Contacts of the helix formed by residues 249 - 258 (chain B) in PDB entry 5YL4
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 ASP 249 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98A ASP* 3.7 26.3 + - - +
100A ALA* 5.5 0.2 - - - +
1B MET* 3.2 48.4 - - + +
46B ARG* 5.9 0.9 - - - +
131B GLN* 3.2 17.0 - - - +
240B LEU* 3.9 4.3 - - - -
248B ALA* 1.3 72.4 - - - +
250B LEU* 1.3 64.7 + - - +
251B ARG* 3.1 5.2 + - - +
252B LYS* 2.8 26.4 + - - +
253B LEU* 3.1 24.2 + - - +
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Residues in contact with LEU 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B MET* 4.4 0.2 - - - +
4B ILE* 3.9 27.1 - - + -
131B GLN* 3.1 18.7 + - + +
132B GLY* 4.1 27.1 - - - +
133B PHE 4.8 3.4 - - - +
134B GLN* 6.2 1.1 - - + -
163B ILE* 3.8 25.8 - - + +
165B ASN* 3.6 23.1 + - + +
198B GLU* 4.9 0.9 - - - +
240B LEU* 3.6 24.2 - - + +
249B ASP* 1.3 75.3 - - - +
251B ARG* 1.3 57.2 + - - +
253B LEU* 3.8 5.6 - - + +
254B ALA* 2.8 30.7 + - - +
506B 8WR 3.8 18.8 - - + +
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Residues in contact with ARG 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A GLU* 3.2 25.7 + - - +
98A ASP 5.4 0.4 + - - -
100A ALA* 3.7 15.0 - - + +
105A ARG* 3.4 41.4 - - - +
407A TRP* 4.6 4.7 - - + -
411A GLU* 4.9 1.8 - - - -
1B MET* 3.3 23.2 - - + +
131B GLN 4.7 1.8 + - - -
161B ASP 2.8 17.8 + - - -
162B ARG* 3.5 14.1 - - - +
163B ILE* 3.8 23.5 - - + +
249B ASP* 3.1 9.3 + - - +
250B LEU* 1.3 76.5 - - - +
252B LYS* 1.3 52.7 + - - +
254B ALA* 3.2 1.0 + - - +
255B VAL* 2.7 47.7 + - + +
503B MES 2.5 39.2 + - - +
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Residues in contact with LYS 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A GLN* 5.6 0.2 + - - -
98A ASP* 3.9 12.4 + - - +
100A ALA* 3.8 25.7 - - - +
101A ASN* 3.3 43.1 - - - +
501A GTP 2.6 28.3 + - - -
502A MG 3.5 6.5 - - - -
247B ASN* 2.8 32.8 + - - +
248B ALA* 4.1 9.6 - - + +
249B ASP* 2.8 24.8 + - - +
251B ARG* 1.3 72.1 - - - +
253B LEU* 1.3 62.7 + - - +
255B VAL* 3.5 1.2 + - - +
256B ASN* 2.9 32.2 + - - +
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Residues in contact with LEU 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239B CYS* 3.9 15.7 - - - -
240B LEU* 4.5 11.7 - - + -
246B LEU* 4.9 0.7 - - + -
248B ALA* 3.6 23.1 - - + -
249B ASP 3.1 20.5 + - - +
250B LEU* 3.8 3.6 - - - +
252B LYS* 1.3 74.3 - - - +
254B ALA* 1.3 64.2 + - - +
256B ASN* 3.1 7.3 + - - +
257B MET* 3.0 27.0 + - - +
506B 8WR 3.0 84.6 - - + +
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Residues in contact with ALA 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407A TRP* 3.7 19.9 - - + -
163B ILE* 4.4 9.0 - - + -
197B ASP* 4.7 5.8 - - + -
198B GLU* 3.5 25.7 + - + +
250B LEU 2.8 19.2 + - - +
251B ARG* 3.5 7.0 - - - +
253B LEU* 1.3 76.4 - - - +
255B VAL* 1.3 62.6 + - - +
257B MET 3.1 0.5 + - - -
258B VAL* 3.0 32.9 + - + +
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Residues in contact with VAL 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A ALA* 3.4 33.0 - - + +
101A ASN 4.5 2.0 - - - +
102A ASN* 5.1 8.1 - - + +
182A VAL* 4.3 24.9 - - + +
404A PHE* 3.1 29.5 - - - -
407A TRP* 3.7 46.3 + - + -
408A TYR* 5.8 1.8 - - + +
251B ARG* 2.7 32.8 + - + +
252B LYS 3.7 3.4 - - - +
254B ALA* 1.3 72.8 - - - +
256B ASN* 1.3 59.2 + - - +
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Residues in contact with ASN 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A ASN* 3.2 28.5 - - - +
179A THR 4.0 6.9 + - - +
180A ALA* 3.4 6.7 - - - +
181A VAL* 2.7 47.9 + - + +
182A VAL* 3.8 10.2 + - - +
404A PHE* 3.9 6.9 - - - -
252B LYS* 2.9 24.3 + - - +
253B LEU* 3.1 8.6 + - - +
255B VAL* 1.3 80.0 - - - +
257B MET* 1.3 61.3 + - - +
312B THR* 3.6 16.6 - - - +
506B 8WR 5.0 9.1 - - + -
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Residues in contact with MET 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198B GLU* 4.3 2.7 - - - +
253B LEU 3.0 19.3 + - - +
254B ALA 4.1 1.6 - - - +
256B ASN* 1.3 78.6 - - - +
258B VAL* 1.3 61.2 + - + +
259B PRO* 3.2 6.6 - - - +
266B PHE* 3.7 24.9 - - + -
312B THR* 3.0 43.0 + - - +
313B VAL 4.3 1.8 - - - +
314B ALA* 3.9 10.5 - - + +
368B ILE* 3.7 43.3 - - + +
370B ASN* 3.0 18.8 + - + -
506B 8WR 3.7 36.6 - - - +
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Residues in contact with VAL 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404A PHE* 3.6 4.9 - - - -
406A HIS* 3.3 4.2 - - + +
407A TRP* 2.9 31.5 + - + +
197B ASP 3.6 20.9 - - - +
198B GLU* 4.6 0.7 - - + -
254B ALA* 3.0 23.9 + - + +
256B ASN 3.8 1.0 - - - -
257B MET* 1.3 80.1 - - + +
259B PRO* 1.4 59.6 - - - +
260B PHE 3.1 26.2 - - - +
261B PRO* 4.2 7.6 - - + +
263B LEU 4.0 2.7 - - - +
264B HIS* 3.9 17.9 - - + -
266B PHE* 4.1 17.3 - - + -
370B ASN* 4.4 1.3 - - - +
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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