Contacts of the helix formed by residues 1040 - 1057 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1038H ALA 4.2 0.6 - - - -
1039H ALA* 1.3 80.6 - - - +
1041H MET* 1.3 59.9 + - - +
1042H ARG* 4.1 9.3 - - - +
1043H GLU* 3.1 32.9 + - - +
1044H ARG* 3.0 21.8 + - - -
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Residues in contact with MET1041 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1243G GLU* 3.3 47.8 - - + +
1246G ARG* 3.5 46.6 - - + +
1247G MET* 3.5 32.1 - - + -
1250G GLN* 4.1 11.9 - - - +
982H SER* 5.8 0.2 - - - -
983H ALA* 4.4 11.0 - - + +
1039H ALA 3.5 1.1 + - - -
1040H SER* 1.3 68.9 - - - +
1042H ARG* 1.3 61.5 + - - +
1044H ARG* 3.2 9.9 + - - +
1045H ILE* 2.8 43.0 + - + +
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Residues in contact with ARG1042 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1250G GLN* 3.9 27.8 + - - +
1252G ASN* 4.6 11.1 - - - +
1255G MET* 4.2 24.7 - - - +
1040H SER* 3.2 8.0 - - - +
1041H MET* 1.3 78.8 - - - +
1043H GLU* 1.3 68.2 + - - +
1045H ILE* 3.3 2.7 + - - +
1046H GLU* 3.0 43.7 + - - +
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Residues in contact with GLU1043 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1009H SER 5.1 1.4 - - - +
1010H PHE* 3.4 37.5 - - + +
1039H ALA* 4.7 7.2 - - + +
1040H SER* 3.1 30.8 + - - +
1041H MET 3.3 0.2 - - - -
1042H ARG* 1.3 85.8 - - - +
1044H ARG* 1.3 62.6 + - - +
1046H GLU* 3.4 5.2 + - - +
1047H PHE* 3.0 24.7 + - - +
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Residues in contact with ARG1044 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
982H SER* 5.2 7.0 - - - -
983H ALA* 4.1 18.4 - - + +
984H ALA* 4.5 4.7 - - - +
1035H VAL* 4.5 22.4 + - + +
1036H ASN 2.6 32.8 + - - -
1037H GLU* 3.7 13.3 + - - +
1039H ALA* 2.7 27.4 + - - -
1040H SER 3.0 10.9 + - - +
1041H MET* 3.8 8.2 - - - +
1043H GLU* 1.3 77.7 - - - +
1045H ILE* 1.3 50.4 + - - +
1047H PHE* 3.5 7.6 - - + +
1048H LEU* 2.7 59.7 + - + +
1073H GLN 5.1 4.9 + - - -
1075H THR* 4.1 21.4 + - - +
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Residues in contact with ILE1045 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1247G MET* 4.4 3.1 - - + -
1250G GLN* 3.8 23.8 - - + +
1255G MET* 3.7 31.4 - - + +
983H ALA* 3.6 13.0 - - + -
987H TYR* 3.5 38.6 - - + +
1041H MET* 2.8 36.0 + - + +
1042H ARG* 3.8 4.9 - - - +
1044H ARG* 1.3 74.5 - - - +
1046H GLU* 1.3 60.2 + - - +
1048H LEU* 3.2 6.5 + - - +
1049H ASN* 2.8 39.8 + - - +
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Residues in contact with GLU1046 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1255G MET* 4.4 9.2 - - + -
1010H PHE* 4.0 18.0 - - + -
1042H ARG* 3.0 41.6 + - - +
1043H GLU* 3.8 6.1 - - - +
1045H ILE* 1.3 76.6 - - - +
1047H PHE* 1.3 60.0 + - - +
1049H ASN* 2.9 23.4 + - + +
1050H GLU* 2.9 25.3 + - - +
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Residues in contact with PHE1047 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8H 741 3.8 33.9 - + - -
1010H PHE* 3.5 48.4 - + + -
1033H LYS* 4.6 4.7 - - + -
1035H VAL* 3.1 39.9 - - + -
1043H GLU 3.0 17.8 + - - +
1044H ARG* 3.5 6.5 - - + +
1046H GLU* 1.3 78.7 + - - +
1048H LEU* 1.3 71.7 + - + +
1049H ASN 3.1 0.5 + - - -
1050H GLU* 3.4 2.9 + - - +
1051H ALA* 3.2 24.9 + - + -
1075H THR* 5.5 2.0 - - + -
1077H VAL* 3.0 32.5 - - + -
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Residues in contact with LEU1048 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
983H ALA* 4.7 1.8 - - + +
984H ALA* 4.4 16.2 - - + +
987H TYR* 4.2 27.8 - - + +
988H VAL* 3.4 30.3 - - + -
1044H ARG* 2.7 57.5 + - + +
1045H ILE* 3.5 7.6 - - - +
1047H PHE* 1.3 83.9 - - + +
1049H ASN* 1.3 57.3 + - - +
1051H ALA* 3.5 9.6 + - + +
1052H SER* 3.1 24.9 + - - -
1068H VAL* 4.9 10.3 - - + -
1075H THR* 5.1 8.1 - - + -
1077H VAL* 6.0 1.8 - - + -
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Residues in contact with ASN1049 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1254G LYS 4.7 4.3 + - - +
1255G MET* 3.7 32.6 - - + +
987H TYR* 4.4 15.0 - - - -
1045H ILE* 2.8 24.8 + - - +
1046H GLU* 2.9 13.2 + - + +
1048H LEU* 1.3 74.5 - - - +
1050H GLU* 1.3 68.4 + - - +
1052H SER* 2.8 25.6 + - - -
1053H VAL* 3.4 9.7 + - - +
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Residues in contact with GLU1050 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8H 741 3.4 23.7 - - + -
1009H SER* 5.7 0.5 - - - -
1010H PHE* 3.6 27.9 - - - -
1046H GLU* 2.9 21.5 + - - +
1047H PHE* 3.4 9.9 - - - +
1049H ASN* 1.3 72.7 - - - +
1051H ALA* 1.3 58.1 + - - +
1053H VAL* 2.8 29.3 + - - +
1054H MET* 3.4 15.0 + - - +
1153H ASP* 4.8 1.9 - - - +
1154H PHE* 4.4 3.6 - - - +
1155H GLY* 3.4 39.4 + - - +
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Residues in contact with ALA1051 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8H 741 4.7 4.2 - - - -
1047H PHE* 3.2 23.8 + - + +
1048H LEU* 3.6 15.5 - - + +
1050H GLU* 1.3 79.4 - - - +
1052H SER* 1.3 62.1 + - - +
1054H MET* 3.1 28.6 - - - +
1055H LYS* 3.3 7.6 + - - +
1065H LEU* 4.0 22.7 - - + +
1068H VAL* 6.0 3.6 - - + -
1077H VAL* 5.0 2.9 - - + -
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Residues in contact with SER1052 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
987H TYR 4.6 11.5 + - - -
989H PRO* 4.8 12.3 - - - +
1048H LEU 3.1 13.0 + - - -
1049H ASN* 2.8 23.5 + - - -
1051H ALA* 1.3 77.9 - - - +
1053H VAL* 1.3 61.8 + - - +
1055H LYS* 3.7 16.9 - - - +
1056H GLU* 4.2 2.8 + - - +
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Residues in contact with VAL1053 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1049H ASN 4.0 11.0 - - - +
1050H GLU* 2.8 10.2 + - - +
1052H SER* 1.3 76.8 - - - +
1054H MET* 1.3 67.8 + - - +
1055H LYS 3.3 0.2 - - - -
1056H GLU* 3.1 26.1 - - - +
1057H PHE* 3.8 17.3 + - + -
1131H PHE* 3.9 35.9 - - + -
1154H PHE* 6.1 2.0 - - + -
1157H THR* 5.0 6.1 - - - +
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Residues in contact with MET1054 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8H 741 3.6 33.9 - - + -
1050H GLU* 3.4 6.9 + - - +
1051H ALA* 3.1 26.0 - - - +
1053H VAL* 1.3 75.5 - - - +
1055H LYS* 1.3 55.9 + - - +
1057H PHE* 2.7 47.4 + - - +
1062H VAL* 6.0 0.2 - - - -
1063H VAL 4.6 4.7 - - - +
1065H LEU* 4.0 18.0 + - + +
1079H MET* 4.2 20.2 - - + -
1152H GLY 4.0 10.5 - - - +
1153H ASP* 5.2 0.9 - - - +
1154H PHE* 3.4 47.1 - - + +
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Residues in contact with LYS1055 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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989H PRO* 6.4 0.2 - - + -
992H TRP* 3.0 60.3 - - + +
1051H ALA 3.3 7.2 + - - +
1052H SER* 3.7 15.5 - - - +
1054H MET* 1.3 78.1 - - - +
1056H GLU* 1.3 65.7 + - - +
1057H PHE 3.8 6.1 - - - +
1058H ASN* 5.5 1.0 - - - +
1065H LEU* 4.7 4.2 - - + +
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Residues in contact with GLU1056 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1052H SER 4.2 2.7 + - - +
1053H VAL* 3.1 19.7 + - - +
1054H MET 2.9 0.6 + - - -
1055H LYS* 1.3 81.8 - - - +
1057H PHE* 1.3 69.8 + - + +
1058H ASN* 3.4 5.9 + - - +
1125H TYR* 3.8 4.3 + - - +
1129H ASN* 4.4 17.5 - - - +
1131H PHE* 3.7 33.6 - - - -
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Residues in contact with PHE1057 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1053H VAL* 3.9 29.6 - - + -
1054H MET* 2.7 27.4 + - - +
1055H LYS* 3.8 4.0 - - - +
1056H GLU* 1.3 76.1 - - + +
1058H ASN* 1.3 59.6 + - - +
1059H CYS 3.8 0.4 - - - -
1062H VAL* 3.9 17.8 - - + +
1064H ARG* 4.1 17.3 - - - +
1065H LEU 5.5 1.0 + - - -
1125H TYR* 3.4 24.7 - + + -
1126H LEU* 3.1 33.9 - - + -
1129H ASN* 5.0 3.4 - - + -
1131H PHE* 3.6 29.8 - + - -
1154H PHE* 3.9 37.5 - + + -
1157H THR* 5.0 2.9 - - - -
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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