Contacts of the helix formed by residues 485 - 494 (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 ASP 485 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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483A TYR* 3.8 26.7 + - + +
484A SER* 1.3 73.4 - - - +
486A ASP* 1.3 70.2 + - - +
487A ASN* 3.1 8.5 - - - -
488A MET* 3.0 24.1 + - + -
489A VAL* 3.0 40.9 + - + +
776A GLY* 5.3 7.1 - - - -
956A PHE* 4.6 8.7 - - - -
957A MET* 4.4 12.8 - - - +
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Residues in contact with ASP 486 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484A SER* 2.9 23.3 + - - +
485A ASP* 1.3 83.3 + - - +
487A ASN* 1.3 63.3 + - - +
489A VAL* 4.2 6.1 - - - -
490A TYR* 2.9 45.2 + - + +
746A ILE* 3.7 4.0 - - + -
747A ASN* 4.8 1.1 - - - +
750A VAL* 3.5 22.7 - - + +
773A MET 4.1 0.2 - - - +
774A GLY* 3.8 2.8 - - - -
775A THR* 2.6 48.5 + - - -
776A GLY* 4.0 7.7 + - - -
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Residues in contact with ASN 487 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A SER* 3.8 18.0 - - - -
484A SER 3.9 6.2 - - - +
485A ASP* 3.7 14.6 - - - -
486A ASP* 1.3 75.6 + - - +
488A MET* 1.3 64.4 + - - +
491A LEU* 3.2 24.9 + - - +
661A MET* 3.4 23.9 - - + +
663A THR* 4.8 2.8 - - - +
671A PHE* 4.3 9.6 - - - -
743A MET* 3.5 40.5 - - + +
746A ILE* 3.6 13.7 - - - +
747A ASN* 3.8 19.0 + - - +
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Residues in contact with MET 488 (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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193A VAL* 3.8 19.7 - - + -
197A SER* 3.4 44.4 - - - +
200A TRP* 3.9 27.2 - - + -
201A GLY* 4.3 6.4 - - - -
483A TYR* 6.4 0.4 - - + -
484A SER 5.3 1.6 - - - +
485A ASP* 3.0 27.2 + - + +
487A ASN* 1.3 85.0 - - - +
489A VAL* 1.3 62.4 + - + +
491A LEU* 3.4 3.2 + - - +
492A GLY* 2.9 25.8 + - - -
663A THR* 3.5 29.8 - - + -
743A MET* 4.2 3.6 - - - -
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Residues in contact with VAL 489 (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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200A TRP* 4.8 13.0 - - + -
204A PHE* 4.8 10.1 - - + -
485A ASP* 3.0 40.1 + - + +
486A ASP* 4.0 10.3 - - - +
488A MET* 1.3 78.4 - - + +
490A TYR* 1.3 72.8 + - + +
492A GLY* 3.2 2.8 + - - -
493A VAL* 3.2 28.9 + - + +
956A PHE* 5.1 8.7 - - + -
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Residues in contact with TYR 490 (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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486A ASP* 2.9 45.2 + - + +
489A VAL* 1.3 80.9 - - + +
491A LEU* 1.3 68.0 + - - +
493A VAL* 4.2 2.7 - - + -
494A MET* 2.9 42.1 + - + +
503A MET* 3.8 30.1 - - + -
506A LEU* 3.6 32.4 - - + +
507A HIS* 3.0 27.0 + + - -
746A ILE* 3.7 19.1 - - + -
750A VAL* 4.2 4.9 - - + -
775A THR* 2.8 29.2 + - - -
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Residues in contact with LEU 491 (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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198A ILE* 4.4 7.6 - - - -
201A GLY* 4.5 6.7 - - - -
205A ARG* 2.7 33.8 + - - -
487A ASN 3.2 18.5 + - - +
488A MET 3.4 3.3 + - - +
489A VAL 3.4 0.2 - - - -
490A TYR* 1.3 78.1 - - - +
492A GLY* 1.3 52.0 + - - +
494A MET* 4.7 2.2 - - - -
688A TRP* 3.9 24.5 - - + -
729A MET* 4.8 2.0 - - + +
733A LEU* 3.7 29.4 - - + -
739A CYS* 4.2 18.4 - - + +
742A GLU* 4.3 17.3 - - + -
743A MET* 3.4 30.1 - - + -
746A ILE* 3.7 7.6 - - + +
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Residues in contact with GLY 492 (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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201A GLY 4.2 4.7 - - - -
204A PHE* 3.8 17.5 - - - -
205A ARG* 3.4 35.1 + - - +
208A TYR* 3.7 9.5 - - - -
488A MET 2.9 15.2 + - - -
489A VAL 3.2 4.7 + - - -
490A TYR 3.1 0.8 - - - -
491A LEU* 1.3 78.3 - - - +
493A VAL* 1.3 61.4 + - - +
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Residues in contact with VAL 493 (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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204A PHE* 3.6 26.2 - - + -
205A ARG* 4.0 0.9 - - - -
208A TYR* 3.8 32.2 + - + +
489A VAL* 3.2 15.2 + - + +
490A TYR* 3.2 3.8 + - + +
492A GLY* 1.3 82.5 - - - +
494A MET* 1.3 71.0 + - - +
495A SER* 3.5 1.9 + - - -
506A LEU* 3.8 34.5 - - + -
541A VAL* 4.4 10.1 - - + -
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Residues in contact with MET 494 (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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205A ARG* 2.9 29.5 + - - +
490A TYR* 2.9 38.1 + - + +
491A LEU* 4.3 1.6 - - - +
493A VAL* 1.3 78.1 - - - +
495A SER* 1.3 58.7 + - - +
496A LYS 3.4 15.0 + - - +
498A THR* 3.5 7.9 - - - +
502A GLY* 3.4 36.6 - - - +
503A MET* 3.7 18.8 - - - -
506A LEU* 4.1 15.3 - - + -
729A MET* 3.8 7.0 - - + +
742A GLU* 3.4 28.9 - - + +
746A ILE* 3.9 5.6 - - + -
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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