Contacts of the helix formed by residues 251 - 263 (chain B) in PDB entry 4H0N
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 PRO 251 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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223B TYR* 5.2 0.2 - - + -
249B ASP 3.8 2.9 - - - +
250B LYS* 1.3 97.8 - - + +
252B ARG* 1.3 65.6 + - - +
253B GLU* 3.4 14.8 - - + +
254B VAL* 3.3 34.6 + - + +
255B VAL* 3.5 12.0 + - - +
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Residues in contact with ARG 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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223B TYR* 3.5 54.5 + - + +
225B THR* 2.5 39.4 + - - -
226B SER* 4.2 8.3 + - - +
250B LYS 3.8 0.4 + - - -
251B PRO* 1.3 71.2 - - - +
253B GLU* 1.3 69.4 + - - +
255B VAL* 3.5 4.0 + - - +
256B GLN* 2.8 40.1 + - - +
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Residues in contact with GLU 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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251B PRO* 3.4 13.1 - - + +
252B ARG* 1.3 92.0 + - + +
254B VAL* 1.3 59.9 + - + +
256B GLN* 3.5 8.3 - - - +
257B LYS* 2.9 41.9 + - - +
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Residues in contact with VAL 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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250B LYS* 4.2 15.3 - - + -
251B PRO* 3.3 36.7 + - + +
253B GLU* 1.3 76.7 - - + +
255B VAL* 1.3 66.0 + - - +
257B LYS* 3.3 10.6 + - - +
258B CYS* 3.1 21.9 + - + +
278B GLU 6.1 0.2 - - - +
279B LEU* 3.9 16.8 - - + -
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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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221B ILE* 4.0 12.3 - - + -
223B TYR* 3.7 28.7 - - + +
248B THR* 4.0 15.7 - - + +
250B LYS* 4.6 3.6 - - + -
251B PRO 3.5 11.8 + - - +
252B ARG 3.6 6.7 - - - +
253B GLU 3.4 0.2 - - - -
254B VAL* 1.3 77.8 - - - +
256B GLN* 1.3 67.0 + - - +
258B CYS* 3.1 4.0 + - - +
259B TYR* 2.9 48.9 + - + -
279B LEU* 3.9 26.0 - - + -
281B LEU* 5.1 1.1 - - + -
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Residues in contact with GLN 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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223B TYR* 4.5 5.9 + - - -
252B ARG* 2.8 33.6 + - - +
253B GLU* 3.5 12.7 - - - +
255B VAL* 1.3 82.8 - - - +
257B LYS* 1.3 61.9 + - - +
259B TYR* 3.3 11.5 + - - +
260B ALA* 3.1 24.1 + - - +
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Residues in contact with LYS 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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253B GLU* 2.9 28.5 + - - +
254B VAL* 3.7 9.9 - - - +
255B VAL 3.2 0.4 - - - -
256B GLN* 1.3 76.8 - - - +
258B CYS* 1.3 57.9 + - - +
260B ALA* 3.7 6.0 + - + +
261B ALA* 3.2 26.3 + - - +
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Residues in contact with CYS 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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254B VAL 3.1 12.3 + - - +
255B VAL 3.1 8.2 + - - +
257B LYS* 1.3 76.2 - - - +
259B TYR* 1.3 65.8 + - - +
261B ALA* 3.3 6.0 + - - +
262B ALA* 3.0 22.5 + - - +
275B LEU* 3.6 45.5 - - + +
276B PHE* 3.9 12.6 - - - -
279B LEU* 3.9 26.0 - - + -
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Residues in contact with TYR 259 (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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216B ALA 2.4 32.2 + - - -
217B LYS* 4.5 8.5 + - - -
219B PHE* 3.6 20.8 + - - +
221B ILE* 3.8 12.6 - - + +
255B VAL* 2.9 43.2 + - + -
256B GLN* 3.3 15.2 + - + +
258B CYS* 1.3 78.3 - - - +
260B ALA* 1.3 63.4 + - - +
261B ALA 3.2 0.9 + - - -
262B ALA* 3.3 2.4 + - - +
263B ALA* 3.2 20.9 + - - +
276B PHE* 3.8 32.3 - + - -
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Residues in contact with ALA 260 (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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256B GLN 3.1 13.5 + - - +
257B LYS* 4.0 7.2 - - + +
259B TYR* 1.3 78.3 - - - +
261B ALA* 1.3 62.1 + - - +
263B ALA* 3.4 17.9 + - - +
264B GLN* 3.8 12.6 + - - +
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Residues in contact with ALA 261 (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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257B LYS 3.2 19.7 + - - +
258B CYS* 3.6 7.2 - - - +
259B TYR 3.1 0.6 - - - -
260B ALA* 1.3 77.8 - - - +
262B ALA* 1.3 61.5 + - - +
263B ALA 3.2 1.0 + - - -
264B GLN* 3.3 18.8 + - - +
265B ASN* 3.1 14.7 + - - -
275B LEU* 4.0 18.4 - - + -
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Residues in contact with ALA 262 (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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258B CYS 3.0 11.2 + - - +
259B TYR 3.9 2.9 - - - +
261B ALA* 1.3 71.3 - - - +
263B ALA* 1.3 56.7 + - - +
264B GLN 2.9 11.0 + - - -
265B ASN* 3.2 20.1 + - - +
266B GLU 4.1 2.8 + - - -
267B ILE* 4.5 3.3 - - - +
272B PHE* 3.5 37.1 - - + -
275B LEU* 3.6 19.2 - - + +
276B PHE* 3.6 20.2 - - + -
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Residues in contact with ALA 263 (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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259B TYR 3.2 11.7 + - - +
260B ALA* 3.5 15.5 - - - +
261B ALA 3.1 1.8 - - - -
262B ALA* 1.3 75.6 - - - +
264B GLN* 1.3 61.6 + - + +
265B ASN 3.6 0.4 - - - -
267B ILE* 4.7 15.4 - - + +
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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