Contacts of the helix formed by residues 931 - 936 (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 PRO 931 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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611A MET 3.6 20.4 - - - +
612A ARG* 4.9 0.9 - - + -
618A ALA* 3.4 20.9 - - + -
901A CYS* 3.9 1.1 - - - +
921A TRP 4.7 1.6 - - - +
923A ALA* 4.0 13.0 - - + +
926A TYR* 3.4 29.2 - - + -
929A TRP 3.3 10.9 - - - +
930A LYS* 1.3 87.4 - - - +
932A TYR* 1.3 67.5 + - - +
933A ASP* 3.5 20.2 - - + +
934A ILE* 3.0 24.0 + - + +
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Residues in contact with TYR 932 (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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845A ILE* 3.5 34.8 - - + -
846A THR 4.3 1.2 - - - -
847A GLY* 3.8 14.0 + - - -
894A LEU* 4.5 2.7 - - + -
901A CYS* 3.7 20.9 - - - -
903A ILE* 5.0 0.4 - - + -
918A VAL* 3.5 53.0 + - + -
920A PHE* 4.4 10.8 - - + -
926A TYR* 3.3 20.1 + - + +
931A PRO* 1.3 71.8 - - - +
933A ASP* 1.3 78.4 + - - +
934A ILE 3.0 1.6 + - - -
935A LEU* 3.1 28.4 + - + +
936A LEU* 3.5 22.5 - - + +
966A ASP* 4.0 2.1 + - - -
967A ARG* 3.9 4.9 + - - -
1987A MD1 2.9 32.3 + - - -
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Residues in contact with ASP 933 (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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611A MET 5.0 0.4 - - - +
612A ARG* 3.0 33.9 - - - +
614A LYS 4.2 9.0 - - - +
615A ARG* 5.0 1.9 - - - -
616A SER 2.7 28.2 + - - -
618A ALA* 5.7 0.7 - - + -
920A PHE* 4.7 5.2 - - - +
921A TRP 4.5 2.8 - - - +
926A TYR* 4.5 1.6 + - - -
931A PRO* 3.0 21.9 - - + +
932A TYR* 1.3 88.2 - - - +
934A ILE* 1.3 57.3 + - - +
935A LEU 3.0 1.3 + - - -
936A LEU* 3.1 20.3 + - + +
1987A MD1 3.0 31.7 + - - -
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Residues in contact with ILE 934 (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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616A SER* 2.7 26.8 + - - +
618A ALA* 4.2 20.0 - - + +
619A LYS* 4.0 33.9 - - + +
898A PHE* 3.2 16.5 - - - -
899A ALA* 3.8 20.6 - - + -
900A ASP 3.6 24.2 - - - +
901A CYS* 4.5 0.4 - - + -
930A LYS* 3.9 31.4 - - + -
931A PRO* 3.0 22.8 + - + +
932A TYR 4.3 0.9 - - - +
933A ASP* 1.3 77.4 - - - +
935A LEU* 1.3 60.6 + - + +
936A LEU 3.4 0.2 - - - -
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Residues in contact with LEU 935 (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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616A SER* 3.9 1.1 - - - -
845A ILE* 4.9 0.4 - - + -
894A LEU* 3.8 37.2 - - + +
895A PHE* 4.0 9.2 - - - -
896A ASN* 3.0 32.8 + - - +
898A PHE* 4.2 6.5 - - - -
899A ALA 4.1 8.1 - - - +
900A ASP* 4.4 3.6 - - - -
901A CYS* 4.5 6.1 - - - -
932A TYR* 3.1 23.8 - - + +
933A ASP 3.0 0.4 - - - -
934A ILE* 1.3 82.8 - - + +
936A LEU* 1.3 75.9 + - + +
937A ILE* 3.5 9.8 - - - +
969A VAL* 3.6 4.7 - - + +
971A VAL* 3.7 26.7 - - + -
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Residues in contact with LEU 936 (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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615A ARG* 3.9 9.9 - - + -
837A VAL* 4.2 0.7 - - - +
845A ILE* 3.7 17.7 - - + -
932A TYR* 3.5 25.4 - - + +
933A ASP* 3.1 33.5 + - + +
934A ILE 3.4 0.4 - - - -
935A LEU* 1.3 96.4 - - + +
937A ILE* 1.3 57.4 + - - +
938A GLY* 2.7 18.2 + - - -
965A THR 4.6 0.5 - - - +
966A ASP* 3.5 31.1 - - + +
969A VAL* 3.5 20.8 - - + +
1987A MD1 3.4 29.8 - - - +
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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