Contacts of the strand formed by residues 898 - 905 (chain B) in PDB entry 2IV9
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 TRP 898 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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829B ASP* 3.8 18.2 - - - -
830B GLY* 3.5 32.3 - - - -
831B LYS 4.0 11.2 - - - -
832B MET* 3.5 43.5 - - + -
890B SER* 4.1 2.7 - - - -
891B LEU 3.4 19.5 - - - -
892B LYS* 3.4 30.6 - - + +
896B GLY 3.3 13.0 + - - -
897B ILE* 1.3 73.9 - - - +
899B ILE* 1.3 61.3 + - - +
900B LEU* 4.5 7.1 - - + +
918B CYS* 3.5 22.5 - - - -
919B ARG 4.8 1.2 + - - -
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Residues in contact with ILE 899 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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832B MET* 5.0 0.7 - - - +
890B SER* 3.4 6.9 - - - -
891B LEU* 2.8 71.4 + - + +
893B LEU* 3.8 27.6 - - + -
897B ILE* 3.8 11.9 - - + +
898B TRP* 1.3 77.7 - - - +
900B LEU* 1.3 73.5 + - - +
916B LEU* 4.2 22.2 - - + -
917B LYS 4.0 6.3 - - - +
918B CYS* 3.7 17.5 - - + -
923B VAL* 4.0 13.0 - - + -
924B SER* 6.0 0.7 - - - +
927B ILE* 4.2 11.9 - - + -
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Residues in contact with LEU 900 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
832B MET* 3.9 24.0 - - + -
837B PHE* 3.6 42.2 - - + +
840B THR* 3.9 21.3 - - + -
841B TRP* 3.6 36.4 - - + +
844B ILE* 4.3 7.4 - - + -
889B GLN 3.7 4.3 - - - -
898B TRP* 4.5 9.6 - - + +
899B ILE* 1.3 79.3 - - - +
901B ALA* 1.3 61.6 + - - +
916B LEU* 3.4 4.0 - - - -
917B LYS* 2.9 43.7 + - + +
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Residues in contact with ALA 901 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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837B PHE* 3.6 2.6 - - - -
841B TRP* 4.2 0.9 - - - -
873B VAL* 6.1 0.4 - - + -
887B LEU 4.3 0.2 - - - -
888B TYR* 3.5 2.8 - - - -
889B GLN* 2.8 53.2 + - + +
891B LEU* 5.2 8.7 - - + -
900B LEU* 1.3 75.3 - - - +
902B GLU* 1.3 65.0 - - - +
903B LEU 4.2 0.2 - - - -
914B LEU* 3.9 11.9 - - + -
915B SER 3.2 5.4 - - - +
916B LEU* 3.5 22.0 - - + -
931B TYR* 5.1 3.8 - - + -
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Residues in contact with GLU 902 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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837B PHE* 3.9 3.6 - - + -
841B TRP* 3.4 52.5 + - + -
886B MET* 3.9 22.2 - - - +
887B LEU 3.3 4.5 - - - -
888B TYR* 3.4 36.3 - - + -
901B ALA* 1.3 79.8 - - - +
903B LEU* 1.3 59.9 + - - +
904B ARG 4.1 0.2 - - - -
913B THR 3.5 2.6 - - - +
914B LEU* 3.6 2.7 - - - -
915B SER* 2.9 37.7 + - - +
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Residues in contact with LEU 903 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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854B ILE* 3.8 28.3 - - + -
864B VAL* 3.7 26.5 - - + -
885B ASP 3.7 0.7 - - - +
886B MET* 3.4 4.4 - - - -
887B LEU* 2.8 56.8 + - + +
889B GLN* 4.1 3.6 + - - +
901B ALA 4.2 0.2 - - - -
902B GLU* 1.3 74.3 - - - +
904B ARG* 1.3 60.3 + - - +
905B ILE* 3.8 14.4 + - + +
912B TYR* 3.9 19.1 - - + -
913B THR 3.4 12.8 - - - +
914B LEU* 3.8 8.7 - - + -
931B TYR* 3.6 27.8 - - + +
935B LEU* 5.1 1.1 - - + -
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Residues in contact with ARG 904 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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884B GLN* 3.0 35.4 + - + +
885B ASP 3.4 7.6 - - - +
886B MET* 3.7 27.1 - - + -
902B GLU 4.1 0.2 - - - -
903B LEU* 1.3 71.6 - - - +
905B ILE* 1.3 62.8 + - - +
906B GLN* 3.6 23.2 + - - +
909B ASN* 4.1 11.5 - - - +
911B ASN 4.7 1.5 + - - +
912B TYR* 3.4 9.9 - - - +
913B THR* 2.9 59.8 + - - +
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Residues in contact with ILE 905 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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859B LEU 5.4 0.2 - - - +
860B ASN* 6.1 0.4 - - - -
861B ALA* 3.8 34.3 - - + +
864B VAL* 4.4 2.7 - - + -
884B GLN* 4.6 0.7 - - - -
885B ASP* 2.7 49.8 + - + +
887B LEU* 3.9 20.6 - - + -
903B LEU* 3.8 14.3 + - + +
904B ARG* 1.3 77.4 - - - +
906B GLN* 1.3 63.9 + - - +
907B PRO* 3.6 6.4 - - + +
912B TYR* 3.7 48.0 - - + +
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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