Contacts of the helix formed by residues 224 - 229 (chain B) in PDB entry 2IVF
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 ASN 224 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B THR* 4.3 2.4 + - - -
150B MET* 4.7 1.2 - - - +
213B LEU* 3.9 17.6 - - + +
214B CYS* 3.7 19.3 - - + -
218B ILE* 3.9 5.9 - - + +
222B ILE 3.6 1.2 + - - -
223B ALA* 1.3 73.3 - - - +
225B ALA* 1.3 59.6 + - - +
226B CYS* 3.4 10.9 - - - -
227B ASN* 2.9 41.3 + - - +
228B ARG* 2.9 23.7 + - - +
237B PHE* 3.5 13.3 - - - -
1359B SF4 3.3 33.5 - - - -
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Residues in contact with ALA 225 (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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37B ALA* 3.9 7.0 - - + +
41B ILE* 3.6 31.2 - - + -
214B CYS* 3.4 7.0 - - - -
217B ARG* 3.7 16.7 - - - +
223B ALA 3.6 1.0 + - - -
224B ASN* 1.3 74.5 - - - +
226B CYS* 1.3 59.4 + - - +
228B ARG* 4.4 0.9 - - - +
229B GLN* 2.8 50.4 + - - +
1359B SF4 3.9 10.8 - - - -
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Residues in contact with CYS 226 (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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34B CYS* 3.5 35.2 - - + +
54B ASN* 3.3 23.1 - - - +
150B MET* 4.0 7.4 - - - -
224B ASN* 3.4 18.6 - - - -
225B ALA* 1.3 78.7 - - - +
227B ASN* 1.3 59.5 - - - +
230B CYS* 3.8 10.9 + - - +
235B ARG* 3.6 22.0 - - - +
1359B SF4 2.3 39.2 - - - -
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Residues in contact with ASN 227 (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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21B THR* 2.9 32.0 + - - +
224B ASN* 2.9 32.8 + - - +
225B ALA 3.2 0.4 - - - -
226B CYS* 1.3 78.1 - - - +
228B ARG* 1.3 65.5 + - - +
229B GLN 3.3 0.4 + - - -
230B CYS* 3.7 13.5 + - - +
235B ARG* 2.9 46.9 + - + +
236B ALA 4.6 0.2 - - - -
237B PHE* 3.4 17.9 - - + +
337B TRP* 5.2 0.3 + - - -
341B PHE* 3.5 22.3 - - + -
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Residues in contact with ARG 228 (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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107A GLU* 2.8 29.1 + - - +
108A GLN* 2.8 25.7 + - - +
109A ALA* 3.1 23.4 + - - +
110A ALA* 3.8 4.4 - - - +
124A PRO* 3.7 7.6 - - - +
217B ARG* 3.7 15.0 - - - +
222B ILE* 4.8 0.4 - - - -
223B ALA* 4.1 7.9 - - + -
224B ASN 2.9 16.9 + - - +
225B ALA 4.2 0.7 - - - +
227B ASN* 1.3 77.3 - - - +
229B GLN* 1.3 60.5 + - - +
230B CYS 3.3 3.9 + - - -
337B TRP* 3.2 37.2 + - + -
341B PHE* 3.8 8.9 - - + -
347B ASP* 4.9 0.2 + - - -
348B PRO* 3.5 21.2 - - - +
1353B GOL 3.1 53.5 + - - -
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Residues in contact with GLN 229 (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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105A ARG* 2.9 24.0 + - - +
106A GLU 3.9 5.3 + - - -
107A GLU* 3.5 36.6 - - + +
108A GLN* 2.8 49.1 + - - +
124A PRO* 4.3 0.4 - - - -
131A SER* 3.8 17.6 + - - -
33B THR* 3.3 8.5 - - + +
34B CYS 5.4 0.4 - - - -
37B ALA* 3.3 29.5 - - + +
225B ALA* 2.8 22.7 + - - +
226B CYS 4.6 1.1 - - - -
228B ARG* 1.3 77.0 - - - +
230B CYS* 1.3 56.8 + - - +
231B PRO* 2.9 10.7 - - - +
1358B SF4 5.0 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