Contacts of the helix formed by residues 244 - 258 (chain A) in PDB entry 1I4A
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 ASN 244 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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240A LYS* 2.8 16.0 + - - +
243A ARG* 1.3 80.7 - - + +
245A LYS* 1.3 63.1 + - - +
246A SER* 3.7 6.8 + - - -
247A ALA* 3.0 31.1 + - + +
248A TYR 3.2 7.8 + - - -
281A ASP* 4.1 4.5 - - - +
285A ASN* 2.9 31.1 + - - +
288A ARG* 3.9 7.3 - - - +
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Residues in contact with LYS 245 (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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113A ALA 5.1 0.4 + - - -
114A SER* 2.8 30.7 + - - +
116A THR* 5.8 4.4 - - - +
240A LYS 3.5 1.6 + - - -
241A CYS* 3.7 41.0 + - - +
244A ASN* 1.3 72.9 + - - +
246A SER* 1.3 63.7 + - - +
248A TYR* 3.0 13.3 + - - +
249A PHE* 3.1 31.7 + - + -
274A ARG* 3.2 33.4 - - - +
278A ASP* 4.5 0.9 - - - +
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Residues in contact with SER 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A ASN* 3.2 3.2 + - - -
245A LYS* 1.3 78.3 - - - +
247A ALA* 1.3 58.7 + - - +
249A PHE* 3.4 0.9 + - - -
250A ALA* 3.0 25.6 + - - +
278A ASP* 2.8 27.8 + - - +
281A ASP* 2.9 46.4 + - - +
282A ILE* 3.8 12.6 - - - +
285A ASN* 3.5 10.8 - - - -
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Residues in contact with ALA 247 (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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240A LYS* 6.2 0.4 - - - -
244A ASN* 3.0 35.0 + - + +
246A SER* 1.3 76.9 - - - +
248A TYR* 1.3 66.9 + - - +
250A ALA* 3.2 2.8 + - - +
251A GLU* 3.0 23.9 + - - +
285A ASN* 3.6 18.1 - - + +
288A ARG* 4.1 9.6 - - - +
289A LEU* 4.2 8.6 - - + +
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Residues in contact with TYR 248 (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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106A GLY 4.9 0.3 + - - -
109A ILE* 4.2 2.8 - - - +
110A GLU* 3.3 37.6 + - + +
113A ALA* 5.9 0.2 - - + -
237A ALA* 3.9 29.4 - - + +
240A LYS* 4.1 39.8 - - + +
241A CYS* 3.5 25.1 - - - -
244A ASN 3.2 3.9 + - - +
245A LYS* 3.0 12.6 + - - +
247A ALA* 1.3 80.8 - - - +
249A PHE* 1.3 87.3 + + - +
251A GLU* 3.3 11.4 + - - +
252A ARG* 3.0 39.4 + - + +
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Residues in contact with PHE 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A GLU* 3.9 27.4 - - + -
114A SER* 3.5 25.4 - - - -
115A ARG* 4.0 6.1 - - - -
245A LYS* 3.1 39.7 + - + -
246A SER 3.9 2.9 - - - +
247A ALA 3.2 0.2 - - - -
248A TYR* 1.3 84.3 - + - +
250A ALA* 1.3 65.2 + - - +
252A ARG* 3.4 5.0 - - + +
253A LEU* 2.9 30.2 + - - +
270A VAL* 3.8 23.1 - - + -
273A SER* 5.2 1.3 - - - -
274A ARG* 3.3 49.4 - - + -
278A ASP* 4.5 2.0 - - - -
282A ILE* 3.7 20.4 - - + -
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Residues in contact with ALA 250 (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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246A SER 3.0 15.8 + - - +
247A ALA* 3.4 12.8 - - - +
249A PHE* 1.3 75.0 - - - +
251A GLU* 1.3 58.3 + - - +
253A LEU* 3.3 4.5 + - - +
254A TYR* 2.9 27.7 + - - +
282A ILE* 3.7 28.9 - - - +
285A ASN* 4.1 0.9 - - + -
286A PHE* 3.6 29.2 - - - +
289A LEU* 4.2 5.2 - - + -
290A TYR* 4.4 1.6 - - - -
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Residues in contact with GLU 251 (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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240A LYS* 2.7 40.3 + - - +
247A ALA 3.0 12.7 + - - +
248A TYR* 3.5 14.8 - - - +
250A ALA* 1.3 75.2 - - - +
252A ARG* 1.3 65.1 + - - +
254A TYR 3.1 0.7 + - - -
255A LYS* 2.9 58.8 + - + +
289A LEU* 4.7 3.3 - - + +
290A TYR* 3.3 23.1 + - - +
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Residues in contact with ARG 252 (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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104A ASP* 4.7 1.8 + - - -
106A GLY* 3.2 41.3 + - - -
107A CYS 3.5 0.8 - - - +
110A GLU* 2.6 32.1 + - + +
248A TYR* 3.0 31.7 + - + +
249A PHE* 3.4 15.9 - - + +
251A GLU* 1.3 76.5 - - - +
253A LEU* 1.3 62.0 + - - +
255A LYS* 3.5 9.0 + - - +
256A SER* 3.2 22.1 + - - -
263A ASP* 5.4 2.0 + - - -
266A THR* 3.5 26.7 + - + +
269A ARG* 3.4 12.7 - - - +
270A VAL* 3.7 9.4 - - + -
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Residues in contact with LEU 253 (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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249A PHE 2.9 20.2 + - - +
250A ALA* 3.5 5.2 - - - +
252A ARG* 1.3 74.7 - - - +
254A TYR* 1.3 64.2 + - - +
256A SER* 2.7 20.6 + - - -
257A MET* 3.3 16.0 + - + +
266A THR* 5.7 0.2 - - - -
267A LEU* 3.9 22.7 - - + +
270A VAL* 3.5 33.4 - - + -
271A MET* 3.7 20.0 - - - -
279A MET* 5.2 0.2 - - - -
282A ILE* 3.6 26.9 - - + -
286A PHE* 4.5 0.4 - - + -
294A LEU* 3.9 32.1 - - + -
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Residues in contact with TYR 254 (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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250A ALA 2.9 7.7 + - - +
251A GLU 3.1 5.4 + - - +
253A LEU* 1.3 75.9 - - - +
255A LYS* 1.3 76.2 + - + +
257A MET* 3.1 4.5 + - - +
258A LYS* 2.9 60.0 + - + +
286A PHE* 3.9 9.4 - + + -
290A TYR* 3.4 67.4 - + + -
297A PHE* 3.5 34.3 - + - -
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Residues in contact with LYS 255 (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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251A GLU* 2.9 56.2 + - + +
252A ARG* 3.8 9.6 - - - +
254A TYR* 1.3 96.1 - - + +
256A SER* 1.3 61.1 + - - +
257A MET 3.5 0.5 + - - -
258A LYS* 4.1 11.9 + - - +
263A ASP* 5.3 0.7 - - - +
290A TYR* 4.9 0.9 - - - -
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Residues in contact with SER 256 (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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252A ARG 3.2 11.4 + - - -
253A LEU* 2.7 24.9 + - - -
255A LYS* 1.3 77.6 - - - +
257A MET* 1.3 61.5 + - - +
262A THR* 3.3 9.0 - - - +
263A ASP* 2.8 56.3 + - - -
266A THR* 4.1 13.0 - - - -
267A LEU* 3.8 17.1 - - - +
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Residues in contact with MET 257 (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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253A LEU* 3.3 22.4 - - + +
254A TYR 3.1 2.9 + - - +
256A SER* 1.3 88.3 + - - +
258A LYS* 1.3 56.7 + - - +
259A GLY 3.6 0.4 + - - -
261A GLY 4.4 1.1 - - - -
267A LEU* 4.1 24.5 - - + -
286A PHE* 4.6 1.3 - - + -
294A LEU* 3.9 28.7 - - + -
297A PHE* 3.7 31.8 - - + +
298A ILE* 3.7 31.6 - - + -
301A ASP* 3.1 28.8 - - + +
410A CA 2.4 27.9 - - - -
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Residues in contact with LYS 258 (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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254A TYR* 2.9 53.2 + - + +
255A LYS* 4.1 9.2 + - - +
256A SER 3.9 0.4 - - - -
257A MET* 1.3 77.0 - - - +
259A GLY* 1.3 74.3 + - - +
297A PHE* 3.9 23.3 - - + -
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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