Contacts of the strand formed by residues 873 - 877 (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 VAL 873 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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869A ARG* 4.1 29.8 - - + +
871A GLN* 3.5 12.1 - - + +
872A PRO* 1.3 80.7 - - - +
874A VAL* 1.3 63.1 + - - +
875A HIS* 3.9 14.7 + - + +
903A ILE* 3.5 10.5 - - - +
904A MET* 3.1 14.8 - - + +
905A VAL 4.4 0.7 - - - -
906A ARG* 3.4 45.5 - - + +
917A ILE 3.9 3.6 - - - +
918A VAL* 3.8 13.0 - - - +
919A TYR* 4.7 1.0 + - - -
921A TRP* 3.3 16.9 + - + +
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Residues in contact with VAL 874 (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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873A VAL* 1.3 74.2 - - - +
875A HIS* 1.3 72.3 + - - +
876A MET* 3.7 9.2 + - + -
892A ALA* 4.9 0.2 - - + -
894A LEU* 4.3 12.1 - - + -
903A ILE* 3.4 30.1 - - + +
904A MET 2.7 16.1 + - - +
905A VAL* 3.5 18.5 - - + +
906A ARG 2.8 24.4 + - - +
916A CYS* 3.9 21.5 - - + -
917A ILE 3.3 10.8 - - - +
918A VAL* 3.8 15.7 - - + -
973A ILE* 5.2 0.2 - - + -
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Residues in contact with HIS 875 (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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259A TYR* 4.4 2.0 + - - -
873A VAL* 3.9 17.3 - - + +
874A VAL* 1.3 75.1 - - - +
876A MET* 1.3 59.7 + - - +
906A ARG* 3.3 46.6 + - + +
908A ALA* 5.4 1.7 - - + +
910A ASN* 5.2 2.8 + - - -
911A VAL* 3.8 21.5 - - + +
916A CYS* 3.3 8.8 - - - +
917A ILE* 2.8 50.1 + - + +
919A TYR* 3.7 34.0 + + - -
133B ASP* 4.1 23.1 + - + +
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Residues in contact with MET 876 (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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843A PHE* 4.1 10.1 - - + -
874A VAL* 4.4 10.5 - - + -
875A HIS* 1.3 78.2 - - - +
877A ASN* 1.3 64.5 + - - +
880A ASP* 4.2 0.9 - - + -
881A ALA* 3.8 29.6 - - + +
884A LEU* 4.0 18.8 - - + -
886A ILE* 4.4 4.0 - - + -
905A VAL* 3.8 31.6 - - + -
906A ARG 2.8 9.0 + - - +
907A THR* 3.3 2.9 - - - -
908A ALA 2.9 24.9 + - - +
911A VAL* 3.7 6.5 - - - +
915A GLN 4.7 2.7 - - - -
916A CYS* 4.5 1.6 - - + -
973A ILE* 3.7 43.5 - - + -
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Residues in contact with ASN 877 (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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876A MET* 1.3 73.7 - - - +
878A SER* 1.3 67.8 + - - +
879A LYS* 2.9 31.2 + - - +
880A ASP* 3.1 30.4 + - - +
881A ALA* 2.9 19.8 + - - +
908A ALA 3.3 6.0 + - - -
909A PRO* 3.9 14.5 + - - +
911A VAL* 2.8 37.1 + - + +
912A GLN 4.1 4.7 - - - +
913A PRO* 4.1 19.2 - - - +
915A GLN 4.5 0.8 + - - -
139B TRP* 4.2 8.1 - - - +
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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