Contacts of the helix formed by residues 828 - 836 (chain B) in PDB entry 1FO4
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 ASP 828 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41B LEU* 4.2 21.5 - - - +
43B CYS 5.8 2.0 - - - +
269B LYS* 3.7 20.8 + - - -
270B PHE* 6.2 2.0 - - + -
606B ARG* 2.9 27.7 + - - -
679B GLU* 3.4 11.1 - - - +
826B MET 3.7 3.0 + - - +
827B LEU* 1.3 78.1 - - - +
829B ARG* 1.3 66.3 + - - +
830B ASN* 3.3 17.2 - - - +
831B GLU* 2.9 15.9 + - + +
832B ASP* 3.0 16.8 + - - +
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Residues in contact with ARG 829 (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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42B GLY 2.8 23.8 + - - +
43B CYS* 3.9 25.9 + - + +
45B GLU* 5.7 1.3 - - - +
270B PHE* 6.5 0.4 - - + -
740B ASP* 4.8 1.4 + - - -
742B PHE* 3.6 49.2 - - + +
743B TYR* 2.9 36.6 + - - +
744B LEU* 3.0 20.2 + - - +
746B THR* 3.6 23.6 - - - +
827B LEU 3.9 0.8 + - - -
828B ASP* 1.3 72.6 - - - +
830B ASN* 1.3 62.3 + - - +
832B ASP* 3.3 4.0 + - - +
833B MET* 3.0 43.0 + - - +
1222B ARG 4.1 5.2 - - - +
1223B GLY* 5.2 0.4 - - - -
1224B PRO* 4.3 11.9 - - + -
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Residues in contact with ASN 830 (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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269B LYS 5.6 1.0 + - - -
270B PHE* 3.6 36.4 - - + -
606B ARG* 4.9 4.5 + - - +
828B ASP* 3.4 18.7 - - - +
829B ARG* 1.3 75.6 - - - +
831B GLU* 1.3 71.8 + - - +
833B MET* 3.7 1.7 + - - +
834B LEU* 3.3 24.1 + - - +
1222B ARG* 3.3 42.9 + - + +
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Residues in contact with GLU 831 (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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606B ARG* 3.0 54.3 + - - +
607B LEU* 4.5 14.0 + - - +
825B CYS* 5.6 1.3 - - - -
826B MET 4.3 1.9 - - - +
827B LEU* 3.5 25.6 - - + +
828B ASP* 2.9 29.0 + - + +
830B ASN* 1.3 89.6 + - - +
832B ASP* 1.3 58.5 + - - +
834B LEU* 3.3 5.1 + - - +
835B ILE* 2.9 48.4 + - + +
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Residues in contact with ASP 832 (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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740B ASP* 5.0 4.9 - - - +
743B TYR* 2.8 34.3 + - - -
746B THR* 3.4 15.1 - - + -
747B HIS* 3.0 42.4 + - - +
827B LEU* 3.9 12.4 - - + +
828B ASP 3.0 12.0 + - - +
829B ARG* 3.6 12.2 + - - +
831B GLU* 1.3 78.2 - - - +
833B MET* 1.3 62.4 + - - +
836B THR* 2.9 32.4 + - - -
837B GLY 4.7 0.2 + - - -
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Residues in contact with MET 833 (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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740B ASP* 3.0 43.8 - - + +
742B PHE* 4.3 4.9 - - - -
829B ARG* 3.0 32.0 + - - +
830B ASN 4.3 2.7 - - - +
832B ASP* 1.3 77.0 - - + +
834B LEU* 1.3 61.8 + - - +
837B GLY* 5.0 6.8 + - - +
1211B LEU* 4.0 6.8 - - + +
1219B LEU* 3.4 17.9 - - + +
1221B THR 3.5 17.0 - - - +
1222B ARG* 3.4 27.1 - - - +
1223B GLY* 3.5 7.4 - - - -
1227B TYR* 3.6 33.9 - - + -
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Residues in contact with LEU 834 (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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609B THR* 4.6 9.9 - - - +
610B SER 5.3 0.7 - - - +
663B VAL* 3.9 30.7 - - + +
664B GLY* 3.9 22.2 - - - -
830B ASN 3.3 16.8 + - - +
831B GLU* 3.7 4.9 - - - +
832B ASP 3.2 0.4 - - - -
833B MET* 1.3 81.0 - - - +
835B ILE* 1.3 58.1 + - + +
837B GLY 4.9 0.3 + - - -
906B SER* 2.7 31.1 + - - +
1219B LEU* 3.9 21.9 - - + +
1222B ARG* 3.9 34.8 - - - +
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Residues in contact with ILE 835 (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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607B LEU* 3.9 21.3 - - + -
609B THR* 3.6 26.7 - - + -
664B GLY* 3.7 25.6 - - - +
666B ILE* 4.3 11.7 - - + -
804B ARG* 4.9 3.6 + - - -
807B LEU* 3.7 27.0 - - + +
808B VAL* 6.4 0.7 - - + -
827B LEU* 5.1 4.0 - - + -
831B GLU* 2.9 31.2 + - + +
834B LEU* 1.3 80.1 - - + +
836B THR* 1.3 65.3 + - + +
837B GLY 3.2 7.9 + - - -
906B SER* 3.7 14.5 + - - -
907B SER 5.2 0.2 + - - -
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Residues in contact with THR 836 (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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740B ASP* 5.6 0.7 + - - -
741B HIS* 5.0 0.5 + - - -
743B TYR* 3.2 16.8 + - - -
747B HIS* 3.3 36.3 - - + +
800B GLY 5.0 1.0 - - - +
804B ARG* 3.1 32.1 - - - +
807B LEU* 4.3 10.8 - - + -
808B VAL* 5.6 1.8 - - + -
827B LEU* 3.9 19.1 - - + -
832B ASP* 2.9 21.9 + - - +
835B ILE* 1.3 81.3 - - + +
837B GLY* 1.3 65.2 + - - +
907B SER 4.5 1.3 - - - -
909B THR* 4.1 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