Contacts of the strand formed by residues 969 - 975 (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 969 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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837A VAL* 3.5 32.8 - - + +
844A LYS* 3.5 1.2 - - - -
845A ILE* 2.9 37.1 + - + +
896A ASN* 3.6 3.4 - - - +
935A LEU* 3.6 24.2 - - + +
936A LEU* 3.5 29.4 - - + +
965A THR 3.8 14.4 - - - +
966A ASP* 3.3 18.5 + - - +
967A ARG 3.4 0.6 - - - -
968A GLY* 1.3 78.7 - - - +
970A ARG* 1.3 72.8 + - - +
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Residues in contact with ARG 970 (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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834A THR 5.1 3.8 + - - -
835A PRO 5.0 1.6 + - - -
836A MET* 3.7 46.3 - - - +
837A VAL 2.9 17.0 + - - +
838A GLY 4.7 0.2 - - - -
839A GLY 3.3 29.4 - - - +
840A ASP* 4.2 2.6 + - - -
841A HIS* 2.9 31.3 + - + +
842A PRO* 4.6 6.2 + - - +
843A PHE 3.3 9.4 - - - -
844A LYS* 3.7 35.8 - - - +
896A ASN* 3.0 30.0 + - - +
968A GLY 3.9 3.7 + - - +
969A VAL* 1.3 73.1 - - - +
971A VAL* 1.3 61.6 + - - +
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Residues in contact with VAL 971 (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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841A HIS* 3.4 9.1 - - - +
843A PHE* 2.9 39.3 + - + +
845A ILE* 4.0 22.7 - - + -
894A LEU* 4.6 3.6 - - + -
895A PHE 3.4 11.0 - - - +
896A ASN* 4.3 1.1 - - - +
916A CYS* 3.7 30.7 - - - -
935A LEU* 3.7 37.7 - - + -
969A VAL 3.7 0.2 + - - -
970A ARG* 1.3 81.6 - - - +
972A SER* 1.3 65.0 + - - +
973A ILE* 4.4 5.4 - - + -
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Residues in contact with SER 972 (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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841A HIS* 2.7 30.1 - - - +
842A PRO* 3.2 19.6 - - - +
843A PHE* 4.5 1.1 - - - -
894A LEU* 3.5 1.9 - - - -
895A PHE* 2.7 55.2 + - - -
971A VAL* 1.3 73.2 - - - +
973A ILE* 1.3 67.0 + - - +
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Residues in contact with ILE 973 (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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842A PRO* 5.8 0.2 - - - +
843A PHE* 3.7 35.4 - - + -
876A MET* 3.7 28.5 - - + -
884A LEU* 3.6 28.8 - - + +
886A ILE* 3.9 22.0 - - + -
892A ALA* 3.9 13.2 - - + -
893A LYS 3.3 9.2 - - - +
894A LEU* 3.9 18.2 - - + -
895A PHE* 4.4 2.9 - - - -
916A CYS* 3.9 21.8 - - + -
971A VAL* 4.4 2.7 - - + -
972A SER* 1.3 81.4 - - - +
974A LYS* 1.3 65.1 + - - +
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Residues in contact with LYS 974 (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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884A LEU* 5.2 4.7 - - + -
886A ILE* 3.9 8.3 - - - -
892A ALA* 3.2 4.5 - - - +
893A LYS* 2.8 57.1 + - + +
895A PHE* 4.0 23.1 - - + -
973A ILE* 1.3 75.9 - - - +
975A LYS* 1.3 67.2 + - - +
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Residues in contact with LYS 975 (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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884A LEU 4.5 8.9 + - - +
885A GLY 3.9 14.6 - - - +
886A ILE* 3.8 25.0 - - + +
890A ASP* 3.9 24.0 - - - +
891A MET 3.8 8.3 - - - +
893A LYS* 5.1 0.3 - - - +
974A LYS* 1.3 86.2 - - - +
976A ALA* 1.3 84.8 + - - +
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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