Contacts of the helix formed by residues 256 - 261 (chain A) 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 256 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255A SER* 1.3 75.7 - - - +
257A TRP* 1.3 60.5 + - - +
258A SER* 4.0 1.0 - - - -
259A TYR* 2.9 45.0 + - - +
260A THR* 2.8 25.6 + - + +
286A ASN* 3.9 1.1 + - - -
287A PRO* 3.5 29.2 - - - +
288A THR* 2.8 28.7 + - - -
849A HIS 5.0 0.4 + - - -
919A TYR* 4.0 10.3 - - - -
1986A MGD 2.9 36.1 + - - +
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Residues in contact with TRP 257 (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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88A PRO* 5.8 0.4 - - + -
239A TYR* 4.3 7.9 - + - -
241A ALA* 4.9 6.3 - - + -
244A LEU* 3.7 35.2 - - + -
252A MET* 3.8 25.5 - - + -
255A SER* 4.0 4.8 + - - -
256A ASN* 1.3 71.4 - - - +
258A SER* 1.3 67.4 + - - +
260A THR* 3.5 11.9 - - - -
261A TYR* 2.8 69.7 + + + +
262A PRO 3.6 0.2 - - - -
264A SER 4.2 10.8 - - - -
265A TYR* 3.8 24.4 - - + -
268A LEU* 4.1 12.1 - - + -
288A THR* 3.1 12.7 + - + +
443A TYR* 3.2 54.7 - + + -
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Residues in contact with SER 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A TRP* 1.3 77.4 - - - +
259A TYR* 1.3 61.9 + - - +
262A PRO* 4.3 5.0 - - - +
265A TYR* 3.6 19.2 - - - -
287A PRO* 3.1 37.2 + - - -
288A THR* 2.9 9.4 + - - -
851A ARG* 3.1 17.0 + - - +
29B LEU* 2.8 40.8 + - - +
31B CYS* 5.1 2.1 - - - +
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Residues in contact with TYR 259 (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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129A LYS* 4.3 1.4 + - - -
256A ASN* 2.9 25.7 + - - +
258A SER* 1.3 81.9 - - - +
260A THR* 1.3 68.7 + - + +
261A TYR 3.6 0.7 - - - -
262A PRO* 3.6 9.8 - - - +
287A PRO* 3.4 19.5 - - + -
849A HIS 3.3 13.2 - - - +
851A ARG* 3.1 75.5 + - + +
875A HIS* 4.4 3.3 + - - -
906A ARG* 5.9 0.2 + - - -
919A TYR* 3.5 39.0 - + + -
1986A MGD 2.8 22.8 + - - -
132B GLU* 5.3 2.6 - - - -
133B ASP* 2.5 21.4 + - - -
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Residues in contact with THR 260 (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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86A CYS* 5.3 2.1 - - - +
87A TRP 2.9 25.0 + - - +
88A PRO 5.1 0.2 - - - +
256A ASN* 2.8 26.8 + - + +
257A TRP* 3.5 8.0 - - - -
259A TYR* 1.3 84.2 - - + +
261A TYR* 1.3 56.8 + - - +
262A PRO* 3.5 5.2 - - - +
443A TYR* 5.8 0.2 - - - -
849A HIS* 4.0 12.6 - - + +
1986A MGD 2.8 78.3 + - - +
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Residues in contact with TYR 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A PRO* 3.4 45.5 - - + -
241A ALA* 3.7 6.7 - - + +
257A TRP* 2.8 71.2 + + + -
260A THR* 1.3 74.3 + - - +
262A PRO* 1.4 62.2 - - - +
263A SER* 3.2 17.7 - - - -
264A SER* 3.1 17.8 + - - -
265A TYR* 2.8 25.6 + - - +
667A GLY* 3.0 25.7 + - - -
668A ASN* 2.5 31.5 + - - -
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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