Contacts of the helix formed by residues 868 - 882 (chain A) in PDB entry 4FM9
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 868 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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780A ASN* 4.5 2.7 - - - +
867A PHE* 1.3 70.9 - - - +
869A VAL* 1.3 67.0 + - - +
870A ARG* 3.3 32.2 - - - +
871A GLU* 3.4 32.1 + - + +
872A ILE* 3.0 25.1 + - - +
889A LEU 5.2 0.6 + - - -
891A SER* 3.3 30.6 + - - +
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Residues in contact with VAL 869 (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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780A ASN* 5.2 1.2 - - + +
781A LEU* 4.6 1.6 - - + -
845A ILE* 4.1 9.2 - - + -
850A ILE* 3.9 24.4 - - + +
867A PHE 3.3 3.7 + - - -
868A ASP* 1.3 73.3 + - - +
870A ARG* 1.3 90.0 + - + +
872A ILE* 2.9 12.1 + - - +
873A VAL* 2.8 25.1 + - + +
1174A PHE* 3.7 34.3 - - + -
1175A ILE* 5.7 0.7 - - + -
1178A LEU* 4.9 16.2 - - + -
1182A GLU* 5.1 4.5 - - - +
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Residues in contact with ARG 870 (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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868A ASP* 3.3 15.2 - - - +
869A VAL* 1.3 81.2 - - + +
871A GLU* 1.3 55.6 + - + +
873A VAL* 2.8 13.0 + - - +
874A ASN* 2.7 35.1 + - - +
1175A ILE* 5.2 14.3 - - - +
1178A LEU* 3.9 11.2 - - - +
1179A GLU* 2.5 39.0 + - - -
1182A GLU* 2.7 34.6 + - - -
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Residues in contact with GLU 871 (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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867A PHE* 6.4 0.2 - - + -
868A ASP* 3.4 32.8 + - + +
869A VAL 3.3 0.4 - - - -
870A ARG* 1.3 78.3 - - + +
872A ILE* 1.3 64.1 + - - +
874A ASN* 3.3 10.3 + - - +
875A ASN* 2.8 33.2 + - - +
887A PRO 4.9 1.7 - - - +
888A MET* 3.9 31.8 - - + +
889A LEU 4.4 11.6 + - - +
891A SER* 5.4 1.2 - - - -
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Residues in contact with ILE 872 (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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845A ILE* 4.2 8.7 - - + -
846A PRO* 3.3 38.4 - - + +
849A LEU* 4.3 17.7 - - + +
850A ILE* 5.2 7.0 - - + -
867A PHE* 4.0 20.2 - - + +
868A ASP 3.0 18.7 + - - +
869A VAL* 2.9 11.4 + - + +
871A GLU* 1.3 77.6 - - - +
873A VAL* 1.3 66.7 + - + +
875A ASN* 3.0 2.4 + - - +
876A ILE* 2.9 30.8 + - + +
888A MET* 3.8 28.5 - - + -
1019A LEU* 5.1 3.4 - - + -
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Residues in contact with VAL 873 (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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845A ILE* 4.3 18.2 - - + -
869A VAL* 2.8 25.3 + - + +
870A ARG* 2.8 13.4 + - - +
872A ILE* 1.3 71.6 - - - +
874A ASN* 1.3 53.9 + - - +
876A ILE* 2.9 11.8 + - - +
877A ARG* 2.7 41.2 + - + +
1171A LEU* 4.7 23.2 - - + +
1174A PHE* 4.9 2.7 - - + -
1175A ILE* 3.9 31.9 - - + -
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Residues in contact with ASN 874 (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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870A ARG 2.7 15.4 + - - +
871A GLU* 3.4 14.3 + - - +
873A VAL* 1.3 73.6 - - - +
875A ASN* 1.3 56.3 + - - +
877A ARG* 2.8 37.4 + - - +
878A ARG* 2.6 39.4 + - - +
886A LEU* 3.7 28.3 - - - +
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Residues in contact with ASN 875 (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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871A GLU* 2.8 31.8 + - - +
872A ILE 3.7 2.7 - - - +
874A ASN* 1.3 82.8 - - - +
876A ILE* 1.3 57.8 + - - +
878A ARG* 3.7 6.6 - - - +
879A LEU* 2.8 31.0 + - - +
885A PRO* 3.1 11.9 - - + +
886A LEU* 2.6 57.3 + - - +
888A MET* 4.0 17.7 - - - +
1019A LEU* 3.8 21.1 - - + +
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Residues in contact with ILE 876 (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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844A ILE 4.1 3.1 - - - +
845A ILE* 3.9 18.6 - - + -
846A PRO* 3.3 31.6 - - + -
872A ILE* 2.9 23.3 + - + +
873A VAL* 3.4 7.6 - - - +
875A ASN* 1.3 73.5 - - - +
877A ARG* 1.3 61.3 + - - +
879A LEU* 4.4 3.4 - - - -
880A MET* 2.8 32.9 + - + +
1019A LEU* 4.0 18.8 - - + -
1022A PHE* 4.6 4.7 - - + -
1023A PHE* 3.7 10.9 - - + -
1167A TRP* 3.6 36.3 - - + +
1171A LEU* 4.8 8.7 - - + -
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Residues in contact with ARG 877 (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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873A VAL* 2.7 22.7 + - + +
874A ASN* 2.8 43.5 + - - +
876A ILE* 1.3 72.2 - - - +
878A ARG* 1.3 79.6 + - - +
880A MET* 3.7 18.9 - - + +
881A ASP* 2.8 45.7 + - - +
883A GLU* 5.4 1.6 + - - -
1171A LEU* 5.6 4.9 - - + -
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Residues in contact with ARG 878 (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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874A ASN* 2.6 27.9 + - - +
875A ASN* 3.7 7.6 - - - +
876A ILE 3.2 0.2 - - - -
877A ARG* 1.3 93.3 - - - +
879A LEU* 1.3 64.6 + - - +
881A ASP* 3.4 5.8 + - - +
882A GLY 3.3 5.9 + - - -
883A GLU* 3.1 49.1 + - + +
884A GLU 2.8 27.8 + - - +
885A PRO* 4.1 0.9 - - + -
886A LEU* 3.3 48.8 - - - +
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Residues in contact with LEU 879 (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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875A ASN 2.8 18.9 + - - +
876A ILE* 3.9 3.1 - - - +
878A ARG* 1.3 78.4 - - - +
880A MET* 1.3 60.5 + - - +
882A GLY* 3.3 12.3 + - - -
883A GLU 3.3 16.2 + - - +
884A GLU* 5.3 4.5 - - - +
885A PRO* 4.5 19.0 - - + -
1019A LEU* 4.7 9.0 - - + +
1020A ARG* 4.7 20.0 - - + -
1023A PHE* 3.1 50.8 - - + -
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Residues in contact with MET 880 (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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876A ILE* 2.8 20.6 + - + +
877A ARG* 3.7 18.4 - - + +
879A LEU* 1.3 76.2 - - - +
881A ASP* 1.3 67.3 + - + +
882A GLY* 3.2 1.6 + - - -
1023A PHE* 3.5 20.3 - - + -
1164A SER* 2.9 44.8 - - - +
1167A TRP* 4.5 19.5 - - + -
1168A LYS* 4.5 24.9 - - + +
1171A LEU* 4.9 7.0 - - + -
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Residues in contact with ASP 881 (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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877A ARG* 2.8 28.5 + - - +
878A ARG* 3.4 9.9 - - - +
880A MET* 1.3 79.9 - - - +
882A GLY* 1.3 57.9 + - - +
883A GLU* 3.8 24.6 - - - +
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Residues in contact with GLY 882 (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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878A ARG 3.3 0.2 + - - -
879A LEU 3.3 7.1 + - - -
880A MET 3.1 4.5 - - - -
881A ASP* 1.3 79.1 - - - +
883A GLU* 1.3 69.8 + - - +
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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