Contacts of the helix formed by residues 249 - 253 (chain A) in PDB entry 5IVK
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 CYS 249 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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245A GLY* 3.9 4.5 - - - -
246A ASN* 3.2 37.1 + - - +
247A ALA 3.8 2.3 - - - +
248A ILE* 1.3 78.9 - - - +
250A PRO* 1.3 72.0 - - + +
251A TRP* 3.3 33.2 - - + +
252A ALA* 3.0 16.3 + - + +
253A ASN* 4.3 2.1 + - - +
420A TYR 3.4 18.6 - - - -
421A PHE* 4.8 1.8 - - - -
424A PRO* 3.6 16.4 - - - -
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Residues in contact with PRO 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 ILE 3.4 4.4 - - - +
249A CYS* 1.3 85.3 - - + +
251A TRP* 1.3 65.5 + - + +
252A ALA 3.2 1.6 + - - -
253A ASN* 3.4 17.8 - - - +
306A LYS 5.6 4.7 - - - +
378A SER* 6.0 1.6 - - - +
419A PHE* 3.6 50.0 - - + +
420A TYR* 4.2 9.2 - - + -
424A PRO* 4.0 6.1 - - + -
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Residues in contact with TRP 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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138A PHE* 4.6 6.8 - + - -
218A SER* 3.4 27.4 - - - -
219A ALA* 3.8 22.9 - - + -
222A ALA* 4.0 18.2 - - + -
244A SER 4.1 0.2 - - - -
245A GLY* 3.9 11.2 - - - -
249A CYS* 3.3 24.7 - - + +
250A PRO* 1.3 77.1 - - + +
252A ALA* 1.3 64.7 + - + +
253A ASN 3.4 2.7 + - - +
306A LYS 5.7 1.6 - - - -
308A MET* 3.9 41.1 - - + +
309A PHE* 3.9 21.6 - + + -
313A PRO* 5.9 0.2 - - - +
420A TYR* 2.9 52.3 + + + +
421A PHE* 4.0 14.2 - + - -
601A DPF 4.2 18.4 - - - -
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Residues in contact with ALA 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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138A PHE* 4.2 4.3 - - - -
222A ALA* 3.9 13.2 - - + -
226A TYR* 2.6 22.5 + - - +
246A ASN 3.6 22.0 - - - +
247A ALA* 3.8 8.5 - - - +
249A CYS* 3.0 15.2 + - + +
251A TRP* 1.3 95.0 - - + +
253A ASN* 1.3 54.6 + - - +
313A PRO* 3.4 19.8 - - - +
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Residues in contact with ASN 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 TYR* 3.2 13.7 - - - +
247A ALA 4.9 5.3 - - - +
249A CYS 4.3 2.0 + - - +
250A PRO 3.4 15.6 + - - +
251A TRP 3.4 4.0 + - - -
252A ALA* 1.3 81.4 - - - +
254A THR* 1.3 73.4 + - - +
255A GLN* 3.5 22.0 + - - +
312A GLY* 5.7 0.2 - - - -
313A PRO* 3.1 16.2 + - - +
314A THR* 3.9 5.7 - - - +
315A VAL* 4.1 10.7 - - - +
325A LEU* 5.8 1.7 - - + +
328A HIS* 4.8 8.2 + - - -
329A PRO* 4.7 14.7 - - + +
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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