Contacts of the helix formed by residues 277 - 292 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130A GLU* 3.7 15.7 - - + +
248A LEU* 5.3 1.1 - - + -
253A ASP* 3.0 21.3 - - + +
254A LEU* 4.1 6.1 - - + -
276A GLY* 1.3 87.4 - - - +
278A LEU* 1.3 62.1 + - - +
279A LYS* 4.6 7.2 - - + +
280A LEU* 3.2 27.3 + - + +
281A VAL* 2.9 27.0 + - - +
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Residues in contact with LEU 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A GLU* 2.8 36.1 + - + +
131A SER* 4.4 17.9 - - - -
277A PRO* 1.3 67.9 - - - +
279A LYS* 1.3 70.2 + - - +
280A LEU 2.8 1.9 + - - -
281A VAL* 3.7 8.5 - - + -
282A SER* 2.8 37.9 + - - -
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Residues in contact with LYS 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A GLU* 4.4 1.6 + - - +
277A PRO* 3.4 6.2 - - + +
278A LEU* 1.3 80.1 - - - +
280A LEU* 1.3 70.6 + - + +
282A SER* 3.4 12.6 + - - -
283A GLU* 3.7 13.7 - - - +
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Residues in contact with LEU 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A LEU* 4.0 23.7 - - + +
232A LEU* 4.2 22.7 - - + -
253A ASP* 4.0 16.8 - - + +
254A LEU* 4.0 29.8 - - + -
277A PRO* 3.2 28.3 + - + +
278A LEU 2.8 4.8 + - - -
279A LYS* 1.3 84.7 - - + +
281A VAL* 1.3 57.7 + - - +
282A SER 3.0 1.6 - - - -
283A GLU* 2.7 35.8 + - + +
284A ILE* 3.5 9.1 + - - +
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Residues in contact with VAL 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A SER* 3.1 42.6 - - - +
133A LEU* 3.9 19.7 - - + +
254A LEU* 4.4 3.5 - - + +
274A ILE* 3.9 30.1 - - + +
276A GLY 4.7 4.3 - - - +
277A PRO 2.9 23.5 + - - +
278A LEU* 3.5 6.5 - - + +
280A LEU* 1.3 73.5 - - - +
282A SER* 1.3 63.5 + - - +
284A ILE* 3.2 13.7 + - + +
285A ARG* 2.9 28.3 + - - +
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Residues in contact with SER 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A LEU* 2.8 33.8 + - - -
279A LYS* 3.4 9.4 + - - -
281A VAL* 1.3 77.6 - - - +
283A GLU* 1.3 71.2 + - - +
285A ARG* 3.2 12.7 + - - +
286A ASN* 3.0 29.8 + - - +
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Residues in contact with GLU 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A ALA* 4.3 17.5 - - - +
149A LEU* 4.5 15.9 - - + +
279A LYS 3.7 14.6 - - - +
280A LEU* 2.7 17.2 + - + +
282A SER* 1.3 80.0 + - - +
284A ILE* 1.3 62.9 + - - +
286A ASN* 3.4 24.9 + - - +
287A LEU* 3.5 4.3 + - - +
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Residues in contact with ILE 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A LEU* 3.7 16.8 - - + -
135A MET* 4.0 4.9 - - + -
144A VAL* 3.6 23.7 - - + +
145A MET* 4.1 27.8 - - + -
148A ALA* 4.0 16.4 - - + -
149A LEU* 4.2 16.6 - - + -
254A LEU* 4.6 5.4 - - + -
274A ILE* 4.1 26.0 - - + -
280A LEU 4.0 5.6 - - - +
281A VAL* 3.5 18.6 - - - +
283A GLU* 1.3 73.8 - - - +
285A ARG* 1.3 66.4 + - - +
286A ASN 3.0 1.6 - - - -
287A LEU* 3.0 4.7 + - - +
288A HIS* 2.8 20.1 + - - +
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Residues in contact with ARG 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A TYR 5.2 5.9 + - - -
117A VAL* 5.8 1.4 - - - +
120A GLU* 2.9 31.7 + - - -
131A SER* 3.5 18.0 + - - -
132A THR 3.4 21.6 + - - -
133A LEU* 3.8 25.9 - - + +
281A VAL* 2.9 16.5 + - - +
282A SER* 3.2 14.9 + - - +
284A ILE* 1.3 75.0 - - - +
286A ASN* 1.3 61.4 + - - +
288A HIS* 3.2 10.7 - - - +
289A HIS* 3.0 56.0 + - + +
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Residues in contact with ASN 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282A SER* 3.0 16.3 + - - +
283A GLU* 3.5 21.3 + - - +
284A ILE 3.0 0.8 - - - -
285A ARG* 1.3 80.8 - - - +
287A LEU* 1.3 66.2 + - - +
289A HIS* 3.1 27.4 + - - +
290A ILE* 3.6 12.3 + - - +
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Residues in contact with LEU 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A VAL* 3.7 9.6 - - + +
147A LEU* 3.7 18.2 - - + +
148A ALA* 3.6 41.1 - - + +
283A GLU 3.5 3.2 + - - +
284A ILE 3.0 7.2 + - - +
286A ASN* 1.3 78.6 - - - +
288A HIS* 1.3 56.7 + - - +
290A ILE* 3.1 17.4 + - + +
291A LEU* 3.0 52.6 + - + +
173C ILE* 3.7 32.1 - - + -
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Residues in contact with HIS 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A ARG* 4.7 5.4 + - - +
133A LEU* 4.0 25.6 - - + -
134A LEU 4.0 10.2 + - - -
135A MET* 3.6 22.5 - - + +
144A VAL* 4.2 14.2 - - + +
284A ILE 2.8 12.5 + - - +
285A ARG* 3.2 12.1 - - - +
286A ASN 3.0 0.2 - - - -
287A LEU* 1.3 73.5 - - - +
289A HIS* 1.3 71.6 + + - +
290A ILE 2.9 4.9 - - - -
291A LEU* 4.5 2.7 - - - +
292A GLY* 2.9 29.3 + - - -
293A GLY* 3.2 42.3 + - - -
294A ALA* 3.7 11.6 - - - +
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Residues in contact with HIS 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A ARG* 3.0 53.5 + - - +
111A TYR* 3.4 47.2 + + + -
285A ARG* 3.0 44.9 + - + +
286A ASN* 3.1 16.7 + - - +
288A HIS* 1.3 85.0 - + - +
290A ILE* 1.3 59.6 + - + +
292A GLY 4.3 0.9 - - - -
165C LYS* 4.6 7.5 - - - +
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Residues in contact with ILE 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286A ASN 3.9 13.5 - - - +
287A LEU* 3.1 19.9 + - + +
288A HIS 2.9 0.4 - - - -
289A HIS* 1.3 81.5 - - + +
291A LEU* 1.3 65.6 + - + +
292A GLY 3.0 5.5 + - - -
139C MET* 3.3 32.3 - - + +
143C THR* 3.7 0.5 + - - -
165C LYS* 4.6 24.0 - - + +
168C ILE* 4.2 24.7 - - + -
169C PHE* 4.0 37.0 - - + +
172C THR* 5.5 2.2 - - - +
173C ILE* 5.4 4.3 - - + -
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Residues in contact with LEU 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A CYS* 6.4 0.4 - - - -
143A THR* 5.3 2.2 - - + -
144A VAL* 3.9 25.6 - - + -
147A LEU* 4.3 17.3 - - + -
287A LEU* 3.0 42.5 + - + +
288A HIS* 4.3 3.8 - - - +
290A ILE* 1.3 75.0 - - + +
292A GLY* 1.3 63.5 + - - +
293A GLY* 3.7 2.6 + - - +
140C CYS* 3.0 27.7 - - - +
143C THR* 3.3 31.0 - - + +
147C LEU* 5.0 4.3 - - + -
169C PHE* 3.8 22.2 - - + -
173C ILE* 5.9 1.1 - - + -
291C LEU* 6.3 2.7 - - + -
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Residues in contact with GLY 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A ARG* 3.8 20.2 - - - -
288A HIS* 2.9 14.3 + - - -
290A ILE 3.0 3.8 - - - -
291A LEU* 1.3 77.6 - - - +
293A GLY* 1.3 55.6 + - - +
294A ALA 3.3 7.1 + - - -
136C ALA* 3.9 3.3 - - - +
137C SER* 2.8 29.4 + - - -
139C MET* 4.3 1.1 - - - -
140C CYS* 3.1 15.1 - - - +
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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