Contacts of the helix formed by residues 132 - 149 (chain D) in PDB entry 3L49
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 ASN 132 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139C GLU* 3.5 23.0 + - - +
142C LEU* 3.7 10.4 - - - +
131D SER* 1.3 71.5 - - - +
133D ASN* 1.3 58.3 + - - +
134D TYR* 3.3 19.8 + - - +
135D SER* 2.9 37.5 + - - -
136D ILE* 2.9 30.8 + - - +
299D PHE* 4.0 31.0 - - + +
300D ALA 4.5 2.8 + - - -
302D ALA* 5.7 0.8 - - - +
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Residues in contact with ASN 133 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119D ASP* 4.5 0.8 + - - -
130D THR* 3.2 18.6 + - - +
131D SER* 2.9 25.7 + - - +
132D ASN* 1.3 70.2 + - - +
134D TYR* 1.3 63.8 + - + +
136D ILE* 3.5 19.1 - - - +
137D GLY* 2.9 25.2 + - - -
165D VAL* 3.4 18.5 - - - +
168D ILE* 3.5 30.8 - - + +
169D ARG* 2.9 41.2 + - + +
272D GLN* 4.5 1.9 + - - +
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Residues in contact with TYR 134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134C TYR 5.9 0.4 - - - -
138C ALA* 3.7 20.2 - - + -
142C LEU* 4.1 24.0 - - + +
172C GLN* 5.0 0.7 - - - -
175C TYR* 3.6 37.4 + + - -
176C VAL* 4.0 25.4 + - + +
179C ALA* 3.9 23.0 - - - +
180C PHE* 5.3 1.6 - - - -
132D ASN* 3.3 13.4 - - - +
133D ASN* 1.3 81.1 - - - +
135D SER* 1.3 56.9 + - - +
138D ALA* 3.0 24.9 + - - +
168D ILE* 3.7 37.7 - - + +
172D GLN* 3.1 20.8 + - - +
299D PHE* 5.2 5.6 - + - -
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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
----------------------------------------------------------
135C SER* 3.8 22.4 + - - +
138C ALA* 4.8 1.7 - - - +
139C GLU* 3.3 19.2 + - - +
132D ASN* 2.9 33.5 + - - -
134D TYR* 1.3 74.7 - - - +
136D ILE* 1.3 66.0 + - - +
138D ALA* 3.8 1.5 - - - +
139D GLU* 2.9 40.8 + - - +
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Residues in contact with ILE 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131D SER* 3.7 21.5 - - - -
132D ASN 2.9 22.6 + - - +
133D ASN* 3.5 25.1 - - - +
135D SER* 1.3 72.2 - - - +
137D GLY* 1.3 65.0 + - - +
139D GLU* 3.8 3.6 - - - +
140D LEU* 2.9 25.5 + - - +
169D ARG* 4.6 2.9 - - + -
249D VAL* 3.7 23.8 - - + -
270D ALA* 3.6 27.1 - - + +
272D GLN* 4.4 11.9 - - + -
302D ALA* 3.9 23.3 - - + -
304D LEU* 5.4 0.6 - - - +
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Residues in contact with GLY 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133D ASN 2.9 23.2 + - - -
134D TYR 3.9 0.4 - - - -
136D ILE* 1.3 78.5 - - - +
138D ALA* 1.3 62.0 + - - +
140D LEU* 3.7 5.5 + - - +
141D ALA* 3.4 18.9 + - - +
169D ARG* 4.2 19.3 - - - +
172D GLN* 3.7 15.3 - - - +
173D MET* 4.3 3.5 + - - +
222D TRP* 5.3 1.5 + - - -
249D VAL* 5.9 0.4 - - - -
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Residues in contact with ALA 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134C TYR* 3.8 24.7 - - + -
135C SER* 4.7 4.7 - - - +
134D TYR 3.0 19.9 + - - +
135D SER* 3.8 4.7 - - - +
137D GLY* 1.3 75.5 - - - +
139D GLU* 1.3 58.4 + - - +
141D ALA* 3.3 5.9 + - - +
142D LEU* 3.0 34.0 + - + +
172D GLN* 3.6 20.4 - - - +
176D VAL* 3.9 10.4 - - + +
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Residues in contact with GLU 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132C ASN* 3.5 23.1 + - - +
135C SER* 3.5 14.3 + - - +
139C GLU* 5.3 1.4 - - - +
135D SER* 2.9 32.6 + - - +
136D ILE* 4.0 3.4 - - - +
138D ALA* 1.3 70.7 - - - +
140D LEU* 1.3 64.5 + - - +
142D LEU* 3.8 8.2 - - - +
143D GLN* 3.0 23.4 + - - +
304D LEU* 3.7 32.0 + - + +
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Residues in contact with LEU 140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136D ILE* 2.9 19.4 + - + +
137D GLY* 3.9 5.2 - - - +
139D GLU* 1.3 73.2 - - - +
141D ALA* 1.3 65.1 + - - +
143D GLN* 3.3 5.4 + - - +
144D MET* 3.1 21.9 + - - +
222D TRP* 3.5 29.8 - - + +
223D ALA 4.3 1.1 - - - +
247D TYR* 4.1 17.3 - - + -
248D GLY* 3.7 28.0 - - - +
249D VAL* 3.8 26.5 - - + -
268D ALA* 4.0 14.6 - - + +
270D ALA* 4.5 1.6 - - + +
304D LEU* 3.8 25.0 - - + +
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Residues in contact with ALA 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137D GLY 3.4 4.1 + - - +
138D ALA 3.3 9.3 + - - +
140D LEU* 1.3 79.4 - - - +
142D LEU* 1.3 55.9 + - - +
144D MET* 3.2 15.7 + - + +
145D VAL* 3.0 31.7 + - - +
173D MET* 3.6 38.3 - - + +
176D VAL* 3.9 16.6 - - + -
177D LEU* 4.7 4.0 - - + -
222D TRP* 5.1 1.3 - - - +
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Residues in contact with LEU 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132C ASN* 3.9 23.3 - - - +
134C TYR* 3.9 21.3 - - + -
297C PHE* 3.2 39.6 - - + -
299C PHE* 3.8 30.3 - - + -
138D ALA* 3.0 26.6 + - + +
139D GLU* 3.8 6.5 - - - +
140D LEU 3.3 0.2 - - - -
141D ALA* 1.3 76.2 - - - +
143D GLN* 1.3 57.0 + - - +
145D VAL* 3.4 2.4 + - - +
146D ALA* 3.0 24.1 + - - +
176D VAL* 4.0 20.2 - - + -
180D PHE* 4.8 5.6 - - + -
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Residues in contact with GLN 143 (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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139D GLU 3.0 13.9 + - - +
140D LEU* 3.6 9.2 - - - +
142D LEU* 1.3 75.2 - - - +
144D MET* 1.3 58.4 + - - +
146D ALA* 3.2 11.1 + - - +
147D ASP* 2.8 69.9 + - - +
247D TYR* 4.4 2.2 - - + -
268D ALA* 4.1 13.2 - - + -
304D LEU* 4.2 12.5 - - + +
306D THR* 3.5 36.2 - - + +
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Residues in contact with MET 144 (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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140D LEU 3.1 11.5 + - - +
141D ALA* 3.2 14.1 + - - +
143D GLN* 1.3 78.6 - - - +
145D VAL* 1.3 56.8 + - + +
147D ASP* 3.6 2.3 + - - +
148D LEU* 3.1 36.9 + - + +
154D VAL* 4.0 29.4 - - + -
173D MET* 4.2 14.6 - - - -
177D LEU* 4.5 11.2 - - + -
183D VAL* 6.1 0.2 - - + -
220D ALA* 3.8 11.9 - - + -
221D ILE 4.6 0.4 - - - +
222D TRP* 4.0 34.8 - - + -
247D TYR* 3.7 45.3 + - + -
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Residues in contact with VAL 145 (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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296C PRO* 4.3 1.1 - - + +
297C PHE* 4.3 7.2 - - + -
141D ALA 3.0 16.7 + - - +
142D LEU 3.9 4.9 - - - +
144D MET* 1.3 75.0 - - + +
146D ALA* 1.3 59.1 + - - +
148D LEU* 3.2 7.3 + - + +
149D GLY 3.0 23.2 + - - -
150D GLY* 3.1 23.8 + - - -
176D VAL* 4.3 4.7 - - + -
177D LEU* 3.9 25.1 - - + -
180D PHE* 3.6 46.7 - - + -
183D VAL* 4.3 12.3 - - + -
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Residues in contact with ALA 146 (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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295C LYS* 3.4 35.4 - - + +
296C PRO* 4.6 7.0 - - - -
297C PHE* 3.9 21.0 - - + +
142D LEU 3.0 16.8 + - - +
143D GLN* 3.2 16.1 + - - +
145D VAL* 1.3 76.0 - - - +
147D ASP* 1.3 62.7 + - - +
149D GLY* 3.4 8.9 + - - +
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Residues in contact with ASP 147 (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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295C LYS* 5.9 1.9 - - - +
143D GLN* 2.8 40.1 + - - +
144D MET 3.8 1.3 - - - +
146D ALA* 1.3 76.8 - - - +
148D LEU* 1.3 62.3 + - - +
149D GLY* 3.2 0.9 + - - -
245D ARG* 3.7 29.0 + - + +
247D TYR* 2.6 38.7 + - - +
267D GLY 4.6 2.6 - - - +
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Residues in contact with LEU 148 (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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144D MET* 3.1 28.1 + - + +
145D VAL* 3.2 7.8 + - + +
147D ASP* 1.3 76.2 - - - +
149D GLY* 1.3 58.5 + - - +
150D GLY* 4.2 2.5 - - - +
151D LYS* 3.0 32.3 + - - +
152D GLY* 4.2 11.4 - - - -
154D VAL* 4.0 16.2 - - + -
183D VAL* 4.0 28.3 - - + -
219D GLY* 3.7 38.8 - - - +
220D ALA* 4.4 6.1 - - + -
247D TYR* 6.0 0.2 - - - +
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Residues in contact with GLY 149 (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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294C VAL 6.1 0.4 - - - -
295C LYS* 5.8 1.3 - - - -
296C PRO* 3.9 19.8 - - - +
145D VAL 3.0 4.7 + - - -
146D ALA 3.4 8.6 + - - -
147D ASP 3.2 4.9 + - - -
148D LEU* 1.3 78.7 - - - +
150D GLY* 1.3 57.3 + - - +
151D LYS* 3.2 4.4 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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