Contacts of the helix formed by residues 137 - 150 (chain D) in PDB entry 1I43
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 137 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110B ARG* 4.0 12.7 - - - -
292B GLY* 2.8 29.8 + - - -
294B ALA* 5.5 1.6 - - - -
135D MET* 3.3 2.1 - - - +
136D ALA* 1.3 82.0 - - - +
138D GLY* 1.3 64.5 + - - +
139D MET* 3.6 0.7 + - - +
140D CYS* 3.1 19.8 + - - +
141D ALA 3.1 9.9 + - - -
270D LEU* 4.6 7.0 - - - -
271D ALA* 3.6 4.5 - - - +
272D GLY* 3.2 17.8 - - - +
500D PLP 3.5 15.0 + - - -
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Residues in contact with GLY 138 (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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137D SER* 1.3 71.8 - - - +
139D MET* 1.3 58.4 + - - -
141D ALA* 3.1 12.0 + - - +
142D SER* 2.9 20.8 + - - -
256D LEU* 4.5 2.7 - - - +
257D HIS 4.2 9.6 - - - -
258D SER* 4.1 4.7 - - - -
271D ALA 3.5 9.2 + - - -
272D GLY* 3.9 10.5 - - - -
500D PLP 2.7 31.4 + - - -
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Residues in contact with MET 139 (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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110B ARG* 3.3 40.2 - - - +
290B ILE* 3.3 28.9 - - + +
291B LEU 3.8 1.8 - - - -
292B GLY* 4.3 1.1 - - - -
137D SER* 3.9 3.1 - - - +
138D GLY* 1.3 71.8 - - - +
140D CYS* 1.3 63.4 + - - +
142D SER* 3.9 6.8 + - - +
143D THR* 2.9 36.6 + - - +
163D TYR* 4.0 17.5 - - - -
165D LYS* 4.1 11.2 - - + +
166D THR* 3.9 40.2 - - + +
169D PHE* 5.1 2.0 - - + -
500D PLP 2.6 19.7 + - - +
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Residues in contact with CYS 140 (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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291B LEU 3.1 14.5 + - - -
292B GLY 3.2 22.4 - - - +
293B GLY* 4.9 1.3 - - - -
135D MET* 3.9 18.4 - - + -
136D ALA 4.4 0.2 - - - -
137D SER* 3.1 18.2 + - - +
139D MET* 1.3 79.4 - - - +
141D ALA* 1.3 54.1 + - - +
143D THR* 3.5 0.8 - - - -
144D VAL* 2.8 53.4 + - - +
288D HIS* 5.2 0.4 - - - -
291D LEU* 6.4 0.7 - - - -
293D GLY* 4.0 23.8 - - - -
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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
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135D MET* 3.4 20.1 - - - -
137D SER 3.1 6.7 + - - +
138D GLY* 3.1 10.4 + - - +
140D CYS* 1.3 78.9 - - - +
142D SER* 1.3 58.3 + - - +
144D VAL* 4.0 0.3 - - - -
145D MET* 2.9 33.3 + - - +
256D LEU* 4.5 4.5 - - + -
273D CYS 4.0 16.8 - - - +
274D ILE* 3.2 28.4 - - + +
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Residues in contact with SER 142 (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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138D GLY 2.9 16.5 + - - -
139D MET* 3.9 10.9 + - - -
141D ALA* 1.3 76.8 - - - +
143D THR* 1.3 58.9 + - - +
145D MET* 3.6 4.1 - - - +
146D LEU* 2.8 40.4 + - - +
166D THR* 4.8 16.0 + - - -
205D PHE* 4.7 14.6 - - - -
236D ASP* 5.5 0.5 + - - -
256D LEU* 3.9 26.6 - - - +
500D PLP 5.1 4.7 - - - -
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Residues in contact with THR 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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290B ILE 3.8 9.7 + - - -
291B LEU* 3.3 41.1 - - + +
139D MET* 2.9 26.1 + - - +
140D CYS* 3.5 4.0 - - - +
142D SER* 1.3 76.2 - - - +
144D VAL* 1.3 65.1 + - + +
146D LEU* 3.2 4.2 + - - +
147D LEU* 2.9 43.0 + - + +
169D PHE* 3.9 24.6 - - + -
291D LEU* 5.3 1.8 - - + -
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Residues in contact with VAL 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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135D MET* 3.4 24.5 - - + -
140D CYS* 2.8 38.3 + - - +
143D THR* 1.3 74.6 - - + +
145D MET* 1.3 60.9 + - - +
147D LEU* 3.4 4.9 + - - +
148D ALA* 3.0 27.9 + - - +
284D ILE* 3.7 22.7 - - + +
287D LEU* 3.6 14.2 - - + +
288D HIS* 4.2 13.2 - - - +
291D LEU* 3.8 23.3 - - + -
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Residues in contact with MET 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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141D ALA 2.9 18.7 + - - +
142D SER* 3.6 5.6 - - - +
144D VAL* 1.3 77.9 - - - +
146D LEU* 1.3 93.8 + - + +
149D LEU* 3.1 42.0 + - + +
150D VAL* 5.7 0.2 - - + -
203D LEU* 3.8 27.1 - - + -
205D PHE* 4.5 6.5 - - + -
234D CYS* 3.6 26.5 - - - -
254D LEU* 4.6 3.8 - - + -
256D LEU* 4.1 11.0 - - - -
274D ILE* 3.6 16.2 - - + -
284D ILE* 4.0 20.2 - - + +
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Residues in contact with LEU 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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142D SER* 2.8 26.7 + - - +
143D THR* 3.5 4.7 - - - +
145D MET* 1.3 94.3 - - + +
147D LEU* 1.3 62.0 + - - +
148D ALA 3.1 5.4 + - - -
150D VAL* 3.2 34.1 + - + +
156D ILE* 3.4 33.0 - - + -
166D THR* 4.8 9.2 - - + -
169D PHE* 3.6 33.7 - - + -
170D ILE* 4.1 18.2 - - + -
174D LEU* 4.4 10.0 - - + +
179D ILE* 5.5 0.2 - - - +
203D LEU* 4.2 2.0 - - + -
205D PHE* 5.2 7.9 - - + -
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Residues in contact with LEU 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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147B LEU* 5.1 17.0 - - + -
173B ILE* 5.9 9.4 - - + +
176B LYS* 4.1 17.7 + - - -
291B LEU* 4.9 3.8 - - + -
143D THR* 2.9 37.1 + - + +
144D VAL 3.4 0.2 + - - -
146D LEU* 1.3 75.5 - - - +
148D ALA* 1.3 58.1 + - - +
150D VAL 4.3 5.9 - - - +
169D PHE* 3.7 21.3 - - + -
173D ILE* 5.4 6.3 - - + -
174D LEU* 4.3 7.9 - - + -
177D MET* 3.9 34.6 - - + +
179D ILE* 6.3 0.2 - - - -
287D LEU* 3.7 17.3 - - + +
291D LEU* 4.4 16.4 - - + -
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Residues in contact with ALA 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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176B LYS* 5.5 3.3 + - - +
144D VAL 3.0 16.9 + - - +
145D MET 4.2 2.0 - - - +
147D LEU* 1.3 81.3 - - - +
149D LEU* 1.3 65.0 + - - +
150D VAL 3.8 1.5 - - - +
283D GLU* 4.2 15.2 - - - +
284D ILE* 4.1 21.8 - - + -
287D LEU* 3.6 24.0 - - + -
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Residues in contact with LEU 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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145D MET* 3.1 33.5 + - + +
148D ALA* 1.3 82.9 - - - +
150D VAL* 1.3 66.3 + - + +
151D PRO* 3.5 10.0 - - - +
202D ASN* 5.4 1.2 + - - +
203D LEU* 4.5 11.7 - - + -
232D LEU* 4.6 11.8 - - + +
254D LEU* 3.4 33.0 - - + -
280D LEU* 4.2 22.2 - - + +
283D GLU* 4.6 13.5 - - + +
284D ILE* 4.2 18.6 - - + -
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Residues in contact with VAL 150 (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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176B LYS* 4.9 2.8 + - - -
146D LEU* 3.2 23.5 + - + +
147D LEU 4.3 8.5 - - - +
148D ALA 4.9 0.7 - - - -
149D LEU* 1.3 79.1 + - + +
151D PRO* 1.3 70.5 - - + +
154D GLY* 4.4 9.6 - - - -
155D HIS 4.7 2.0 - - - +
156D ILE* 4.1 25.6 - - + -
174D LEU* 6.0 2.0 - - + -
177D MET* 4.6 4.7 - - - +
179D ILE* 3.6 45.1 - - + +
202D ASN* 4.5 8.3 - - + +
203D LEU* 4.2 20.2 - - + -
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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