Contacts of the helix formed by residues 250 - 257 (chain B) in PDB entry 1IRD
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 THR 250 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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248B LEU 3.4 0.4 - - - -
249B SER* 1.3 92.3 + - - +
251B PRO* 1.3 76.8 - - - +
252B ASP* 3.4 7.1 + - - +
253B ALA* 2.9 23.8 + - - +
254B VAL* 2.9 26.2 + - - +
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Residues in contact with PRO 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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119A PRO* 4.8 5.2 - - + -
120A ALA* 4.2 28.3 - - + +
233B VAL* 4.0 35.2 - - + -
250B THR* 1.3 85.5 - - - +
252B ASP* 1.3 58.9 + - - +
254B VAL* 3.1 2.9 + - - +
255B MET* 2.9 35.2 + - + +
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Residues in contact with ASP 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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250B THR* 3.2 6.8 + - - +
251B PRO* 1.3 82.9 - - - +
253B ALA* 1.3 63.6 + - - +
255B MET* 4.2 5.6 - - - +
256B GLY* 2.9 22.9 + - - -
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Residues in contact with ALA 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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247B ASP* 3.6 42.4 - - + +
249B SER* 4.0 1.6 - - - +
250B THR* 2.9 26.9 + - - +
252B ASP* 1.3 77.8 - - - +
254B VAL* 1.3 61.9 + - - +
256B GLY* 3.8 1.0 - - - -
257B ASN* 3.1 24.6 + - - +
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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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229B GLY* 3.6 37.0 - - - +
232B LEU* 4.2 20.6 - - + -
233B VAL* 3.9 14.1 - - + -
239B GLN* 5.1 3.4 - - - +
247B ASP 4.3 0.2 + - - -
248B LEU* 3.7 34.5 - - + +
250B THR 2.9 19.0 + - - +
251B PRO 3.5 5.8 - - - +
253B ALA* 1.3 76.6 - - - +
255B MET* 1.4 62.8 + - - +
257B ASN* 3.2 19.5 + - - +
260B VAL* 3.7 12.6 - - + +
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Residues in contact with MET 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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119A PRO* 3.8 30.1 - - + -
225B GLY 4.2 2.5 - - - +
226B GLU* 3.6 56.5 - - - +
229B GLY* 3.6 29.4 - - - +
230B ARG* 3.8 2.2 - - + +
233B VAL* 4.5 1.8 - - - -
251B PRO 2.9 21.8 + - - +
252B ASP* 4.2 5.2 - - - +
254B VAL* 1.4 77.9 - - - +
256B GLY* 1.3 58.6 + - - +
257B ASN 3.7 2.6 + - - +
260B VAL* 5.3 2.7 - - - +
261B LYS* 5.6 5.0 + - - +
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Residues in contact with GLY 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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252B ASP 2.9 16.4 + - - -
253B ALA 3.8 2.2 - - - -
255B MET* 1.3 77.8 - - - +
257B ASN* 1.3 63.1 + - - +
258B PRO* 3.3 9.7 - - - +
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Residues in contact with ASN 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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245B PHE* 2.9 24.4 + - - +
247B ASP* 2.9 29.0 + - - +
248B LEU* 3.9 5.1 - - - +
253B ALA 3.1 10.5 + - - +
254B VAL* 3.2 16.4 + - - +
255B MET 3.4 1.2 - - - +
256B GLY* 1.3 75.2 - - - +
258B PRO* 1.3 72.8 - - - +
259B LYS* 2.8 25.3 + - - +
260B VAL* 3.1 23.4 + - + +
261B LYS* 3.2 10.6 + - - +
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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