Contacts of the helix formed by residues 897 - 910 (chain B) in PDB entry 6VSB
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 897 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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707A TYR* 3.6 8.3 - - - +
708A SER 3.6 6.9 - - - +
709A ASN* 3.4 30.7 - - + +
711A SER 3.1 24.5 - - - +
712A ILE* 4.6 1.3 - - + -
1077A THR* 3.8 5.6 - - - +
896B ILE* 1.3 89.5 - - + +
898B PHE* 1.3 67.1 + - - +
899B ALA* 4.6 2.9 - - + +
900B MET* 3.2 37.5 + - + +
901B GLN* 3.1 17.2 + - - +
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Residues in contact with PHE 898 (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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707A TYR* 2.9 20.3 + - + +
797B PHE* 3.3 31.9 - - + +
800B PHE* 3.4 37.9 - + + -
802B PHE* 3.6 22.4 - + - -
882B ILE* 3.4 32.1 - - + +
896B ILE 3.3 3.8 + - - -
897B PRO* 1.3 71.8 - - - +
899B ALA* 1.3 66.0 + - - +
901B GLN* 2.9 15.3 + - + +
902B MET* 2.8 46.3 + - + +
927B PHE* 6.0 0.9 - + - -
1050B MET* 3.9 23.3 - - + -
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Residues in contact with ALA 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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1130A ILE* 5.7 0.7 - - + -
797B PHE 5.1 0.8 + - - -
798B GLY* 5.0 6.0 - - - -
800B PHE* 5.5 2.7 - - + -
897B PRO* 3.3 3.2 - - + +
898B PHE* 1.3 80.9 - - - +
900B MET* 1.3 58.8 + - + +
902B MET* 3.3 6.0 + - - +
903B ALA* 2.9 24.3 + - - +
916B LEU* 3.2 13.4 - - + +
917B TYR* 4.0 11.3 - - + -
920B GLN* 3.6 36.3 - - - +
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Residues in contact with MET 900 (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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709A ASN 5.5 0.2 - - - +
712A ILE* 4.7 4.7 - - + -
1077A THR* 3.5 29.8 - - + -
1078A ALA 4.5 9.0 - - - +
1079A PRO* 4.6 17.0 - - + -
1094A VAL* 3.6 35.2 - - + -
1095A PHE 5.1 0.4 - - - +
1107A ARG* 3.9 11.1 + - - +
896B ILE* 4.3 8.5 - - + -
897B PRO* 3.2 36.5 + - + +
898B PHE 3.2 0.8 - - - -
899B ALA* 1.3 74.9 - - + +
901B GLN* 1.3 65.6 + - - +
903B ALA* 3.2 3.1 + - - +
904B TYR* 3.1 18.4 + - - +
917B TYR* 3.3 24.7 - - + +
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Residues in contact with GLN 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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881B THR 2.7 21.4 + - - -
882B ILE 2.9 24.1 + - - +
885B GLY* 3.0 28.1 + - - -
886B TRP* 4.5 8.6 - - + -
896B ILE* 3.9 18.6 - - + +
897B PRO 3.1 11.5 + - - +
898B PHE* 2.9 15.5 + - - +
900B MET* 1.3 76.9 - - - +
902B MET* 1.3 63.1 + - - +
904B TYR* 3.3 7.6 + - - +
905B ARG* 3.1 52.7 + - - +
1050B MET* 3.8 10.3 - - - +
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Residues in contact with MET 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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720B ILE* 6.3 1.6 - - + -
800B PHE* 4.2 18.6 - - + -
898B PHE* 2.8 34.5 + - + +
899B ALA* 3.7 5.2 - - - +
901B GLN* 1.3 76.9 - - - +
903B ALA* 1.3 58.3 + - - +
905B ARG* 3.0 20.4 + - - +
906B PHE* 2.8 47.1 + - + +
916B LEU* 3.5 28.5 - - + -
923B ILE* 5.4 2.5 - - + -
927B PHE* 5.8 2.0 - - + -
1049B LEU* 4.7 11.7 - - + -
1050B MET* 3.6 28.9 - - + -
1065B VAL* 5.5 5.4 - - + -
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Residues in contact with ALA 903 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1107A ARG* 5.1 2.5 - - - +
899B ALA 2.9 8.8 + - - +
900B MET 3.2 5.6 + - - +
902B MET* 1.3 76.0 - - - +
904B TYR* 1.3 62.5 + - - +
906B PHE* 3.3 4.9 + - - +
907B ASN* 3.0 20.6 + - - +
913B GLN* 4.1 21.4 - - + +
916B LEU* 3.1 15.3 - - + +
917B TYR* 3.4 41.3 - - + +
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Residues in contact with TYR 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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909A ILE 5.5 2.8 + - - -
910A GLY* 6.1 0.7 - - - -
1093A GLY 6.3 0.4 - - - -
1107A ARG* 3.1 51.5 - - - +
886B TRP* 3.3 38.3 - + + -
900B MET 3.1 6.4 + - - +
901B GLN 3.6 8.3 - - - +
902B MET 3.2 0.2 - - - -
903B ALA* 1.3 77.1 - - - +
905B ARG* 1.3 60.9 + - + +
907B ASN* 2.9 23.4 + - + +
908B GLY* 2.8 29.4 + - - -
1036B GLN* 4.8 8.1 - - - -
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Residues in contact with ARG 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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881B THR* 4.2 11.5 + - - -
885B GLY 4.3 1.2 - - - -
886B TRP* 4.2 31.3 - - + +
901B GLN* 3.1 45.5 + - + +
902B MET* 3.0 21.9 + - - +
904B TYR* 1.3 77.4 - - + +
906B PHE* 1.3 63.3 + - - +
908B GLY 3.2 1.2 + - - -
909B ILE* 3.1 13.3 + - - +
1033B VAL 5.1 2.6 + - - -
1035B GLY 3.5 24.2 + - - -
1036B GLN* 3.0 44.5 + - + +
1049B LEU* 2.7 45.5 + - + +
1050B MET* 3.7 17.0 - - - +
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Residues in contact with PHE 906 (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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718B PHE* 4.2 11.2 - + - -
720B ILE* 4.7 1.6 - - + -
902B MET* 2.8 25.1 + - + +
903B ALA* 3.5 9.9 - - - +
905B ARG* 1.3 75.9 - - - +
907B ASN* 1.3 63.1 + - - +
909B ILE* 2.9 28.9 - - + +
911B VAL* 3.0 31.3 + - + +
912B THR 5.1 2.2 - - - +
913B GLN* 5.1 1.3 - - - -
915B VAL* 4.8 2.0 - - + -
916B LEU* 3.6 29.6 - - + -
923B ILE* 3.5 39.5 - - + -
1049B LEU* 3.4 37.7 - - + -
1067B TYR* 4.2 16.4 - + - -
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Residues in contact with ASN 907 (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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1091A ARG 5.0 9.9 + - - -
1092A GLU* 6.2 0.4 - - - +
903B ALA 3.0 12.6 + - - +
904B TYR* 2.9 28.9 + - + +
906B PHE* 1.3 76.7 - - - +
908B GLY* 1.3 60.6 + - - +
910B GLY* 3.0 16.1 + - - -
911B VAL 3.3 12.7 + - - +
912B THR* 5.8 1.3 - - - -
913B GLN* 4.9 20.8 + - + +
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Residues in contact with GLY 908 (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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904B TYR* 2.8 22.4 + - - -
905B ARG 3.2 4.4 + - - -
907B ASN* 1.3 74.4 - - - +
909B ILE* 1.3 61.9 + - - +
910B GLY* 3.3 0.5 + - - -
1036B GLN* 4.1 13.9 - - - -
1038B LYS* 4.6 20.5 - - - +
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Residues in contact with ILE 909 (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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905B ARG 3.1 14.0 + - - +
906B PHE* 2.9 27.8 - - + +
908B GLY* 1.3 76.2 - - - +
910B GLY* 1.3 57.0 + - - +
911B VAL* 3.5 22.2 - - + -
1036B GLN* 3.7 1.1 - - - +
1047B TYR* 3.9 29.1 - - + -
1048B HIS 3.4 26.0 - - - +
1049B LEU* 3.7 9.9 - - + -
1067B TYR* 3.4 41.5 - - + -
1108B ASN* 3.7 10.8 + - + +
904C TYR* 5.8 0.2 + - - -
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Residues in contact with GLY 910 (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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907B ASN 3.0 12.7 + - - -
908B GLY 3.2 0.6 - - - -
909B ILE* 1.3 77.7 - - - +
911B VAL* 1.3 60.1 + - - +
912B THR 4.2 0.7 + - - -
1106B GLN* 4.6 10.6 - - - +
1108B ASN* 3.2 27.3 + - - +
904C TYR* 6.0 1.6 - - - -
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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