Contacts of the helix formed by residues 277 - 292 (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 PRO 277 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130L GLU* 3.7 17.0 - - + +
248L LEU* 5.3 1.3 - - + -
253L ASP* 3.0 22.4 - - + +
254L LEU* 4.3 0.9 - - + -
276L GLY* 1.3 84.2 - - - +
278L LEU* 1.3 61.3 + - - +
279L LYS* 4.6 6.7 - - + +
280L LEU* 3.3 28.5 + - + +
281L VAL* 2.8 29.7 + - - +
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Residues in contact with LEU 278 (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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130L GLU* 2.9 35.6 + - + +
131L SER* 4.3 18.8 - - - -
277L PRO* 1.3 68.5 - - - +
279L LYS* 1.3 68.8 + - - +
280L LEU 2.7 2.1 + - - -
281L VAL* 3.7 7.6 - - + -
282L SER* 2.8 38.6 + - - +
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Residues in contact with LYS 279 (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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130L GLU* 4.5 1.4 + - - -
277L PRO* 3.5 5.4 - - + -
278L LEU* 1.3 77.9 - - - +
280L LEU* 1.3 71.5 - - + +
282L SER* 3.4 14.0 + - - -
283L GLU* 3.7 13.9 - - - +
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Residues in contact with LEU 280 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149L LEU* 4.1 19.5 - - + +
232L LEU* 3.7 32.8 - - + -
253L ASP* 4.1 13.5 - - + -
254L LEU* 3.9 28.5 - - + -
277L PRO* 3.3 22.0 + - + +
278L LEU 2.7 4.8 + - - -
279L LYS* 1.3 88.2 - - + +
281L VAL* 1.3 66.7 + - - +
282L SER 3.0 1.8 - - - -
283L GLU* 2.9 25.4 + - + +
284L ILE* 3.5 9.7 + - - +
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Residues in contact with VAL 281 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131L SER* 3.1 43.5 - - - +
133L LEU* 3.9 20.1 - - + +
254L LEU* 4.5 4.2 - - + +
274L ILE* 3.7 30.5 - - + +
276L GLY 4.6 4.5 - - - +
277L PRO 2.8 22.9 + - - +
278L LEU* 3.5 5.8 - - + +
280L LEU* 1.3 73.3 - - - +
282L SER* 1.3 60.8 + - - +
284L ILE* 3.4 12.4 + - + +
285L ARG* 3.0 28.0 + - - +
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Residues in contact with SER 282 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278L LEU* 2.8 33.8 + - - -
279L LYS* 3.4 10.2 + - - -
281L VAL* 1.3 77.2 - - - +
283L GLU* 1.3 71.5 + - - +
285L ARG* 3.2 12.8 + - - +
286L ASN* 3.1 28.2 + - - +
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Residues in contact with GLU 283 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148L ALA* 4.2 17.1 - - - +
149L LEU* 4.5 15.1 - - + +
279L LYS 3.7 14.8 - - - +
280L LEU* 2.9 12.7 + - + +
282L SER* 1.3 84.1 + - - +
284L ILE* 1.3 61.5 - - - +
286L ASN* 3.4 26.3 + - - +
287L LEU* 3.6 5.2 + - - +
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Residues in contact with ILE 284 (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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133L LEU* 3.6 18.4 - - + -
135L MET* 4.0 5.2 - - + -
144L VAL* 3.6 23.3 - - + +
145L MET* 3.8 32.8 - - + -
148L ALA* 3.9 18.2 - - + -
149L LEU* 4.0 17.0 - - + -
254L LEU* 4.6 4.7 - - + -
274L ILE* 4.1 21.8 - - + -
280L LEU 3.5 10.3 + - - +
281L VAL* 3.4 12.2 + - - +
282L SER 3.2 0.2 - - - -
283L GLU* 1.3 72.9 - - - +
285L ARG* 1.3 61.4 + - - +
286L ASN 3.0 2.3 + - - -
287L LEU* 3.1 4.2 + - - +
288L HIS* 2.9 26.0 + - - +
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Residues in contact with ARG 285 (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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111L TYR 5.5 3.5 + - - -
117L VAL* 6.0 1.0 - - - +
120L GLU* 3.1 31.7 + - - -
131L SER* 3.4 23.4 + - - -
132L THR 3.5 13.1 + - - -
133L LEU* 3.8 25.4 - - + +
281L VAL* 3.0 15.9 + - - +
282L SER* 3.2 15.1 + - - +
284L ILE* 1.3 76.7 - - - +
286L ASN* 1.3 62.0 + - - +
288L HIS* 3.2 10.5 - - - +
289L HIS* 3.0 55.5 + - + +
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Residues in contact with ASN 286 (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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282L SER* 3.1 14.3 + - - +
283L GLU* 3.5 22.0 + - - +
284L ILE 3.0 0.6 - - - -
285L ARG* 1.3 80.5 - - - +
287L LEU* 1.3 63.5 + - - +
289L HIS* 3.3 23.4 + - - +
290L ILE* 3.7 15.0 + - - +
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Residues in contact with LEU 287 (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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173J ILE* 4.0 30.5 - - + -
144L VAL* 3.6 10.5 - - + +
147L LEU* 3.6 21.8 - - + +
148L ALA* 3.6 37.2 - - + +
283L GLU 3.6 3.4 + - - +
284L ILE 3.1 7.0 + - - +
286L ASN* 1.3 77.1 - - - +
288L HIS* 1.3 59.4 + - - +
290L ILE* 3.1 13.6 + - + +
291L LEU* 2.9 53.8 + - + +
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Residues in contact with HIS 288 (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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110L ARG 4.9 4.8 + - - +
133L LEU* 3.9 24.5 - - + -
134L LEU 3.9 11.0 + - - -
135L MET* 3.4 27.1 - - + +
144L VAL* 4.2 12.5 - - + +
284L ILE 2.9 13.2 + - - +
285L ARG* 3.2 12.3 - - - +
286L ASN 3.1 0.2 - - - -
287L LEU* 1.3 74.1 - - - +
289L HIS* 1.3 72.5 + + - +
290L ILE 2.9 4.5 - - - -
291L LEU* 4.5 3.1 - - - +
292L GLY* 2.9 30.7 + - - -
293L GLY* 3.4 39.0 + - - -
294L ALA* 3.6 12.5 + - - +
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Residues in contact with HIS 289 (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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165J LYS* 4.5 7.7 - - - +
110L ARG* 3.1 48.6 + - - +
111L TYR* 3.5 50.6 + + + -
285L ARG* 3.0 43.3 + - + +
286L ASN* 3.6 16.6 + - - +
287L LEU 3.3 0.4 - - - -
288L HIS* 1.3 86.0 - + - +
290L ILE* 1.3 61.3 + - + +
292L GLY 4.3 0.9 - - - -
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Residues in contact with ILE 290 (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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139J MET* 3.4 30.0 - - + +
143J THR* 3.7 1.4 + - - -
165J LYS* 4.5 25.8 - - + +
168J ILE* 4.2 25.1 - - + -
169J PHE* 4.0 36.8 - - + +
172J THR* 5.6 1.8 - - - +
173J ILE* 5.5 4.5 - - + -
286L ASN 3.9 13.7 - - - +
287L LEU* 3.1 17.9 + - + +
288L HIS 2.9 1.0 - - - -
289L HIS* 1.3 81.8 - - + +
291L LEU* 1.3 68.9 + - + +
292L GLY 3.0 1.9 + - - -
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Residues in contact with LEU 291 (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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139J MET 3.8 0.2 - - - -
140J CYS* 3.0 31.1 - - - +
143J THR* 3.5 30.9 + - + +
147J LEU* 5.2 4.3 - - + -
169J PHE* 3.7 20.0 - - + -
173J ILE* 5.8 1.1 - - + -
291J LEU* 6.4 1.8 - - + -
140L CYS* 6.5 0.7 - - - -
143L THR* 5.4 1.8 - - + -
144L VAL* 3.6 31.4 - - + -
147L LEU* 4.2 16.6 - - + -
287L LEU* 2.9 46.3 + - + +
288L HIS* 4.4 2.5 - - - +
290L ILE* 1.3 76.4 - - - +
292L GLY* 1.3 60.8 + - - +
293L GLY 5.0 1.1 - - - +
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Residues in contact with GLY 292 (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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136J ALA* 3.8 4.0 - - - +
137J SER* 3.0 18.6 + - - -
140J CYS* 2.9 26.4 - - - +
110L ARG* 3.9 19.1 - - - -
288L HIS* 2.9 15.4 + - - -
290L ILE 3.0 3.0 - - - -
291L LEU* 1.3 76.6 - - - +
293L GLY* 1.3 57.0 + - - +
294L ALA 3.3 6.1 + - - -
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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