Contacts of the helix formed by residues 909 - 917 (chain B) in PDB entry 1FVR
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 ASN 909 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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833B GLY 5.5 2.0 - - - +
907B HIS 4.1 0.3 - - - +
908B GLY* 1.3 74.6 - - - -
910B LEU* 1.3 61.1 + - - +
911B LEU* 3.0 13.7 + - - +
912B ASP* 2.7 47.0 + - - +
913B PHE* 3.1 18.4 + - - +
967B ALA 4.3 0.2 - - - +
968B ARG* 3.6 23.2 - - - +
970B ILE 3.2 13.7 - - - +
971B LEU* 3.9 10.4 - - + +
972B VAL* 4.4 0.7 - - - -
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Residues in contact with LEU 910 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
908B GLY 3.9 1.0 + - - -
909B ASN* 1.3 70.2 - - - +
911B LEU* 1.3 61.1 + - - +
913B PHE* 4.1 2.7 - - + -
914B LEU* 2.8 55.2 + - + +
944B PHE* 4.0 31.6 - - + -
948B VAL* 5.2 2.5 - - + -
967B ALA* 3.4 12.1 + - + +
970B ILE* 2.8 38.7 + - + +
972B VAL* 3.9 22.2 - - + +
978B ALA* 6.0 0.2 - - + -
1027B LEU* 4.3 12.1 - - + -
1031B ILE* 4.1 27.8 - - + -
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Residues in contact with LEU 911 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
909B ASN* 3.0 9.7 + - - +
910B LEU* 1.3 77.5 - - - +
912B ASP* 1.3 68.4 + - - +
914B LEU* 3.3 4.1 + - + +
915B ARG* 3.0 70.1 + - - +
967B ALA* 3.4 17.6 + - + +
968B ARG* 4.1 22.0 - - + +
1004B TRP* 6.2 2.0 - - + -
1030B GLU* 3.7 21.3 - - + +
1035B GLY* 3.8 20.4 - - - +
1036B GLY 5.2 0.9 - - - +
1121B GLU* 4.1 9.2 - - - +
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Residues in contact with ASP 912 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
909B ASN* 2.7 38.4 + - - +
911B LEU* 1.3 81.9 - - - +
913B PHE* 1.3 58.0 + - - +
915B ARG* 3.8 13.1 + - - +
916B LYS* 2.8 55.3 + - + +
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Residues in contact with PHE 913 (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 HIS* 3.9 34.0 + + + +
909B ASN 3.1 15.0 + - - +
910B LEU* 3.5 9.2 - - + +
911B LEU 3.2 0.2 - - - -
912B ASP* 1.3 77.2 - - - +
914B LEU* 1.3 63.2 + - - +
916B LYS* 3.4 9.8 + - + +
917B SER* 3.2 21.3 + - - -
936B LEU* 3.9 26.5 - - + -
944B PHE* 3.8 28.5 - + - -
972B VAL* 4.0 19.7 - - + -
976B TYR* 3.6 29.8 - + - -
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Residues in contact with LEU 914 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
910B LEU* 2.8 52.3 + - + +
911B LEU* 3.6 7.4 - - - +
913B PHE* 1.3 74.2 - - - +
915B ARG* 1.3 61.3 + - - +
917B SER* 2.5 25.1 + - - -
918B ARG* 3.8 3.3 + - - +
936B LEU* 4.3 7.9 - - + -
941B LEU* 3.7 31.0 - - + -
944B PHE* 4.9 1.1 - - + -
967B ALA* 4.6 5.6 - - + -
1030B GLU 3.7 23.6 - - - +
1031B ILE* 3.7 22.0 - - + +
1034B LEU* 3.6 22.7 - - + +
1035B GLY* 3.9 5.6 - - - +
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Residues in contact with ARG 915 (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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911B LEU* 3.0 42.2 + - - +
912B ASP* 3.8 13.2 + - - +
914B LEU* 1.3 70.3 - - - +
916B LYS* 1.3 62.9 + - + +
917B SER 3.0 5.3 + - - -
918B ARG* 3.2 25.0 + - - +
922B THR* 5.0 3.3 - - - +
1034B LEU 3.9 4.9 - - - +
1035B GLY* 2.7 35.6 + - - +
1036B GLY 4.4 0.8 + - - -
1037B THR* 3.5 15.0 + - - +
1116B ILE* 3.5 35.8 - - + +
1118B CYS* 5.9 0.8 - - - -
1121B GLU* 2.6 42.2 + - - -
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Residues in contact with LYS 916 (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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912B ASP* 2.8 40.1 + - + +
913B PHE* 3.8 10.1 - - + +
915B ARG* 1.3 77.2 - - + +
917B SER* 1.3 59.0 + - - +
918B ARG 3.3 0.8 + - - -
922B THR* 4.0 23.3 + - + +
935B THR* 5.5 2.1 - - - +
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Residues in contact with SER 917 (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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913B PHE* 3.2 11.3 + - - -
914B LEU* 2.5 21.7 + - - -
915B ARG 3.0 0.6 - - - -
916B LYS* 1.3 76.9 - - - +
918B ARG* 1.3 50.8 + - - +
919B VAL* 2.6 21.7 + - - +
934B SER* 3.0 34.9 + - - -
935B THR* 3.1 28.1 + - - -
936B LEU* 3.8 16.7 - - - +
1034B LEU* 4.2 5.4 - - - +
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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