Contacts of the helix formed by residues 240 - 247 (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 SER 240 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122A TYR* 3.4 16.4 - - - -
239A TYR* 1.3 77.5 - - - +
241A ALA* 1.3 62.1 + - - +
242A ASP* 2.6 19.6 + - - -
243A ASN* 2.8 28.9 + - - +
666A SER 2.9 20.8 + - - -
669A PRO* 4.0 6.5 - - - -
791A PRO* 3.4 1.4 - - - +
792A ILE* 2.9 36.5 + - - +
1979A GOL 3.5 2.6 - - - -
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Residues in contact with ALA 241 (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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122A TYR* 4.1 0.6 + - - -
239A TYR* 4.6 7.9 - - - -
240A SER* 1.3 72.3 - - - +
242A ASP* 1.3 60.7 + - - +
243A ASN 3.1 0.2 - - - -
244A LEU* 3.2 18.5 + - - +
257A TRP* 4.9 3.8 - - + -
261A TYR* 3.7 27.1 - - + +
264A SER* 3.8 9.9 - - - +
267A PHE* 3.3 42.2 - - + +
667A GLY* 2.9 13.7 + - - +
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Residues in contact with ASP 242 (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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115A CYS* 3.5 18.2 + - - +
119A TYR* 4.0 5.7 - - + +
120A VAL 4.6 3.4 - - - +
122A TYR* 3.3 9.4 + - - -
240A SER* 2.6 28.4 + - - -
241A ALA* 1.3 68.7 - - - +
243A ASN* 1.3 58.8 + - - +
244A LEU 3.1 2.2 - - - -
245A LEU* 2.9 33.6 + - + +
267A PHE* 3.5 32.3 - - + -
791A PRO* 3.3 17.1 - - - +
1979A GOL 2.5 26.6 + - - -
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Residues in contact with ASN 243 (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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239A TYR* 3.5 18.8 - - + +
240A SER 2.8 16.6 + - - +
242A ASP* 1.3 80.7 + - - +
244A LEU* 1.3 57.0 + - - +
246A ASP* 2.9 25.0 + - - +
247A ALA 3.6 3.1 + - - -
441A CYS* 3.6 16.6 - - - -
474A PRO* 4.3 1.4 - - - +
475A GLY* 2.9 23.5 + - - -
476A THR 2.8 31.9 + - - +
791A PRO* 3.6 14.5 - - + +
792A ILE 3.8 11.1 - - - +
793A TYR* 3.7 9.6 - - - +
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Residues in contact with LEU 244 (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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239A TYR* 4.0 16.4 - - + +
241A ALA 3.2 14.7 + - - +
242A ASP 3.1 0.4 - - - -
243A ASN* 1.3 77.7 - - - +
245A LEU* 1.3 61.7 + - - +
246A ASP 3.1 0.2 - - - -
247A ALA* 3.1 22.3 + - - +
250A ILE* 3.9 25.8 - - + +
252A MET* 4.1 1.3 - - + -
257A TRP* 3.7 33.0 - - + -
267A PHE 4.1 4.3 - - - +
268A LEU* 3.7 35.0 - - + +
271A ALA* 3.6 17.1 - - + +
441A CYS* 3.9 26.5 - - + -
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Residues in contact with LEU 245 (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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118A ASP 5.6 0.4 - - - +
119A TYR* 3.9 17.0 - - + -
120A VAL* 3.7 46.0 - - + +
242A ASP* 2.9 17.3 + - + +
244A LEU* 1.3 76.8 - - - +
246A ASP* 1.3 58.0 + - - +
247A ALA 3.5 3.3 - - - +
267A PHE* 3.9 24.7 - - + +
270A GLU* 4.2 6.1 - - + +
271A ALA* 3.8 29.6 - - - +
274A LYS* 2.5 51.8 + - + +
333B ILE* 5.9 0.9 - - + -
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Residues in contact with ASP 246 (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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119A TYR* 2.6 40.8 + - - -
243A ASN* 2.9 11.6 + - - +
245A LEU* 1.3 81.3 - - - +
247A ALA* 1.3 58.7 + - - +
248A GLU* 4.1 2.6 + - - +
274A LYS* 4.5 3.3 + - - -
439A ARG* 3.8 12.1 + - - +
474A PRO* 4.2 15.5 - - + +
475A GLY* 3.7 22.4 - - - +
791A PRO* 3.8 11.3 - - - +
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Residues in contact with ALA 247 (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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243A ASN 3.6 0.8 + - - -
244A LEU* 3.1 17.8 + - - +
245A LEU 4.5 3.5 - - - +
246A ASP* 1.3 79.5 - - - +
248A GLU* 1.3 60.5 + - - +
249A LEU 3.9 4.9 - - - +
250A ILE* 3.8 15.3 - - + -
276A ALA* 3.6 16.5 + - - +
439A ARG 3.7 4.0 - - - +
441A CYS* 3.7 18.6 - - + -
475A GLY 3.6 20.2 - - - +
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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