Contacts of the helix formed by residues 132 - 150 (chain A) in PDB entry 3T79
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 132 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130A PHE* 3.3 12.2 - - - +
131A LYS* 1.3 97.1 - - + +
133A CYS* 1.3 59.9 + - - +
134A GLN* 2.5 33.5 + - + +
135A ASP* 3.0 25.6 + - - +
136A LYS* 3.4 14.8 + - - +
217A TYR* 5.0 18.6 - - + -
360A ASP* 4.4 8.3 - - - -
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Residues in contact with CYS 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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117A LEU 5.8 0.2 - - - -
118A TRP 4.6 1.1 - - - -
120A PRO* 3.6 39.9 - - - -
132A THR* 1.3 75.0 + - - +
134A GLN* 1.3 59.8 + - - +
135A ASP 3.4 0.7 - - - -
136A LYS* 3.3 14.8 - - - +
137A LEU* 2.9 31.7 + - - +
208A LEU* 4.7 2.7 - - + -
359A HIS* 3.7 33.0 - - + +
360A ASP* 3.4 29.9 + - + -
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Residues in contact with GLN 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A THR* 2.5 17.4 + - + +
133A CYS* 1.3 71.3 - - - +
135A ASP* 1.3 59.9 + - - +
137A LEU* 3.8 4.7 - - - +
138A LYS* 2.9 36.7 + - - +
205A TYR* 3.5 22.9 + - + -
208A LEU* 3.9 28.1 + - + +
209A ARG* 3.2 41.0 - - - +
217A TYR* 5.4 7.6 - - - +
220A ASP* 5.6 1.2 + - - -
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Residues in contact with ASP 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A LYS 5.0 0.2 - - - +
129A HIS* 4.5 2.8 - - - -
130A PHE* 3.3 35.2 + - + +
131A LYS* 3.5 3.1 + - - +
132A THR* 3.0 34.0 + - - +
134A GLN* 1.3 73.8 - - - +
136A LYS* 1.3 68.7 + - - +
138A LYS* 3.2 24.2 + - - +
139A LEU* 3.0 18.7 + - - +
251A TRP* 3.6 19.6 - - + -
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Residues in contact with LYS 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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116A ASN 4.6 0.4 + - - -
117A LEU* 3.3 42.4 - - + +
119A ASN 2.4 33.4 + - - +
120A PRO* 3.6 13.5 + - - -
122A THR* 3.1 32.9 + - - +
125A LEU* 5.5 1.3 - - - -
130A PHE* 3.9 33.1 - - + -
131A LYS 5.6 0.9 - - - -
132A THR 3.4 17.0 - - - +
133A CYS* 3.3 16.8 - - - +
135A ASP* 1.3 79.7 - - - +
137A LEU* 1.3 61.9 - - + +
139A LEU* 3.1 2.8 + - - +
140A LEU* 2.9 28.9 + - - +
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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
----------------------------------------------------------
117A LEU 4.4 8.7 - - - +
118A TRP* 3.7 32.3 - - + -
133A CYS* 2.9 16.7 + - + +
134A GLN* 4.1 3.6 - - - +
136A LYS* 1.3 81.2 - - + +
138A LYS* 1.3 56.7 + - - +
140A LEU* 4.0 19.1 - - + -
141A LEU* 2.9 30.5 + - - +
201A THR* 3.8 5.6 - - + +
204A VAL* 3.3 39.3 - - + -
205A TYR* 3.9 24.1 - - + +
208A LEU* 4.4 3.6 - - + -
359A HIS* 4.1 11.9 - - + +
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Residues in contact with LYS 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 GLN* 2.9 22.1 + - - +
135A ASP* 3.2 36.4 + - - +
137A LEU* 1.3 72.3 - - - +
139A LEU* 1.3 69.2 + - - +
141A LEU* 3.1 6.7 + - - +
142A ASP* 3.0 19.2 + - - +
205A TYR* 3.5 34.4 - - + +
234A ILE* 3.6 27.5 - - + +
235A ARG 3.6 26.2 - - - +
243A PRO* 4.7 5.6 - - + -
251A TRP* 3.9 17.1 - - + -
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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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117A LEU* 4.1 11.2 - - + -
130A PHE* 3.4 31.6 - - + -
135A ASP 3.0 9.0 + - - +
136A LYS 3.6 5.8 - - - +
138A LYS* 1.3 78.4 - - - +
140A LEU* 1.3 59.2 + - - +
142A ASP* 2.8 25.3 + - + +
143A PHE* 3.0 13.2 + - + +
234A ILE* 5.5 1.1 - - - -
248A LEU* 4.9 10.5 - - + -
251A TRP* 3.7 28.2 - - + +
252A TYR* 3.8 33.9 - - + +
255A ILE* 3.8 27.6 - - + -
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Residues in contact with LEU 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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113A ILE* 5.3 2.2 - - + -
114A SER* 3.5 24.9 - - - +
117A LEU* 3.5 26.2 - - + +
118A TRP* 3.5 29.8 - - + +
136A LYS 2.9 14.4 + - - +
137A LEU* 4.0 10.1 - - + +
139A LEU* 1.3 74.2 - - - +
141A LEU* 1.3 62.7 + - - +
143A PHE* 4.6 12.3 - - + +
144A GLN* 2.9 69.0 + - + +
201A THR* 3.6 16.8 - - + +
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Residues in contact with LEU 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 21.6 + - - +
138A LYS* 3.4 4.9 - - - +
139A LEU 3.1 0.2 - - - -
140A LEU* 1.3 74.9 - - - +
142A ASP* 1.3 70.4 + - - +
144A GLN* 3.9 1.2 - - - +
145A TRP* 2.9 26.7 + - + +
198A PRO* 3.0 34.3 - - + +
201A THR* 3.7 7.4 - - + -
202A MET* 3.4 29.4 - - + +
205A TYR* 4.6 7.9 - - + -
233A ILE* 3.6 25.4 - - + +
234A ILE* 3.5 25.8 - - + -
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Residues in contact with ASP 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 LYS 3.0 10.7 + - - +
139A LEU* 2.8 18.7 + - + +
141A LEU* 1.3 71.7 - - - +
143A PHE* 1.3 52.7 + - - +
145A TRP* 2.6 40.8 + - - +
146A LYS 2.9 6.1 + - - -
156A ARG* 2.8 36.6 + - - -
234A ILE* 4.2 13.6 - - + +
242A TYR* 3.1 22.8 + - - -
248A LEU* 5.0 9.4 - - + +
252A TYR* 2.9 30.0 + - + +
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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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109A ILE* 4.6 1.1 - - + -
110A LEU* 3.3 38.8 - - + -
113A ILE* 2.8 46.4 - - + -
114A SER* 4.7 1.8 - - - -
117A LEU* 6.4 0.2 - - + -
139A LEU* 3.0 11.2 + - + +
140A LEU* 4.1 9.4 - - + +
142A ASP* 1.3 75.7 - - - +
144A GLN* 1.3 77.4 + - + +
146A LYS* 3.2 5.1 + - - +
147A PHE* 2.9 33.9 + + - +
252A TYR* 2.7 39.7 - + + +
255A ILE* 6.4 0.9 - - + -
256A PHE* 4.6 6.7 - + - -
268A TRP* 4.0 17.4 - + - -
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Residues in contact with GLN 144 (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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110A LEU* 4.6 4.0 - - + -
114A SER* 3.1 11.5 + - - +
140A LEU* 2.9 56.4 + - + +
141A LEU 3.9 1.6 - - - +
143A PHE* 1.3 89.4 - - + +
145A TRP* 1.3 58.2 + - - +
147A PHE* 3.4 3.6 + - - +
148A ASN* 2.9 34.8 + - - +
195A PHE 2.9 25.4 + - - -
196A THR* 3.4 8.7 - - - +
197A CYS 2.9 7.6 - - - +
198A PRO* 2.8 41.0 - - + +
201A THR* 3.6 8.3 - - - -
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Residues in contact with TRP 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 LEU* 2.9 17.9 + - + +
142A ASP* 2.6 19.9 + - - +
144A GLN* 1.3 74.1 - - - +
146A LYS* 1.3 63.7 + - - -
148A ASN* 3.1 3.8 + - - +
149A THR* 2.8 42.0 + - + +
151A VAL* 5.8 2.2 - - + -
156A ARG* 3.2 50.3 - - + -
159A VAL* 3.5 17.3 - - + -
183A PRO* 6.3 0.2 - - + -
185A PHE* 3.6 39.1 - + - -
187A LEU* 4.0 21.5 - - + +
198A PRO* 4.5 6.3 - - + +
233A ILE* 4.3 24.5 - - + -
242A TYR* 3.1 30.5 - + - -
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Residues in contact with LYS 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 ASP 2.9 12.6 + - - +
143A PHE* 3.2 8.0 + - - +
145A TRP* 1.3 73.2 - - - +
147A PHE* 1.3 59.7 - - - +
149A THR* 4.0 5.8 - - - -
150A ASN* 2.5 54.9 + - - +
151A VAL 3.0 37.5 - - - +
156A ARG* 4.0 16.8 - - - +
267A HIS 2.6 28.4 + - - -
268A TRP* 3.7 35.4 - - + +
270A GLN 3.4 17.4 + - - -
271A VAL* 4.7 0.4 - - - +
272A ASN* 4.0 6.1 - - - +
275A TRP* 4.8 8.7 - - + -
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Residues in contact with PHE 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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103A TYR* 4.2 22.0 + + - -
106A VAL* 3.2 43.1 - - + -
107A ILE* 4.3 1.8 - - - -
109A ILE* 4.9 4.3 - - + -
110A LEU* 3.5 48.5 - - + -
143A PHE* 2.9 33.1 + + + +
144A GLN 3.4 6.7 - - - +
146A LYS* 1.3 79.4 - - - +
148A ASN* 1.3 68.9 + - - +
150A ASN* 4.3 2.4 + - - +
268A TRP* 5.1 7.2 - + - +
275A TRP* 4.1 25.7 - + - -
312A ARG* 3.9 21.1 - - - -
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Residues in contact with ASN 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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103A TYR* 4.8 1.2 + - - -
110A LEU* 5.0 3.8 - - - +
144A GLN* 2.9 19.7 + - - +
145A TRP 3.9 2.0 - - - +
147A PHE* 1.3 90.3 - - - +
149A THR* 1.3 61.1 + - - +
150A ASN* 5.1 0.5 - - - +
187A LEU* 3.9 14.6 - - + -
188A VAL 4.9 2.2 + - - -
196A THR 5.1 3.2 + - - +
198A PRO* 3.9 27.1 - - + +
278A PHE* 4.9 0.7 - - - -
310A MET* 3.3 39.9 - - - +
311A ASN* 3.6 36.7 + - - +
312A ARG* 4.7 10.1 + - - +
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Residues in contact with THR 149 (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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145A TRP* 2.8 54.0 + - + +
146A LYS* 4.0 1.1 - - - -
148A ASN* 1.3 73.7 - - - +
150A ASN* 1.3 71.8 + - - +
151A VAL* 3.0 30.3 - - + +
185A PHE* 2.9 35.8 - - - +
187A LEU* 4.6 4.9 - - - -
278A PHE* 4.1 13.0 + - - -
310A MET* 3.8 11.2 - - - +
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Residues in contact with ASN 150 (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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103A TYR* 6.2 0.2 - - - +
146A LYS* 2.5 36.0 + - - +
147A PHE 4.3 2.4 + - - +
148A ASN 3.5 1.8 - - - +
149A THR* 1.3 75.9 - - - +
151A VAL* 1.3 59.3 + - - +
271A VAL* 3.4 10.5 - - - +
272A ASN* 3.2 37.0 + - - +
275A TRP* 3.8 14.3 - - + +
276A PRO* 3.1 20.9 + - + +
277A GLN* 2.8 30.0 + - - +
310A MET* 4.9 2.2 - - + -
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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