Contacts of the helix formed by residues 254 - 262 (chain A) in PDB entry 5ID6
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 GLY 254 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A LYS* 3.6 8.6 + - - -
239A ALA 4.3 0.7 - - - -
240A ILE 3.2 13.2 - - - -
241A ILE 3.3 9.6 - - - -
243A GLY* 3.6 13.8 - - - -
253A LYS 1.3 70.9 - - - +
255A LEU* 1.3 66.2 + - - +
256A ASN 3.4 0.4 - - - -
257A GLU* 2.4 33.5 + - - +
258A TYR* 3.6 10.2 + - - -
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Residues in contact with LEU 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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190A PHE* 4.9 0.2 - - + -
197A PHE* 3.7 33.6 - - + -
202A VAL* 5.7 4.0 - - + -
206A LYS* 3.4 28.5 - - + +
216A VAL* 4.2 10.1 - - + -
220A PHE* 3.8 19.7 - - + -
240A ILE* 2.8 35.3 + - + +
241A ILE* 3.1 2.6 + - - +
254A GLY* 1.3 72.9 - - - -
256A ASN* 1.3 64.3 + - - +
258A TYR* 3.0 18.8 + - + +
259A ILE* 3.1 17.2 + - - +
273A PHE* 3.5 32.8 - - + -
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Residues in contact with ASN 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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241A ILE* 3.1 33.3 + - + +
242A GLY* 5.4 2.2 - - - +
255A LEU* 1.3 74.8 - - - +
257A GLU* 1.3 56.9 + - - +
259A ILE* 3.4 8.1 + - - +
260A ASN* 2.9 29.3 + - - +
272A LYS* 3.2 29.6 - - + +
273A PHE* 3.0 48.0 - - - +
492A LEU* 3.7 11.8 - - - +
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Residues in contact with GLU 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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242A GLY 2.8 19.8 - - - +
243A GLY* 4.9 0.7 - - - -
251A LYS* 5.4 9.9 + - - +
252A ILE 4.7 1.4 - - - +
253A LYS* 3.7 29.9 - - + +
254A GLY* 2.4 40.1 + - - +
255A LEU 3.3 0.8 - - - -
256A ASN* 1.3 76.7 - - - +
258A TYR* 1.3 53.8 + - - +
260A ASN* 3.2 8.8 - - - +
261A LEU* 2.7 39.7 + - + +
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Residues in contact with TYR 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A ILE* 4.6 6.7 - - + +
197A PHE* 4.0 25.4 - + + -
201A GLU* 3.3 61.8 + - + +
205A ILE* 3.8 16.3 - - - +
206A LYS* 3.1 30.7 + - - -
252A ILE* 4.6 0.9 - - - +
253A LYS* 3.5 38.6 + - + +
254A GLY 3.6 4.2 + - - -
255A LEU* 3.0 10.8 + - + +
257A GLU* 1.3 75.9 - - - +
259A ILE* 1.3 60.8 + - - +
261A LEU* 3.1 14.8 + - + +
262A TYR* 3.0 26.7 + - - +
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Residues in contact with ILE 259 (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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193A VAL* 4.1 20.0 - - + -
196A ILE* 5.1 2.5 - - + -
197A PHE* 4.3 9.6 - - + -
255A LEU 3.1 24.8 + - - +
256A ASN* 3.7 15.9 - - - +
258A TYR* 1.3 74.7 - - - +
260A ASN* 1.3 62.4 + - - +
262A TYR* 2.9 10.2 + - + +
268A GLN* 2.9 34.4 + - - +
270A LEU* 3.2 33.9 - - + +
271A PRO 3.9 14.4 - - - +
272A LYS* 4.2 11.0 - - + -
273A PHE* 3.9 23.1 - - + -
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Residues in contact with ASN 260 (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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256A ASN 2.9 12.9 + - - +
257A GLU* 3.2 13.7 - - - +
259A ILE* 1.3 76.1 - - - +
261A LEU* 1.3 58.3 + - + +
263A ASN* 2.8 36.3 + - - +
268A GLN* 4.7 2.4 + - - +
272A LYS* 3.1 28.5 + - - +
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Residues in contact with LEU 261 (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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201A GLU* 6.0 0.9 - - - +
253A LYS* 4.1 31.9 - - + -
257A GLU* 2.7 25.0 + - + +
258A TYR* 3.1 17.4 + - + +
260A ASN* 1.3 73.2 - - + +
262A TYR* 1.3 56.2 + - - +
263A ASN* 3.1 14.3 + - - +
264A ALA* 3.7 10.9 + - - +
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Residues in contact with TYR 262 (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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196A ILE* 3.4 48.5 - - + +
258A TYR 3.0 10.0 + - - +
259A ILE* 2.9 14.7 + - - +
261A LEU* 1.3 78.8 - - - +
263A ASN* 1.3 55.7 + - - +
264A ALA* 3.0 10.1 - - + -
265A LYS* 3.4 51.1 + - + +
268A GLN* 2.6 22.0 + - - +
270A LEU* 4.0 16.6 - - + -
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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