Contacts of the helix formed by residues 121 - 136 (chain D) in PDB entry 3CMT
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 121 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119D PRO* 3.9 4.7 - - - +
120D ASP* 1.3 87.9 - - + +
122D GLY* 1.3 62.9 + - - +
123D GLU* 3.7 14.8 + - - +
124D GLN* 3.1 28.1 + - - +
125D ALA* 3.1 20.6 + - - +
150D THR 3.5 8.7 - - - -
152D LYS* 3.9 36.3 - - + +
155D ILE* 4.1 13.0 - - + -
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Residues in contact with GLY 122 (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 THR* 1.3 69.1 - - - +
123D GLU* 1.3 64.9 + - - +
125D ALA* 3.2 5.7 + - - +
126D LEU* 3.0 27.4 + - - +
149D LEU* 3.9 30.3 - - - -
150D THR 2.7 22.1 + - - +
170D MET* 4.1 9.6 - - - -
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Residues in contact with GLU 123 (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 THR* 3.3 5.2 - - - +
122D GLY* 1.3 75.5 - - - +
124D GLN* 1.3 52.6 + - - +
126D LEU* 3.3 6.3 + - - +
127D GLU* 2.8 41.2 + - + +
151D PRO* 3.5 8.0 - - - +
152D LYS* 2.7 47.4 + - + +
153D ALA 5.3 0.3 + - - -
166D LEU* 5.6 2.4 - - - +
170D MET* 3.6 31.0 - - + +
173D GLN* 6.3 1.6 - - - +
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Residues in contact with GLN 124 (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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118D GLN 4.9 0.2 - - - +
119D PRO* 3.4 10.0 - - + +
120D ASP* 3.4 48.5 + - - +
121D THR* 3.1 20.5 + - - +
123D GLU* 1.3 78.4 - - - +
125D ALA* 1.3 63.8 + - - +
127D GLU* 3.2 6.7 + - - +
128D ILE* 2.9 40.2 + - + +
1021D PHE* 3.7 47.9 + - + +
1025D SER* 4.5 8.3 - - - +
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Residues in contact with ALA 125 (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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93D ILE* 4.0 12.6 - - + +
119D PRO* 3.6 30.4 - - + +
121D THR 3.1 7.0 + - - +
122D GLY 3.2 9.8 + - - +
124D GLN* 1.3 78.7 - - - +
126D LEU* 1.3 57.8 + - + +
128D ILE* 3.4 6.5 + - - +
129D CYS* 3.2 29.8 + - - -
143D VAL* 5.5 1.6 - - + -
149D LEU* 3.8 23.6 - - + -
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Residues in contact with LEU 126 (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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122D GLY 3.0 21.1 + - - +
123D GLU* 3.9 4.7 - - - +
125D ALA* 1.3 74.6 - - - +
127D GLU* 1.3 60.6 + - - +
128D ILE 3.2 0.4 - - - -
129D CYS* 3.3 10.8 + - - +
130D ASP* 3.0 27.7 + - - +
143D VAL* 5.6 0.9 - - + -
149D LEU* 4.2 8.1 - - + -
170D MET* 3.9 22.7 - - + +
171D MET* 3.5 35.4 - - + -
174D ALA* 3.8 27.1 - - + -
178D LEU* 4.5 8.6 - - + +
191D PHE* 4.2 22.7 - - + -
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Residues in contact with GLU 127 (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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123D GLU* 2.8 22.0 + - + +
124D GLN 3.7 4.0 - - - +
126D LEU* 1.3 72.7 - - - +
128D ILE* 1.3 60.3 + - - +
130D ASP* 3.4 10.3 + - - +
131D ALA* 3.0 28.6 + - - +
134D ARG* 5.1 8.5 + - - -
177D LYS* 3.5 24.5 + - - +
1020D GLN* 4.7 9.5 + - - +
1021D PHE* 3.9 24.5 - - + -
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Residues in contact with ILE 128 (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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93D ILE* 3.9 22.4 - - + -
117D SER* 3.5 22.4 - - - +
119D PRO* 4.7 1.3 - - + -
124D GLN* 2.9 41.6 + - + +
125D ALA* 3.6 8.5 - - - +
126D LEU 3.2 0.2 - - - -
127D GLU* 1.3 73.6 - - - +
129D CYS* 1.3 66.7 + - - +
131D ALA* 3.2 6.9 + - - +
132D LEU* 3.0 34.9 + - + +
1017D ILE* 4.0 28.0 - - + -
1021D PHE* 4.4 10.3 - - + -
1025D SER* 4.6 4.7 - - - +
1026D ILE* 4.3 13.2 - - + -
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Residues in contact with CYS 129 (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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93D ILE* 4.1 5.6 - - - -
125D ALA 3.2 16.6 + - - -
126D LEU* 3.4 16.4 - - - +
128D ILE* 1.3 78.9 - - - +
130D ASP* 1.3 51.8 + - - +
132D LEU* 3.2 4.3 + - - +
133D ALA* 2.7 35.9 + - - +
141D ILE* 3.9 26.3 - - + +
143D VAL* 3.6 30.7 - - - -
178D LEU* 4.1 17.3 - - + -
189D LEU* 4.7 9.6 - - + -
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Residues in contact with ASP 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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126D LEU 3.0 16.3 + - - +
127D GLU* 3.7 13.2 - - - +
128D ILE 3.2 0.2 - - - -
129D CYS* 1.3 76.4 - - - +
131D ALA* 1.3 59.1 + - - +
133D ALA* 3.3 2.8 + - - +
134D ARG* 2.5 59.1 + - - +
177D LYS* 3.4 36.5 + - - +
178D LEU* 3.6 20.4 - - + +
181D ASN* 2.8 24.2 - - - +
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Residues in contact with ALA 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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127D GLU 3.0 13.5 + - - +
128D ILE* 3.5 8.3 - - - +
130D ASP* 1.3 77.6 - - - +
132D LEU* 1.3 57.7 + - - +
134D ARG* 3.4 21.7 + - - +
135D SER* 3.0 29.0 + - - -
1013D ALA* 4.4 7.4 - - + +
1016D GLN* 5.3 8.7 - - + +
1017D ILE* 4.0 25.4 - - + -
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Residues in contact with LEU 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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91D ALA* 3.7 28.9 - - + -
93D ILE* 4.7 5.8 - - + -
115D LEU* 4.7 1.3 - - + -
128D ILE* 3.0 34.2 + - + +
129D CYS 3.7 2.9 - - - +
131D ALA* 1.3 71.4 - - - +
133D ALA* 1.3 68.6 + - - +
135D SER* 2.7 23.6 + - - +
136D GLY* 3.6 2.1 + - - -
138D VAL* 3.8 30.1 + - + +
141D ILE* 3.8 16.8 - - + -
187D THR* 5.7 0.2 - - - -
1010D LEU* 5.4 0.4 - - + -
1013D ALA* 5.0 4.3 - - + -
1014D LEU* 4.5 14.8 - - + -
1017D ILE* 4.0 20.0 - - + -
1026D ILE* 4.3 13.7 - - + -
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Residues in contact with ALA 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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129D CYS 2.7 21.6 + - - +
130D ASP* 3.5 7.9 - - - +
132D LEU* 1.3 75.8 - - - +
134D ARG* 1.3 58.4 + - - +
136D GLY* 3.2 2.8 + - - -
141D ILE* 4.2 4.4 - - + +
178D LEU* 4.8 2.0 - - + -
181D ASN* 4.0 21.1 - - + +
182D LEU* 4.0 26.0 - - + -
185D SER* 2.5 31.9 + - - -
187D THR* 4.3 8.7 - - - -
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Residues in contact with ARG 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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127D GLU* 5.1 7.7 + - - -
130D ASP* 2.5 54.7 + - - +
131D ALA* 3.6 24.3 - - - +
133D ALA* 1.3 72.3 - - - +
135D SER* 1.3 62.2 + - - +
136D GLY* 3.2 1.7 + - - -
177D LYS* 5.0 1.6 - - - +
181D ASN* 3.2 34.7 + - - +
185D SER* 4.2 4.8 + - - -
1016D GLN* 5.3 9.7 - - - +
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Residues in contact with SER 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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131D ALA 3.0 15.7 + - - -
132D LEU* 2.7 22.2 + - - +
134D ARG* 1.3 76.2 - - - +
136D GLY* 1.3 59.2 + - - +
137D ALA* 3.1 17.6 + - - +
138D VAL* 4.1 3.5 + - - +
1009D ALA* 3.6 30.9 - - - +
1010D LEU* 5.0 0.7 - - - +
1013D ALA* 3.7 24.8 - - - +
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Residues in contact with GLY 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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132D LEU 3.6 0.8 + - - -
133D ALA 3.2 12.0 + - - -
134D ARG 3.1 4.6 - - - -
135D SER* 1.3 77.7 + - - +
137D ALA* 1.3 58.9 + - - +
138D VAL 3.6 5.4 - - - +
185D SER* 4.0 22.5 - - - +
1006D LYS* 3.7 18.6 - - - +
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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