Contacts of the helix formed by residues 1040 - 1055 (chain R) in PDB entry 3F5P
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 SER1040 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1246L ARG* 5.9 1.3 - - - +
1038R ALA 4.1 2.0 + - - -
1039R ALA* 1.3 79.2 - - - +
1041R MET* 1.3 66.2 + - - +
1042R ARG* 3.8 7.7 + - - +
1043R GLU* 2.6 42.4 + - - +
1044R ARG* 3.2 19.4 + - - +
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Residues in contact with MET1041 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1243L GLU* 3.8 46.2 - - + +
1246L ARG* 3.6 48.3 - - + +
1247L MET* 3.8 25.4 - - + -
1250L GLN* 4.1 7.0 - - - +
982R SER* 5.8 0.7 - - - -
983R ALA* 4.7 10.1 - - + +
1039R ALA 3.7 0.2 + - - -
1040R SER* 1.3 73.9 - - - +
1042R ARG* 1.3 64.2 + - - +
1044R ARG* 3.1 9.6 + - - +
1045R ILE* 3.0 44.2 + - + +
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Residues in contact with ARG1042 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1250L GLN* 3.9 25.7 - - - +
1252L ASN* 6.0 4.9 - - - +
1255L MET* 5.5 8.5 - - + +
1040R SER* 3.2 9.4 + - - +
1041R MET* 1.3 80.4 - - - +
1043R GLU* 1.3 74.7 + - - +
1045R ILE* 4.0 2.2 - - - +
1046R GLU* 3.1 58.2 + - - +
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Residues in contact with GLU1043 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1010R PHE* 3.4 26.7 - - + -
1035R VAL* 5.8 0.4 - - - +
1039R ALA* 5.2 7.6 - - + -
1040R SER* 2.6 35.6 + - - +
1042R ARG* 1.3 94.4 + - - +
1044R ARG* 1.3 57.4 + - - +
1045R ILE 3.5 0.2 - - - -
1046R GLU* 4.1 6.7 - - - -
1047R PHE* 3.2 25.1 + - - +
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Residues in contact with ARG1044 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
982R SER* 5.0 10.9 - - - -
983R ALA* 4.2 23.8 - - + +
984R ALA 4.9 2.7 - - - +
1035R VAL* 3.5 33.6 + - + +
1036R ASN 3.4 23.6 + - - -
1037R GLU* 3.8 14.5 + - - +
1039R ALA* 3.1 27.8 + - + +
1040R SER 3.2 15.1 + - - +
1041R MET* 3.1 8.9 + - - +
1042R ARG 3.1 0.6 - - - -
1043R GLU* 1.3 78.6 - - - +
1045R ILE* 1.3 60.3 + - - +
1047R PHE* 3.7 5.7 - - + +
1048R LEU* 3.1 35.7 + - + +
1073R GLN 4.1 11.7 + - - -
1075R THR* 3.7 19.8 + - - +
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Residues in contact with ILE1045 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1247L MET* 4.8 0.9 - - - -
1250L GLN* 3.3 30.3 - - - +
1255L MET* 3.6 22.0 - - + +
983R ALA* 3.9 17.9 - - + -
987R TYR* 3.1 53.6 - - + +
1041R MET* 3.0 29.7 + - + +
1042R ARG* 4.0 2.9 - - - +
1044R ARG* 1.3 74.8 - - - +
1046R GLU* 1.3 62.0 + - - +
1048R LEU* 3.0 6.4 + - - +
1049R ASN* 2.8 31.3 + - - +
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Residues in contact with GLU1046 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1255L MET* 4.0 20.7 - - + +
1010R PHE* 3.4 22.4 - - + -
1042R ARG* 3.1 41.9 + - - +
1043R GLU* 3.9 8.7 - - - +
1045R ILE* 1.3 77.8 - - - +
1047R PHE* 1.3 60.5 + - - +
1049R ASN* 3.3 2.3 + - - +
1050R GLU* 3.1 30.0 + - - +
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Residues in contact with PHE1047 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14R 741 3.2 42.2 - + - -
1010R PHE* 3.1 41.6 - + + -
1033R LYS* 4.2 7.4 - - + -
1035R VAL* 3.2 31.9 - - + -
1043R GLU 3.2 17.9 + - - +
1044R ARG* 3.7 5.4 - - + +
1046R GLU* 1.3 79.1 - - - +
1048R LEU* 1.3 80.4 + - + +
1050R GLU* 3.5 3.5 + - - +
1051R ALA* 3.2 26.3 + - + +
1075R THR* 5.1 0.4 - - + -
1077R VAL* 3.0 37.5 - - + -
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Residues in contact with LEU1048 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
983R ALA* 4.1 9.6 - - + +
984R ALA* 3.5 37.7 - - + +
987R TYR* 4.3 15.8 - - + +
988R VAL* 3.9 25.5 - - + +
1044R ARG* 3.1 22.6 + - + +
1045R ILE* 3.0 9.2 + - - +
1047R PHE* 1.3 104.2 - - + +
1049R ASN* 1.3 61.6 + - - +
1051R ALA* 4.0 8.6 + - + +
1052R SER* 3.3 22.3 + - - -
1068R VAL* 5.3 2.2 - - + -
1075R THR* 4.5 13.7 - - + -
1077R VAL* 5.1 2.9 - - + -
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Residues in contact with ASN1049 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1254L LYS 4.1 7.8 - - - +
1255L MET* 3.1 35.1 - - + +
1261L GLU* 5.4 3.4 + - - -
987R TYR* 4.3 23.0 + - - -
1045R ILE* 2.8 19.0 + - - +
1046R GLU 4.0 2.2 - - - +
1048R LEU* 1.3 78.0 + - - +
1050R GLU* 1.3 62.8 + - - +
1051R ALA 3.2 0.4 - - - -
1052R SER* 3.0 36.2 + - - -
1053R VAL* 3.4 11.3 + - - +
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Residues in contact with GLU1050 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14R 741 3.3 34.0 - - + -
1009R SER* 5.1 1.2 + - - -
1010R PHE* 3.8 20.6 - - - -
1046R GLU* 3.1 21.3 + - - +
1047R PHE 3.6 7.0 - - - +
1049R ASN* 1.3 77.1 - - - +
1051R ALA* 1.3 60.9 + - - +
1053R VAL* 3.3 16.0 + - - +
1054R MET* 3.7 14.1 + - + +
1153R ASP* 4.7 3.3 - - - +
1154R PHE* 4.7 6.2 - - - +
1155R GLY* 3.5 35.5 + - - +
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Residues in contact with ALA1051 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14R 741 5.0 7.8 - - - +
1047R PHE* 3.2 15.4 + - + +
1048R LEU* 4.0 11.9 - - + +
1050R GLU* 1.3 78.5 - - - +
1052R SER* 1.3 63.0 + - - +
1053R VAL 3.2 1.2 + - - -
1054R MET* 3.2 26.7 + - - +
1055R LYS* 3.4 6.2 + - - +
1065R LEU* 3.6 23.0 - - + +
1068R VAL* 6.0 4.0 - - + -
1077R VAL* 4.9 10.3 - - + -
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Residues in contact with SER1052 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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987R TYR 4.0 10.7 + - - -
988R VAL* 5.6 0.3 - - - +
989R PRO* 5.1 7.1 - - - +
1048R LEU 3.3 14.7 + - - -
1049R ASN* 3.0 28.8 + - - -
1051R ALA* 1.3 78.6 - - - +
1053R VAL* 1.3 61.2 + - - +
1055R LYS* 4.0 13.4 + - - +
1056R GLU* 4.4 4.0 + - - +
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Residues in contact with VAL1053 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1049R ASN 4.1 9.2 - - - +
1050R GLU* 3.3 9.5 + - - +
1051R ALA 3.1 1.0 - - - -
1052R SER* 1.3 80.9 - - - +
1054R MET* 1.3 64.5 + - - +
1055R LYS 3.3 0.2 - - - -
1056R GLU* 3.3 19.4 - - + +
1057R PHE* 3.3 31.1 - - + -
1131R PHE* 4.1 20.4 - - + -
1154R PHE* 5.4 4.7 - - + +
1157R THR* 4.6 10.8 - - - +
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Residues in contact with MET1054 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14R 741 3.8 33.4 - - + -
1050R GLU* 3.7 14.3 + - + +
1051R ALA* 3.2 18.4 - - - +
1053R VAL* 1.3 77.8 - - - +
1055R LYS* 1.3 54.2 + - - +
1057R PHE* 2.7 44.7 + - - +
1063R VAL 4.7 3.6 - - - +
1065R LEU* 3.8 24.4 + - + +
1079R MET* 4.5 16.4 - - + -
1152R GLY 4.2 9.4 - - - +
1153R ASP* 5.7 0.2 - - - +
1154R PHE* 3.5 48.0 - - + +
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Residues in contact with LYS1055 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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992R TRP* 3.0 59.7 - - + +
1051R ALA 3.4 7.1 + - - +
1052R SER* 4.1 12.3 - - - +
1053R VAL 3.3 1.0 - - - -
1054R MET* 1.3 79.2 - - - +
1056R GLU* 1.3 63.5 + - - +
1057R PHE 3.4 5.1 + - - +
1058R ASN* 5.4 2.3 - - - +
1065R LEU* 4.6 6.5 - - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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