Contacts of the helix formed by residues 252 - 263 (chain A) in PDB entry 5WWW
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 252 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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248A VAL* 3.2 31.6 - - - +
249A GLY 3.1 4.0 + - - -
250A ARG 3.0 2.8 - - - -
251A GLN* 1.3 77.6 - - - +
253A CYS* 1.3 57.5 + - - +
254A LYS 3.2 0.2 + - - -
255A ILE* 3.4 1.2 + - - +
256A LYS* 2.9 35.8 + - - +
8B A 3.2 18.1 + - - -
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Residues in contact with CYS 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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248A VAL 3.4 1.4 + - - -
249A GLY* 4.3 0.4 - - - -
250A ARG 3.1 19.9 + - - +
251A GLN* 3.1 15.3 - - - -
252A GLY* 1.3 76.5 - - - +
254A LYS* 1.3 61.8 + - + +
256A LYS* 4.0 7.9 - - - +
257A ALA* 3.1 26.7 + - - +
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Residues in contact with LYS 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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246A GLU 3.9 19.3 + - - +
247A ILE* 3.3 14.6 - - - +
248A VAL 3.0 6.1 + - - +
249A GLY* 4.2 12.3 - - - -
253A CYS* 1.3 80.2 - - + +
255A ILE* 1.3 60.5 + - - +
257A ALA* 3.4 6.6 + - - +
258A LEU* 3.0 26.2 + - - +
300A PHE* 5.2 0.2 - - - -
5B U 2.5 44.6 + - - -
6B U 5.3 3.9 + - - -
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Residues in contact with ILE 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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247A ILE* 3.9 16.3 + - + +
248A VAL* 3.2 21.2 + - + -
252A GLY 3.4 9.4 - - - +
254A LYS* 1.3 78.7 - - - +
256A LYS* 1.3 60.1 + - - +
258A LEU* 3.3 26.1 + - + +
259A ARG* 2.9 32.3 + - - +
266A ILE* 4.1 25.4 - - + -
268A THR* 4.2 5.2 - - - +
277A PHE* 4.0 21.3 - - + -
293A ILE* 4.5 3.1 - - + -
8B A 3.5 39.9 - - + +
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Residues in contact with LYS 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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251A GLN 3.8 16.4 + - - +
252A GLY 2.9 22.0 + - - +
253A CYS* 4.0 7.5 - - - +
255A ILE* 1.3 74.5 - - - +
257A ALA* 1.3 65.1 + - - +
259A ARG* 3.3 8.8 + - - +
260A ALA* 3.0 23.4 + - - +
8B A 3.5 43.4 + - + +
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Residues in contact with ALA 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 CYS 3.1 18.7 + - - +
254A LYS* 3.4 7.6 + - - +
256A LYS* 1.3 75.7 - - - +
258A LEU* 1.3 57.6 + - - +
260A ALA* 3.3 7.0 + - - +
261A LYS* 2.8 31.0 + - - +
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Residues in contact with LEU 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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247A ILE* 6.0 0.9 - - + -
254A LYS 3.0 14.5 + - - +
255A ILE* 3.5 22.0 - - + +
256A LYS 3.2 0.2 - - - -
257A ALA* 1.3 74.1 - - - +
259A ARG* 1.3 59.7 + - - +
261A LYS* 3.3 6.2 + - + -
262A THR* 2.6 51.7 + - + +
266A ILE* 4.1 10.8 - - + -
289A ALA* 4.0 9.9 - - + +
292A GLU* 3.4 39.9 - - + +
293A ILE* 3.8 29.6 - - + +
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Residues in contact with ARG 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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255A ILE 2.9 17.8 + - - +
256A LYS* 3.3 10.3 + - - +
258A LEU* 1.3 74.5 - - - +
260A ALA* 1.3 54.2 + - - +
263A ASN* 2.7 33.3 + - - -
264A THR* 3.1 32.3 + - - +
265A TYR* 3.5 28.7 - - - +
266A ILE* 3.4 31.0 - - + +
8B A 2.8 41.4 + - - +
9B G 3.0 17.8 + - - +
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Residues in contact with ALA 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 LYS 3.0 13.2 + - - +
257A ALA* 3.6 10.8 - - - +
259A ARG* 1.3 80.0 - - - +
261A LYS* 1.3 63.4 + - - +
263A ASN* 3.6 6.9 + - - +
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Residues in contact with LYS 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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257A ALA 2.8 21.5 + - - +
258A LEU* 3.8 9.0 - - + +
260A ALA* 1.3 74.1 - - - +
262A THR* 1.3 62.4 + - + +
263A ASN* 3.9 0.3 + - - +
288A MET* 4.5 16.0 - - - +
292A GLU* 2.6 36.2 + - - +
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Residues in contact with THR 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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258A LEU* 2.6 37.8 + - + +
261A LYS* 1.3 80.9 - - + +
263A ASN* 1.3 70.3 + - - +
264A THR* 2.7 24.2 + - - +
285A ASP* 3.0 36.8 - - - +
288A MET* 3.8 34.5 - - + -
289A ALA* 3.8 13.9 - - - +
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Residues in contact with ASN 263 (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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230A VAL* 6.0 0.9 - - - +
259A ARG 2.7 16.8 + - - -
260A ALA 3.6 7.4 + - - +
261A LYS 3.6 0.4 - - - +
262A THR* 1.3 76.8 - - - +
264A THR* 1.3 58.2 + - - +
280A THR 4.6 1.6 - - - +
281A GLY* 4.6 6.9 - - - -
282A ARG* 5.1 6.9 + - - +
285A ASP* 3.9 17.5 + - - +
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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