Contacts of the helix formed by residues 133 - 148 (chain A) in PDB entry 3CMM
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 SER 133 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131A THR 3.9 2.8 + - - -
132A VAL* 1.3 78.7 - - - +
134A LEU* 1.3 60.4 + - - +
135A GLU* 3.6 9.4 + - - +
136A ASP* 3.2 23.1 + - - +
137A LYS* 2.8 27.3 + - - +
300A HIS* 4.4 10.5 - - - -
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Residues in contact with LEU 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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133A SER* 1.3 70.7 - - - +
135A GLU* 1.3 68.2 + - - +
137A LYS* 3.3 12.2 + - + +
138A VAL* 2.9 30.2 + - + +
155A GLU* 5.8 0.2 - - - +
269A LEU* 4.3 17.7 - - + -
273A LEU* 4.1 34.8 - - + -
297A GLN* 4.4 22.0 - - + +
300A HIS* 3.4 51.8 + - + +
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Residues in contact with GLU 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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133A SER* 3.3 9.1 + - - +
134A LEU* 1.3 80.4 - - - +
136A ASP* 1.3 66.5 + - - +
138A VAL* 3.2 13.8 + - - +
139A LYS* 3.2 47.7 + - - +
304A VAL* 5.3 12.9 - - + +
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Residues in contact with ASP 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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132A VAL* 3.9 13.4 - - + +
133A SER* 3.2 19.0 + - - +
135A GLU* 1.3 82.9 - - - +
137A LYS* 1.3 60.8 + - - +
139A LYS* 3.3 26.1 + - - +
140A ILE* 3.0 41.7 + - + +
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Residues in contact with LYS 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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128A ALA* 3.9 31.9 - - + -
129A THR 3.4 18.6 + - - -
130A ASP* 4.7 0.6 - - - +
132A VAL* 3.4 28.3 + - + +
133A SER 2.8 13.1 + - - +
134A LEU* 3.4 19.7 - - + +
136A ASP* 1.3 73.4 - - - +
138A VAL* 1.3 59.7 + - - +
140A ILE* 4.8 2.7 - - - -
141A ASN* 3.0 32.2 + - - +
151A PHE* 3.8 11.2 - - + -
153A SER* 4.0 13.1 + - - +
154A SER 4.2 3.6 + - - -
155A GLU* 3.2 35.7 + - - +
269A LEU* 3.9 13.1 - - + +
300A HIS* 4.9 0.2 - - - -
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Residues in contact with VAL 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 LEU* 2.9 20.7 + - + +
135A GLU* 3.2 9.8 + - - +
137A LYS* 1.3 76.3 - - - +
139A LYS* 1.3 60.9 + - + +
141A ASN* 4.0 4.6 - - - +
142A GLU* 3.1 28.0 + - + +
269A LEU* 4.2 15.9 - - + -
270A LYS* 4.2 32.5 - - + +
273A LEU* 3.9 28.0 - - + -
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Residues in contact with LYS 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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135A GLU* 3.2 41.2 + - + +
136A ASP* 3.5 27.0 + - - +
137A LYS 3.2 0.2 - - - -
138A VAL* 1.3 79.4 - - + +
140A ILE* 1.3 66.5 + - + +
142A GLU* 3.4 6.6 + - - +
143A PHE* 3.2 18.7 + - - +
723C TYR* 3.0 67.9 + - + +
759C LYS* 4.5 9.7 - - - +
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Residues in contact with ILE 140 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A LEU* 3.9 22.7 - - + -
114A LEU* 4.2 17.5 - - + -
120A LEU* 6.6 0.2 - - + -
126A VAL* 4.3 14.8 - - + -
128A ALA* 5.5 0.9 - - + -
132A VAL* 4.3 13.0 - - + -
136A ASP* 3.0 29.7 + - + +
137A LYS* 4.2 3.1 - - - +
138A VAL 3.4 0.2 - - - -
139A LYS* 1.3 75.2 - - + +
141A ASN* 1.3 62.1 + - - +
143A PHE* 3.1 9.6 + - + +
144A CYS* 2.9 39.7 + - - -
151A PHE* 3.9 17.0 - - + -
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Residues in contact with ASN 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 LYS 3.0 19.0 + - - +
138A VAL 4.0 4.1 - - - +
140A ILE* 1.3 79.4 - - - +
142A GLU* 1.3 57.7 + - - +
144A CYS* 4.3 0.9 - - - -
145A HIS* 2.8 30.6 + - - +
151A PHE* 3.5 41.1 - - + +
166A ASP* 2.8 31.7 + - - +
268A SER* 3.5 9.2 - - - -
269A LEU* 2.8 36.0 + - + +
270A LYS 4.2 1.4 + - - -
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Residues in contact with GLU 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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138A VAL* 3.1 20.7 + - + +
139A LYS* 3.6 9.4 - - - +
140A ILE 3.1 0.6 - - - -
141A ASN* 1.3 79.5 - - - +
143A PHE* 1.3 54.0 + - - +
145A HIS* 4.0 4.7 - - - +
146A SER* 2.5 36.6 + - - -
268A SER* 4.5 15.1 + - - -
270A LYS* 5.6 7.6 - - - +
721C ASP* 3.6 24.1 - - - +
723C TYR* 4.0 2.2 - - + -
724C ASN* 2.7 43.8 + - - +
727C HIS* 5.6 0.2 - - - -
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Residues in contact with PHE 143 (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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117A VAL* 3.5 33.4 - - + -
120A LEU* 3.8 34.5 - - + -
121A SER* 4.5 7.4 - - - -
139A LYS 3.2 8.3 + - - +
140A ILE* 3.1 13.3 + - + +
142A GLU* 1.3 77.5 - - - +
144A CYS* 1.3 69.5 + - - +
146A SER* 3.5 2.7 + - - -
147A SER* 2.7 45.7 + - - -
149A ILE* 4.2 13.0 - - + -
723C TYR* 3.1 28.9 + + + +
725C ASN* 3.4 27.8 - - + -
728C PHE* 5.6 3.6 - + + -
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Residues in contact with CYS 144 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126A VAL* 3.8 23.3 - - - -
140A ILE* 2.9 28.5 + - - +
141A ASN 3.7 3.1 - - - +
143A PHE* 1.3 83.9 - - - +
145A HIS* 1.3 68.7 + - - +
147A SER* 2.8 11.8 + - - -
148A GLY 2.8 11.8 + - - -
149A ILE* 3.0 49.8 + - + +
151A PHE* 4.0 14.8 - - + -
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Residues in contact with HIS 145 (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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141A ASN* 2.8 22.3 + - - +
142A GLU* 4.0 8.1 - - - +
144A CYS* 1.3 76.3 - - - +
146A SER* 1.3 62.5 + - - +
147A SER 3.2 0.3 + - - -
148A GLY* 3.2 10.3 + - - -
149A ILE 4.0 3.3 + - - -
151A PHE* 5.6 0.4 - - - +
166A ASP* 2.7 35.3 + - - +
168A GLY* 3.7 19.2 - - - -
169A ASP* 3.0 28.0 + - + +
266A PHE 3.2 26.0 + - - -
268A SER* 4.0 21.1 + - - -
271A GLN* 5.7 0.8 + - - -
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Residues in contact with SER 146 (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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142A GLU* 2.5 24.4 + - - -
143A PHE 3.5 3.8 + - - -
145A HIS* 1.3 80.9 - - - +
147A SER* 1.3 58.5 + - - +
148A GLY 3.5 0.2 - - - -
724C ASN* 3.8 28.1 - - - -
725C ASN* 3.2 29.9 + - - +
726C ASP* 4.2 14.9 - - - +
843C GLN* 5.1 1.1 - - - -
849C THR* 5.1 6.3 + - - -
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Residues in contact with SER 147 (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 SER* 5.5 2.9 - - - -
143A PHE* 2.7 30.8 + - - -
144A CYS 2.8 4.6 + - - -
146A SER* 1.3 77.7 - - - +
148A GLY* 1.3 61.5 + - - +
149A ILE* 3.4 24.4 - - - +
725C ASN* 3.3 29.0 + - - +
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Residues in contact with GLY 148 (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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124A GLN* 5.1 0.5 - - - +
144A CYS 2.8 3.4 + - - -
145A HIS* 3.2 10.4 + - - -
146A SER 3.5 0.4 - - - -
147A SER* 1.3 80.2 - - - +
149A ILE* 1.3 61.2 + - - +
150A ARG* 3.7 22.6 + - - -
167A LEU 6.0 0.2 - - - -
168A GLY* 6.0 5.8 - - - -
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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