Contacts of the helix formed by residues 248 - 260 (chain A) in PDB entry 4X4W
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 SER 248 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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246A ASN 4.1 0.2 + - - -
247A ALA* 1.3 71.5 - - - +
249A LEU* 1.3 64.3 + - - +
250A GLU* 3.5 9.7 + - - +
251A GLU* 3.2 27.5 + - - +
252A PHE* 3.0 19.4 + - - +
272A SER 3.6 8.8 - - - +
273A LEU* 4.2 7.8 + - - +
275A LYS* 4.1 21.2 - - - +
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Residues in contact with LEU 249 (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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229A ILE* 4.7 2.7 - - + -
230A HIS* 4.0 26.9 - - + +
233A TYR* 4.1 36.8 - - + -
234A ASP* 5.8 0.2 - - - +
247A ALA* 3.2 11.3 + - + +
248A SER* 1.3 74.6 - - - +
250A GLU* 1.3 56.1 + - - +
252A PHE* 3.3 11.2 + - + +
253A ASP* 2.9 33.7 + - - +
273A LEU* 4.0 22.7 - - + -
188B ASP* 3.5 41.3 - - + +
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Residues in contact with GLU 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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248A SER* 3.1 8.6 + - - +
249A LEU* 1.3 78.6 - - - +
251A GLU* 1.3 61.6 + - - +
253A ASP* 3.2 10.3 + - - +
254A LYS* 3.1 53.8 + - + +
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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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248A SER* 3.2 18.8 + - - +
250A GLU* 1.3 76.7 - - - +
252A PHE* 1.3 60.1 + - - +
254A LYS* 3.1 20.7 + - - +
255A VAL* 2.8 38.4 + - - +
272A SER* 3.4 22.0 - - - +
304A ARG* 4.2 10.2 - - - +
342A TYR* 2.6 37.9 + - - +
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Residues in contact with PHE 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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220A LEU* 5.4 1.1 - - + -
225A VAL* 3.8 10.1 - - + -
226A ASN* 3.5 32.5 - - - -
229A ILE* 3.4 44.6 - - + -
230A HIS* 4.4 7.2 - + - -
248A SER 3.0 13.5 + - - +
249A LEU* 3.5 11.7 - - + +
251A GLU* 1.3 78.0 - - - +
253A ASP* 1.3 63.8 + - - +
256A SER* 2.9 36.3 + - - -
269A LEU* 3.8 28.3 - - + -
270A LEU* 6.3 0.2 - - - -
272A SER* 3.3 24.1 + - - +
273A LEU* 3.8 23.1 - - + -
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Residues in contact with ASP 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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226A ASN* 2.9 14.1 + - - +
230A HIS* 2.7 33.1 + - - -
249A LEU* 2.9 19.7 + - - +
250A GLU* 3.6 11.3 - - + +
251A GLU 3.2 0.2 - - - -
252A PHE* 1.3 76.0 - - - +
254A LYS* 1.3 63.2 + - + +
256A SER* 3.3 15.3 + - - -
257A LYS* 3.3 15.7 + - - +
185B LYS* 3.4 34.7 - - + +
188B ASP* 5.9 0.2 - - - +
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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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250A GLU* 3.1 47.8 + - + +
251A GLU* 3.6 22.3 + - - +
253A ASP* 1.3 78.1 - - + +
255A VAL* 1.3 60.4 + - + +
257A LYS* 3.3 9.7 + - - +
258A ASN* 2.9 37.5 + - - +
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Residues in contact with VAL 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* 2.8 26.7 + - - +
254A LYS* 1.3 76.6 - - + +
256A SER* 1.3 65.5 + - - +
258A ASN* 3.0 8.3 + - - +
259A VAL* 2.9 35.0 + - + +
268A THR 4.4 2.9 - - - +
269A LEU* 3.7 16.8 - - + -
272A SER* 3.6 13.2 - - - +
342A TYR* 3.6 58.3 - - + +
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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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225A VAL* 4.8 6.8 - - - +
226A ASN* 3.0 34.9 + - - +
252A PHE* 2.9 25.2 + - - -
253A ASP 3.3 3.3 + - - -
255A VAL* 1.3 76.8 - - - +
257A LYS* 1.3 61.9 + - - +
259A VAL* 3.7 5.1 - - - +
260A ASP* 3.4 23.9 + - - +
269A LEU* 3.6 23.3 - - - +
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Residues in contact with LYS 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 ASP 3.3 10.6 + - - +
254A LYS* 3.5 12.1 - - - +
255A VAL 3.2 0.4 - - - -
256A SER* 1.3 80.3 + - - +
258A ASN* 1.3 69.5 + - - +
259A VAL 3.4 0.2 + - - -
260A ASP* 3.5 17.2 + - - +
346A HIS* 4.9 3.5 + - - -
185B LYS* 6.1 4.3 - - - +
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Residues in contact with ASN 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 LYS* 2.9 23.2 + - - +
255A VAL* 3.0 12.2 + - - +
257A LYS* 1.3 82.9 - - - +
259A VAL* 1.3 60.1 + - - +
260A ASP 3.6 0.2 + - - -
262A PHE* 4.2 1.7 - - - +
341A LYS* 3.5 10.5 - - - +
342A TYR 2.9 27.6 + - - +
343A GLN* 3.4 14.1 + - - +
344A GLY* 3.5 13.7 - - - -
346A HIS* 2.8 32.2 + - - -
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Residues in contact with VAL 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 VAL* 2.9 27.9 + - + +
256A SER* 3.7 12.1 - - - +
258A ASN* 1.3 72.5 - - - +
260A ASP* 1.3 62.5 + - - +
261A GLY 3.1 0.3 + - - -
262A PHE* 2.8 31.6 + - - +
264A PRO* 3.6 37.6 - - + +
268A THR* 4.5 5.6 - - + -
269A LEU* 4.2 15.5 - - + -
341A LYS* 3.5 32.3 - - + +
342A TYR* 4.0 9.0 - - - +
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Residues in contact with ASP 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 SER 3.4 17.2 + - - +
257A LYS* 3.6 14.0 - - - +
258A ASN 3.4 1.5 - - - +
259A VAL* 1.3 76.3 - - - +
261A GLY* 1.3 61.9 + - - +
262A PHE* 3.3 17.0 - - - -
264A PRO* 5.7 0.4 - - - -
346A HIS* 5.3 0.2 + - - -
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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