Contacts of the helix formed by residues 1050 - 1057 (chain A) in PDB entry 5FLM
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 CYS1050 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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920A PHE* 3.8 25.1 - - + -
955A GLU* 3.5 13.7 - - - +
959A MET* 3.5 30.3 - - + -
1046A ARG 3.5 13.1 + - - +
1047A SER 3.6 15.5 - - - +
1048A THR 3.3 3.4 + - - -
1049A LEU* 1.3 80.4 - - - +
1051A SER* 1.3 63.3 + - - +
1052A ARG 3.9 9.2 - - - -
1053A ARG* 3.2 12.1 + - + +
1054A MET* 2.9 25.8 + - - +
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Residues in contact with SER1051 (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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920A PHE 5.5 0.2 + - - -
922A PHE* 4.0 18.2 - - - +
952A LEU* 4.5 4.9 - - - +
955A GLU* 2.9 31.8 + - - -
1006A PRO* 4.0 30.6 - - - +
1009A VAL* 4.0 14.9 - - - +
1010A VAL* 4.6 0.2 - - - -
1049A LEU 3.5 0.6 + - - -
1050A CYS* 1.3 74.2 - - - +
1052A ARG* 1.3 65.1 + - - +
1054A MET* 3.0 6.3 + - - +
1055A ALA* 2.9 28.4 + - - +
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Residues in contact with ARG1052 (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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918A LYS* 3.5 16.9 + - - +
919A LYS 3.1 23.8 - - - +
920A PHE 4.4 5.8 - - - +
921A ARG* 3.9 1.3 - - - +
922A PHE* 3.1 43.2 - - + +
923A ASP* 2.9 44.8 + - - +
926A ASN* 5.7 4.0 - - - +
1050A CYS* 3.4 2.5 - - - -
1051A SER* 1.3 81.4 + - - +
1053A ARG* 1.3 57.3 + - - +
1055A ALA* 3.3 3.6 + - + +
1056A GLU* 2.4 61.8 + - + +
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Residues in contact with ARG1053 (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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907A ALA* 4.7 14.0 - - - +
919A LYS* 4.9 8.2 + - - +
920A PHE* 3.3 34.8 - - + -
984A LEU* 5.9 2.2 - - - +
1047A SER 3.5 13.3 + - - -
1048A THR* 3.1 30.0 - - - +
1050A CYS* 3.2 19.7 + - + +
1052A ARG* 1.3 77.1 - - - +
1054A MET* 1.3 65.0 + - - +
1056A GLU* 4.7 5.8 - - - -
1057A GLU* 3.0 54.1 + - - +
1058A PHE* 3.5 32.0 + - + -
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Residues in contact with MET1054 (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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987A ILE* 4.4 0.9 - - + -
1002A SER* 5.6 1.0 + - - -
1004A LEU* 4.4 10.2 - - + +
1009A VAL* 3.7 31.9 - - + -
1048A THR 3.4 18.6 - - - +
1049A LEU* 3.7 20.4 - - + +
1050A CYS 2.9 15.3 + - - +
1051A SER 3.0 7.6 + - - +
1053A ARG* 1.3 77.2 - - - +
1055A ALA* 1.3 57.8 + - + +
1058A PHE* 3.4 34.5 - - + -
1059A ARG* 3.1 30.3 + - - -
1060A LEU* 3.8 30.4 + - + +
1065A PHE* 4.3 15.7 - - - -
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Residues in contact with ALA1055 (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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922A PHE* 4.8 14.8 - - + -
933A THR* 3.3 26.4 - - - +
934A LEU* 5.8 8.7 - - + -
1002A SER* 5.9 5.4 - - - -
1006A PRO* 6.1 2.9 - - + -
1051A SER 2.9 14.6 + - - +
1052A ARG* 3.6 8.5 - - + +
1053A ARG 3.3 0.4 - - - -
1054A MET* 1.3 74.5 - - + +
1056A GLU* 1.3 54.5 + - + +
1059A ARG* 2.5 26.0 + - - +
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Residues in contact with GLU1056 (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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918A LYS 4.5 1.7 - - - +
919A LYS* 4.0 13.6 - - - +
933A THR* 5.2 5.8 - - + -
1052A ARG* 2.4 64.3 + - + +
1053A ARG* 4.4 3.5 - - - +
1054A MET 3.3 0.6 - - - -
1055A ALA* 1.3 79.3 - - + +
1057A GLU* 1.3 76.7 + - + +
1058A PHE 3.6 0.2 - - - -
1059A ARG* 2.6 27.4 + - - +
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Residues in contact with GLU1057 (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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991A GLN* 4.3 2.6 + - - -
998A PRO* 5.1 6.2 - - - +
1053A ARG* 3.0 40.0 + - + +
1056A GLU* 1.3 91.6 - - + +
1058A PHE* 1.3 86.5 + - + +
1059A ARG* 4.1 4.7 - - - +
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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