Contacts of the helix formed by residues 129 - 132 (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 LYS 129 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A CYS* 3.3 15.0 - - - +
128A GLN* 1.3 102.5 + - + +
130A GLY* 1.3 64.5 + - - +
132A ALA 3.2 4.3 + - - -
133A PHE* 3.2 21.7 + - - +
259A TYR 4.3 4.2 + - - -
262A PRO* 4.5 4.0 - - - +
851A ARG* 2.7 30.7 + - - +
852A VAL 3.8 6.3 - - - +
853A SER* 3.7 13.5 - - - +
854A ILE* 3.6 26.0 - - + +
858A HIS* 3.5 42.4 + - + +
864A LEU* 3.8 14.4 - - + +
1986A MGD 3.2 15.3 + - - -
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Residues in contact with GLY 130 (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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82A HIS* 3.1 47.6 + - - -
94A PHE* 4.2 2.2 - - - -
106A GLU* 3.2 15.6 - - - +
127A CYS* 3.5 7.9 + - - -
128A GLN 3.4 0.2 - - - -
129A LYS* 1.3 80.1 - - - +
131A SER* 1.3 55.9 + - - +
132A ALA 3.1 2.6 + - - -
133A PHE* 3.3 6.7 + - - -
1984A SF4 3.7 11.7 - - - -
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Residues in contact with SER 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A PHE* 3.4 18.2 - - - -
106A GLU* 3.4 25.6 - - - +
108A GLN* 3.8 2.9 + - - -
127A CYS 2.8 22.4 + - - -
128A GLN 3.9 0.2 - - - -
129A LYS 3.3 0.4 - - - -
130A GLY* 1.3 76.2 - - - +
132A ALA* 1.3 57.5 + - - +
33B THR* 3.4 16.0 - - - +
36B VAL* 3.6 23.4 - - - +
37B ALA* 5.4 0.9 - - - -
40B ASN* 4.2 10.9 + - - +
229B GLN* 3.8 15.8 + - - -
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Residues in contact with ALA 132 (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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106A GLU* 3.8 2.0 - - - -
128A GLN 3.3 15.6 + - - +
129A LYS 3.2 4.0 + - - -
130A GLY 3.1 0.4 - - - -
131A SER* 1.3 78.4 - - - +
133A PHE* 1.3 58.6 + - - +
134A ASN* 3.2 4.3 - - - -
135A ASN* 2.8 45.9 + - - +
136A ASN* 4.1 3.1 + - - +
863A HIS* 3.8 10.8 - - + -
864A LEU* 3.8 20.0 - - + +
36B VAL* 4.0 4.5 - - + -
40B ASN* 3.9 7.4 - - - +
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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