Contacts of the helix formed by residues 137 - 150 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110J ARG* 4.1 11.5 - - - -
292J GLY* 3.1 26.6 + - - -
294J ALA* 5.6 2.2 - - - -
135L MET* 3.2 2.1 - - - +
136L ALA* 1.3 82.1 - - - +
138L GLY* 1.3 64.8 - - - +
139L MET* 3.7 0.9 + - - +
140L CYS* 3.1 18.5 + - - +
141L ALA 3.2 9.4 + - - -
270L LEU* 4.5 8.5 - - - -
271L ALA* 3.4 9.6 - - - +
272L GLY* 3.4 11.5 - - - -
500L PLP 3.3 16.2 + - - -
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Residues in contact with GLY 138 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137L SER* 1.3 71.0 - - - +
139L MET* 1.3 61.0 + - - -
141L ALA* 3.1 11.6 + - - +
142L SER* 3.0 18.8 + - - -
256L LEU* 4.5 3.0 - - - +
257L HIS 4.2 8.7 - - - -
258L SER* 4.0 5.4 - - - -
271L ALA 3.3 10.2 + - - -
272L GLY* 3.9 10.5 - - - -
500L PLP 2.6 29.5 + - - -
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Residues in contact with MET 139 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110J ARG* 3.2 41.7 - - - +
290J ILE* 3.3 28.5 - - + +
291J LEU 3.8 1.6 - - - -
292J GLY* 4.3 1.1 - - - -
137L SER* 3.3 3.8 - - - +
138L GLY* 1.3 70.3 - - - +
140L CYS* 1.3 58.0 + - - +
142L SER* 3.4 7.9 + - - +
143L THR* 2.8 41.7 + - - +
163L TYR* 3.8 26.0 - - - -
165L LYS* 4.0 10.3 - - + +
166L THR* 4.0 29.8 - - + +
169L PHE* 5.2 2.2 - - + -
500L PLP 2.6 19.1 + - - +
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Residues in contact with CYS 140 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291J LEU 3.0 14.5 + - - -
292J GLY 3.1 23.6 - - - +
293J GLY* 5.1 0.7 - - - -
135L MET* 3.8 20.2 - - + -
136L ALA 4.4 0.4 - - - -
137L SER* 3.1 17.9 + - - +
139L MET* 1.3 78.9 - - - +
141L ALA* 1.3 52.2 + - - +
143L THR* 4.2 1.1 - - - -
144L VAL* 2.8 52.2 + - - +
288L HIS* 5.1 0.2 - - - -
291L LEU* 6.5 0.2 - - - -
293L GLY* 4.1 24.2 - - - -
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Residues in contact with ALA 141 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135L MET* 3.5 19.4 - - - +
137L SER 3.2 6.3 + - - +
138L GLY* 3.1 11.5 + - - +
140L CYS* 1.3 76.3 - - - +
142L SER* 1.3 61.5 + - - +
145L MET* 2.9 31.9 + - - +
256L LEU* 4.5 5.4 - - + -
272L GLY* 4.3 0.2 - - - -
273L CYS 4.1 17.3 - - - +
274L ILE* 3.2 28.4 - - + +
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Residues in contact with SER 142 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138L GLY 3.0 16.1 + - - -
139L MET* 3.8 9.2 + - - +
141L ALA* 1.3 75.3 - - - +
143L THR* 1.3 57.9 + - - +
145L MET* 3.3 3.4 + - - +
146L LEU* 2.9 40.9 + - - +
166L THR* 4.8 16.8 + - - -
205L PHE* 4.5 15.8 - - - -
236L ASP* 5.6 0.5 + - - -
256L LEU* 4.1 27.3 - - - +
500L PLP 5.3 4.3 - - - -
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Residues in contact with THR 143 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290J ILE 3.8 13.0 + - - -
291J LEU* 3.4 33.9 - - + +
139L MET* 2.8 27.7 + - - +
140L CYS* 3.6 4.5 - - - +
142L SER* 1.3 78.0 - - - +
144L VAL* 1.3 70.1 + - + +
146L LEU* 3.5 3.1 + - - +
147L LEU* 3.1 35.5 + - + +
169L PHE* 3.8 26.4 - - + -
291L LEU* 5.4 1.8 - - + -
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Residues in contact with VAL 144 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135L MET* 3.4 16.6 - - + -
140L CYS* 2.8 36.6 + - - +
143L THR* 1.3 74.3 - - + +
145L MET* 1.3 60.6 + - - +
147L LEU* 3.4 4.8 + - - -
148L ALA* 2.9 28.8 + - - +
284L ILE* 3.6 31.6 - - + +
287L LEU* 3.6 13.8 - - + +
288L HIS* 4.2 11.9 - - - +
291L LEU* 3.6 25.4 - - + -
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Residues in contact with MET 145 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141L ALA 2.9 20.2 + - - +
142L SER* 3.5 4.5 - - - +
144L VAL* 1.3 77.9 - - - +
146L LEU* 1.3 99.0 + - + +
148L ALA* 3.2 1.2 + - - +
149L LEU* 2.9 53.3 + - + +
150L VAL* 5.3 0.2 - - + -
203L LEU* 3.8 26.9 - - + -
205L PHE* 4.5 5.6 - - + -
234L CYS* 3.5 30.7 - - - -
254L LEU* 4.5 3.6 - - + -
256L LEU* 4.5 7.4 - - + -
274L ILE* 3.9 13.7 - - + -
284L ILE* 3.8 19.9 - - + +
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Residues in contact with LEU 146 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142L SER* 2.9 27.1 + - - +
143L THR 3.7 3.1 - - - +
145L MET* 1.3 99.3 - - + +
147L LEU* 1.3 63.1 + - - +
148L ALA 3.0 1.4 + - - -
150L VAL* 3.0 32.6 + - + +
156L ILE* 3.4 32.3 - - + -
166L THR* 4.9 8.5 - - + -
169L PHE* 3.7 31.4 - - + -
170L ILE* 4.2 17.5 - - + -
174L LEU* 4.5 9.8 - - + +
179L ILE* 5.9 0.2 - - - +
203L LEU* 4.0 2.5 - - + -
205L PHE* 5.0 10.1 - - + -
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Residues in contact with LEU 147 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147J LEU* 5.3 13.7 - - + -
173J ILE* 5.9 7.0 - - + -
176J LYS* 4.2 15.2 + - - -
291J LEU* 5.1 3.8 - - + -
143L THR* 3.1 30.1 + - + +
144L VAL 3.8 0.4 - - - +
146L LEU* 1.3 79.6 - - - +
148L ALA* 1.3 59.9 + - - +
150L VAL 4.1 8.6 - - - +
169L PHE* 3.8 23.3 - - + -
173L ILE* 5.6 5.8 - - + -
174L LEU* 4.5 6.1 - - + -
177L MET* 4.0 34.1 - - + +
287L LEU* 3.6 19.0 - - + +
291L LEU* 4.2 17.7 - - + -
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Residues in contact with ALA 148 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176J LYS* 5.7 1.4 + - - -
144L VAL 2.9 17.5 + - - +
145L MET 3.7 2.7 - - - +
147L LEU* 1.3 79.6 - - - +
149L LEU* 1.3 65.4 + - - +
150L VAL 4.9 1.3 - - - +
283L GLU* 4.2 14.5 - - - +
284L ILE* 3.9 30.7 - - + +
287L LEU* 3.7 17.0 - - + -
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Residues in contact with LEU 149 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145L MET* 2.9 33.8 + - + +
148L ALA* 1.3 80.7 - - - +
150L VAL* 1.3 67.6 + - + +
151L PRO* 3.5 10.0 - - - +
202L ASN* 5.4 1.2 + - - +
203L LEU* 4.5 5.6 - - + -
232L LEU* 4.4 16.4 - - + -
254L LEU* 3.4 33.7 - - + -
280L LEU* 4.1 22.9 - - + +
283L GLU* 4.5 13.9 - - + +
284L ILE* 4.0 18.8 - - + -
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Residues in contact with VAL 150 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176J LYS* 5.2 1.9 + - - -
146L LEU* 3.0 25.4 + - + +
147L LEU 4.1 9.2 - - - +
148L ALA 4.9 1.0 - - - -
149L LEU* 1.3 78.6 - - + +
151L PRO* 1.3 79.6 - - + +
154L GLY* 4.7 4.0 - - - -
155L HIS 5.1 1.8 - - - +
156L ILE* 4.2 13.9 - - + -
174L LEU* 5.9 2.5 - - + -
177L MET* 4.5 4.7 - - - +
179L ILE* 3.5 36.2 - - + +
202L ASN* 4.6 11.4 - - + -
203L LEU* 4.1 32.5 - - + -
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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