +
137L LEU* 1.3 76.3 - - - +
139L LEU* 1.3 62.6 + - - +
141L ALA* 3.7 4.0 + - - +
142L SER 3.9 1.4 + - - -
158L THR* 5.4 6.1 - - + -
159L ILE 3.4 30.1 - - - +
160L PRO* 3.6 7.2 - - - +
161L ALA* 2.7 35.7 + - - +
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Residues in contact with LEU 139 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34L LEU* 4.7 6.1 - - + -
114L LEU* 3.8 30.0 - - + +
117L LYS* 3.8 18.2 - - + -
118L ALA* 3.5 38.1 - - + +
121L LEU* 3.9 17.3 - - + -
135L GLN* 3.0 18.7 + - + +
136L ILE* 2.9 8.6 + - - +
138L THR* 1.3 77.8 + - - +
140L LYS* 1.3 65.0 + - - +
142L SER* 3.2 13.0 + - - -
143L LEU* 3.2 13.1 + - - +
161L ALA* 3.8 20.2 - - + -
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Residues in contact with LYS 140 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34L LEU* 2.5 47.4 + - + +
36L VAL* 3.8 23.8 - - + +
136L ILE* 2.8 17.9 + - + +
137L LEU* 3.9 3.6 - - + +
139L LEU* 1.3 71.0 - - - +
141L ALA* 1.3 66.4 + - - +
143L LEU* 3.0 31.0 + - + +
146L GLY* 3.3 17.6 + - - +
147L LEU* 3.6 18.4 - - + +
148L SER 5.5 0.7 - - - +
151L LEU* 3.7 25.1 - - + -
19P G 4.8 11.5 + - - -
20P A 3.8 19.2 + - - -
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Residues in contact with ALA 141 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137L LEU 2.9 18.4 + - - +
138L THR* 3.7 4.0 - - - +
139L LEU 3.2 0.4 - - - -
140L LYS* 1.3 77.3 - - - +
142L SER* 1.3 56.9 + - - +
146L GLY* 3.3 14.9 - - - -
147L LEU* 3.6 27.3 + - + +
158L THR* 5.7 2.7 - - - +
159L ILE 5.4 0.2 - - - -
160L PRO* 3.7 33.7 - - + +
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Residues in contact with SER 142 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114L LEU* 3.5 18.8 - - - -
138L THR 4.4 1.6 - - - -
139L LEU 3.2 4.9 + - - -
140L LYS 3.1 0.2 - - - -
141L ALA* 1.3 76.0 - - - +
143L LEU* 1.3 60.2 - - - +
144L ASN 3.8 3.9 + - - +
160L PRO* 3.3 16.0 - - - +
161L ALA 2.6 30.0 + - - -
163L ARG* 2.9 39.7 + - - +
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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