Contacts of the helix formed by residues 1040 - 1057 (chain M) 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 M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1038M ALA 4.2 0.6 + - - -
1039M ALA* 1.3 76.9 - - - +
1041M MET* 1.3 60.2 + - - +
1042M ARG* 3.9 11.3 - - - +
1043M GLU* 2.9 34.3 + - - +
1044M ARG* 2.8 27.0 + - - +
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Residues in contact with MET1041 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1243K GLU* 3.7 35.2 - - + +
1246K ARG* 4.0 36.5 - - + +
1247K MET* 3.9 27.6 - - + -
1250K GLN* 3.6 22.4 - - - +
982M SER* 5.6 0.7 - - - -
983M ALA* 4.6 11.7 - - + +
1039M ALA 3.6 2.0 + - - -
1040M SER* 1.3 72.7 - - - +
1042M ARG* 1.3 62.2 + - - +
1044M ARG* 3.8 9.5 - - - +
1045M ILE* 3.0 44.7 + - + +
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Residues in contact with ARG1042 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1250K GLN* 4.0 19.7 - - + +
1252K ASN* 6.2 1.8 - - - +
1255K MET* 5.4 4.6 - - - +
1040M SER* 3.1 10.7 - - - -
1041M MET* 1.3 79.4 - - - +
1043M GLU* 1.3 70.3 + - - +
1045M ILE* 3.3 3.6 + - - +
1046M GLU* 2.6 67.2 + - - +
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Residues in contact with GLU1043 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1009M SER 5.1 1.8 - - - +
1010M PHE* 3.3 48.4 - - - +
1035M VAL* 6.1 1.2 - - - +
1039M ALA* 4.7 9.6 - - + +
1040M SER* 2.9 34.4 + - - +
1042M ARG* 1.3 87.1 - - - +
1044M ARG* 1.3 57.4 + - - +
1046M GLU* 3.5 4.5 + - - +
1047M PHE* 3.0 30.5 + - - +
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Residues in contact with ARG1044 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
982M SER* 4.8 9.2 - - - -
983M ALA* 4.1 22.7 - - + +
984M ALA* 4.2 9.9 - - - +
1035M VAL* 3.4 22.8 + - + +
1036M ASN 3.0 29.3 + - - -
1037M GLU* 3.7 10.1 + - - +
1039M ALA* 3.4 26.5 + - + +
1040M SER 2.8 11.1 + - - +
1041M MET* 3.8 8.8 - - - +
1042M ARG 3.2 0.2 - - - -
1043M GLU* 1.3 78.2 - - - +
1045M ILE* 1.3 57.4 + - - +
1047M PHE* 3.7 8.4 - - + +
1048M LEU* 2.9 40.6 + - + +
1073M GLN 4.6 6.3 + - - -
1075M THR* 3.8 21.5 + - - +
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Residues in contact with ILE1045 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1247K MET* 5.1 0.7 - - - -
1250K GLN* 3.7 24.9 - - + +
1255K MET* 3.7 35.7 - - + +
983M ALA* 3.7 17.7 - - + -
987M TYR* 3.5 44.0 - - + +
1041M MET* 3.0 27.0 + - + +
1042M ARG* 3.9 4.3 - - - +
1044M ARG* 1.3 77.9 - - - +
1046M GLU* 1.3 59.2 + - - +
1047M PHE 3.3 0.2 - - - -
1048M LEU* 3.7 5.0 - - - -
1049M ASN* 3.0 28.2 + - - +
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Residues in contact with GLU1046 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1252K ASN* 5.6 2.3 + - - -
1255K MET* 4.4 27.4 - - + +
1010M PHE* 4.7 10.5 - - + -
1042M ARG* 2.6 61.4 + - - +
1043M GLU* 3.9 4.3 - - - +
1045M ILE* 1.3 72.4 - - - +
1047M PHE* 1.3 61.1 + - - +
1048M LEU 3.0 0.2 - - - -
1049M ASN* 3.2 4.2 + - - +
1050M GLU* 2.9 31.6 + - - +
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Residues in contact with PHE1047 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12M 741 3.3 30.7 - + - -
1010M PHE* 2.9 45.7 - + + -
1033M LYS* 3.7 14.6 - - + -
1035M VAL* 3.2 38.4 - - + -
1043M GLU 3.0 18.9 + - - +
1044M ARG* 3.7 8.5 - - + +
1046M GLU* 1.3 78.1 - - - +
1048M LEU* 1.3 74.8 + - + +
1050M GLU* 3.7 3.7 + - - +
1051M ALA* 3.4 21.5 + - + +
1075M THR* 5.2 0.4 - - + -
1077M VAL* 3.1 33.7 - - + -
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Residues in contact with LEU1048 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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983M ALA* 4.0 8.7 - - + +
984M ALA* 3.6 36.3 - - + +
987M TYR* 4.2 15.5 - - + +
988M VAL* 3.9 23.0 - - + +
1044M ARG* 2.9 28.6 + - + +
1045M ILE* 3.7 7.6 - - - +
1046M GLU 3.0 0.4 - - - -
1047M PHE* 1.3 99.5 - - + +
1049M ASN* 1.3 60.4 + - - +
1051M ALA* 4.0 9.7 - - + +
1052M SER* 3.4 22.0 + - - -
1068M VAL* 4.9 5.6 - - + -
1075M THR* 4.6 12.3 - - + -
1077M VAL* 5.3 1.3 - - + -
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Residues in contact with ASN1049 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1254K LYS 4.0 8.0 - - - +
1255K MET* 3.3 33.6 - - + +
987M TYR* 4.2 22.3 + - - +
1045M ILE* 3.0 19.7 + - - +
1046M GLU 3.2 3.1 + - - +
1048M LEU* 1.3 82.8 + - - +
1050M GLU* 1.3 60.6 + - - +
1051M ALA 3.2 1.1 - - - -
1052M SER* 3.3 20.6 + - - -
1053M VAL* 3.1 23.2 - - - +
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Residues in contact with GLU1050 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12M 741 3.6 33.4 - - + -
1009M SER* 5.0 1.2 + - - -
1010M PHE* 3.8 20.1 - - - -
1046M GLU 2.9 15.8 + - - +
1047M PHE 3.8 6.3 - - - +
1049M ASN* 1.3 78.8 - - - +
1051M ALA* 1.3 59.2 + - - +
1053M VAL* 3.4 16.3 + - - +
1054M MET* 3.7 15.2 + - + +
1153M ASP* 4.5 4.0 - - - +
1154M PHE* 4.4 7.5 - - - +
1155M GLY* 3.4 36.9 + - - +
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Residues in contact with ALA1051 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12M 741 5.1 6.5 - - - +
1047M PHE* 3.4 15.2 + - + +
1048M LEU* 4.1 12.6 - - + +
1049M ASN 3.2 0.4 - - - -
1050M GLU* 1.3 77.7 - - - +
1052M SER* 1.3 61.4 + - - +
1053M VAL 3.0 6.6 + - - -
1054M MET* 3.1 25.9 + - - +
1055M LYS* 3.3 5.7 + - - +
1065M LEU* 3.9 21.5 - - + +
1068M VAL* 5.9 5.6 - - + -
1077M VAL* 5.1 11.2 - - + -
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Residues in contact with SER1052 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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987M TYR 3.9 13.7 + - - -
989M PRO* 4.9 9.2 - - - +
1048M LEU 3.4 14.8 + - - -
1049M ASN* 3.3 22.9 + - - -
1051M ALA* 1.3 78.8 - - - +
1053M VAL* 1.3 60.6 + - - +
1055M LYS* 3.4 19.8 - - - +
1056M GLU* 4.3 2.1 + - - +
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Residues in contact with VAL1053 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1049M ASN 3.1 19.3 - - - +
1050M GLU* 3.8 11.2 - - - +
1051M ALA 3.0 0.6 - - - -
1052M SER* 1.3 78.7 - - - +
1054M MET* 1.3 66.9 + - - +
1056M GLU* 3.4 17.4 - - + +
1057M PHE* 3.6 16.5 - - + -
1131M PHE* 3.7 33.7 - - + -
1154M PHE* 5.7 7.9 - - + +
1157M THR* 5.2 6.3 - - - +
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Residues in contact with MET1054 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12M 741 3.8 26.7 - - + -
1050M GLU* 3.7 15.7 - - + +
1051M ALA* 3.2 17.0 - - - +
1053M VAL* 1.3 74.4 - - - +
1055M LYS* 1.3 71.3 + - - +
1057M PHE* 2.5 35.1 + - - +
1063M VAL 4.9 5.4 - - - +
1065M LEU* 3.8 23.6 - - + +
1079M MET* 4.1 21.3 - - - -
1152M GLY 4.5 5.2 - - - +
1153M ASP* 5.3 0.4 - - - -
1154M PHE* 3.5 48.7 - - + +
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Residues in contact with LYS1055 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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989M PRO* 6.1 0.7 - - + -
992M TRP* 3.0 57.6 - - + +
1051M ALA 3.3 5.5 + - - +
1052M SER* 3.4 20.4 - - - +
1054M MET* 1.3 76.7 - - - +
1056M GLU* 1.3 67.8 + - - +
1057M PHE 3.2 6.1 + - - +
1058M ASN* 5.5 0.9 - - - +
1065M LEU* 4.6 4.1 - - + +
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Residues in contact with GLU1056 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1052M SER 4.3 1.5 + - - +
1053M VAL* 3.4 17.5 + - + +
1054M MET 2.7 1.8 + - - -
1055M LYS* 1.3 77.9 - - - +
1057M PHE* 1.3 77.0 + - + +
1058M ASN* 3.3 6.8 + - - +
1125M TYR* 3.8 5.2 + - - +
1129M ASN* 5.0 14.8 - - + +
1131M PHE* 4.0 20.3 - - + -
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Residues in contact with PHE1057 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1053M VAL* 3.6 32.3 - - + -
1054M MET* 2.5 23.1 + - - +
1055M LYS 3.7 4.2 - - - +
1056M GLU* 1.3 76.1 - - + +
1058M ASN* 1.3 61.5 + - - +
1059M CYS 3.8 0.9 - - - -
1062M VAL* 4.1 14.8 - - + +
1063M VAL 5.6 0.2 - - - +
1064M ARG* 4.4 13.9 - - - +
1065M LEU 5.4 1.4 + - - -
1125M TYR* 3.5 22.9 - + + -
1126M LEU* 3.6 26.7 - - + -
1129M ASN* 5.2 3.8 - - + -
1131M PHE* 3.6 40.4 - + - -
1154M PHE* 4.0 41.3 - + + -
1157M THR* 4.9 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
------------------------------------------------------------
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