Contacts of the helix formed by residues 137 - 150 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110F ARG* 3.9 12.8 - - - -
292F GLY* 3.0 27.5 + - - -
294F ALA* 5.5 2.0 - - - -
135H MET 3.2 2.4 - - - -
136H ALA* 1.3 83.8 - - - +
138H GLY* 1.3 65.7 + - - +
139H MET 3.6 0.5 + - - -
140H CYS* 2.9 18.7 + - - +
141H ALA 3.0 9.5 + - - -
270H LEU* 4.5 6.7 - - - -
271H ALA* 3.4 10.8 - - - +
272H GLY* 3.4 10.6 - - - -
500H PLP 3.1 17.9 + - - -
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Residues in contact with GLY 138 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137H SER* 1.3 69.0 - - - +
139H MET* 1.3 61.2 + - - -
141H ALA* 2.9 17.0 + - - +
142H SER* 3.0 14.3 + - - -
256H LEU* 4.5 2.8 - - - +
257H HIS 4.2 11.4 - - - -
258H SER* 4.2 2.9 - - - -
271H ALA 3.1 15.0 + - - -
272H GLY* 3.8 6.3 - - - -
500H PLP 2.5 28.8 + - - -
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Residues in contact with MET 139 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110F ARG* 3.3 39.3 - - - +
290F ILE* 3.3 32.5 - - + +
291F LEU 3.8 1.8 - - - -
292F GLY* 4.3 1.1 - - - -
137H SER* 3.9 2.2 - - - +
138H GLY* 1.3 69.9 - - - +
140H CYS* 1.3 57.7 + - - +
142H SER* 3.4 7.4 + - - +
143H THR* 2.8 42.0 + - - +
163H TYR* 3.8 17.5 - - - -
165H LYS* 4.1 10.3 - - + +
166H THR* 3.6 42.2 - - + +
169H PHE* 5.0 2.5 - - + -
500H PLP 2.5 20.0 + - - +
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Residues in contact with CYS 140 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291F LEU 3.0 13.8 + - - +
292F GLY 3.0 24.0 - - - +
293F GLY* 5.2 0.9 - - - -
135H MET* 3.6 24.5 - - + -
136H ALA 4.3 1.1 - - - -
137H SER* 2.9 17.0 + - - +
139H MET* 1.3 79.4 - - - +
141H ALA* 1.3 57.4 + - - +
143H THR* 4.2 0.9 - - - -
144H VAL* 2.9 48.8 + - - +
288H HIS* 5.0 0.2 - - - -
293H GLY* 4.2 20.4 - - - -
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Residues in contact with ALA 141 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135H MET* 3.5 19.3 - - - +
137H SER 3.0 9.3 + - - +
138H GLY* 2.9 11.5 + - - +
140H CYS* 1.3 77.1 - - - +
142H SER* 1.3 62.3 + - - +
145H MET* 2.9 26.0 + - - +
256H LEU* 4.4 5.2 - - + -
272H GLY* 4.1 0.2 - - - -
273H CYS 4.0 17.0 - - - +
274H ILE* 3.2 28.6 - - + +
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Residues in contact with SER 142 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138H GLY 3.0 16.3 + - - -
139H MET* 3.6 12.5 + - - -
141H ALA* 1.3 77.6 - - - +
143H THR* 1.3 65.1 + - - +
145H MET* 3.1 8.5 + - - +
146H LEU* 2.8 33.3 + - - +
166H THR* 4.7 15.5 + - - -
205H PHE* 4.6 14.3 - - - -
236H ASP* 5.7 0.3 + - - -
256H LEU* 4.1 23.3 - - - +
500H PLP 5.2 3.8 - - - -
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Residues in contact with THR 143 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290F ILE 3.8 13.9 + - - -
291F LEU* 3.3 37.5 - - + +
139H MET* 2.8 27.3 + - - +
140H CYS 3.6 4.5 - - - +
142H SER* 1.3 78.0 - - - +
144H VAL* 1.3 70.8 + - + +
146H LEU* 3.2 3.1 + - - +
147H LEU* 3.0 36.7 + - + +
169H PHE* 3.9 22.7 - - + -
291H LEU* 5.2 2.0 - - + -
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Residues in contact with VAL 144 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135H MET* 3.4 15.3 - - + -
140H CYS* 2.9 35.9 + - - +
143H THR* 1.3 78.4 - - + +
145H MET* 1.3 63.8 + - - +
147H LEU* 3.3 5.5 + - - -
148H ALA* 3.0 22.9 + - - +
284H ILE* 3.5 31.2 - - + +
287H LEU* 3.6 13.8 - - + +
288H HIS* 4.2 13.5 - - - +
291H LEU* 3.6 25.8 - - + -
293H GLY 6.3 0.2 - - - +
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Residues in contact with MET 145 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141H ALA 2.9 20.0 + - - +
142H SER 3.3 5.2 - - - +
144H VAL* 1.3 77.3 - - - +
146H LEU* 1.3 96.1 + - + +
148H ALA* 3.4 0.5 + - - -
149H LEU* 3.0 47.0 + - + +
203H LEU* 3.8 27.1 - - + -
205H PHE* 4.4 8.7 - - + -
234H CYS* 3.4 29.2 - - - -
254H LEU* 4.7 1.3 - - + -
256H LEU* 4.3 10.1 - - - -
274H ILE* 3.9 14.4 - - + -
284H ILE* 4.1 19.2 - - + +
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Residues in contact with LEU 146 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142H SER* 2.8 24.8 + - - +
143H THR 3.6 3.4 - - - +
145H MET* 1.3 95.7 - - + +
147H LEU* 1.3 61.2 + - - +
148H ALA 3.1 5.4 + - - -
150H VAL* 3.2 33.5 + - + +
156H ILE* 3.4 33.0 - - + -
166H THR* 4.8 9.0 - - + -
169H PHE* 3.6 34.8 - - + -
170H ILE* 4.2 17.7 - - + -
174H LEU* 4.4 9.9 - - + +
179H ILE* 5.5 0.2 - - - +
203H LEU* 4.1 3.1 - - + -
205H PHE* 5.0 8.5 - - + -
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Residues in contact with LEU 147 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147F LEU* 5.3 15.7 - - + -
173F ILE* 5.8 10.5 - - + +
176F LYS* 4.1 17.2 + - - -
291F LEU* 5.1 3.8 - - + -
143H THR* 3.0 35.7 + - + +
144H VAL 3.3 0.2 + - - -
146H LEU* 1.3 75.1 - - - +
148H ALA* 1.3 58.0 + - - +
150H VAL 4.3 6.6 - - - +
169H PHE* 3.8 20.2 - - + -
173H ILE* 5.4 4.9 - - + -
174H LEU* 4.3 7.4 - - + -
177H MET* 3.9 35.4 - - + +
287H LEU* 3.6 18.5 - - + +
291H LEU* 4.2 18.4 - - + -
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Residues in contact with ALA 148 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176F LYS* 5.8 1.7 + - - +
144H VAL 3.0 17.1 + - - +
145H MET 4.0 2.7 - - - +
147H LEU* 1.3 79.6 - - - +
149H LEU* 1.3 64.8 + - + +
150H VAL 4.9 1.1 - - - -
283H GLU* 4.4 14.7 - - - +
284H ILE* 4.0 28.5 - - + +
287H LEU* 3.6 18.2 - - + -
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Residues in contact with LEU 149 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145H MET* 3.0 28.2 + - + +
148H ALA* 1.3 80.9 - - - +
150H VAL* 1.3 68.5 + - + +
151H PRO* 3.5 10.0 - - - +
202H ASN* 5.4 1.4 + - - +
203H LEU* 4.5 17.0 - - + -
232H LEU* 4.5 11.1 - - + +
254H LEU* 3.3 33.9 - - + -
280H LEU* 4.1 23.1 - - + +
283H GLU* 4.4 14.1 - - + -
284H ILE* 4.0 18.6 - - + -
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Residues in contact with VAL 150 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176F LYS* 5.0 2.8 + - - -
146H LEU* 3.2 24.0 + - + +
147H LEU 4.3 8.8 - - - +
148H ALA 4.9 0.8 - - - -
149H LEU* 1.3 78.6 - - + +
151H PRO* 1.3 80.2 - - + +
154H GLY* 4.4 9.2 - - - -
155H HIS 4.6 2.2 - - - +
156H ILE* 4.2 13.9 - - + -
174H LEU* 5.9 1.1 - - + -
177H MET* 4.7 4.7 - - - +
179H ILE* 3.6 36.2 - - + +
202H ASN* 4.6 7.6 - - + -
203H LEU* 4.1 33.2 - - + -
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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