Contacts of the helix formed by residues 1040 - 1057 (chain J) 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 J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1246I ARG* 6.0 0.4 - - - +
1038J ALA 3.7 3.4 + - - -
1039J ALA* 1.3 75.5 - - - +
1041J MET* 1.3 65.8 + - - +
1042J ARG* 3.7 12.1 - - - +
1043J GLU* 3.0 37.5 + - - +
1044J ARG* 3.0 22.0 + - - +
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Residues in contact with MET1041 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1243I GLU* 3.6 47.8 - - + +
1246I ARG* 3.5 47.8 - - + +
1247I MET* 4.0 20.9 - - + -
1250I GLN* 4.0 11.4 - - - +
982J SER* 5.8 0.4 - - - -
983J ALA* 4.7 11.4 - - + +
1039J ALA 3.6 2.0 + - - -
1040J SER* 1.3 72.4 - - - +
1042J ARG* 1.3 62.2 + - - +
1044J ARG* 3.9 9.7 - - - +
1045J ILE* 3.0 40.3 + - + +
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Residues in contact with ARG1042 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1250I GLN* 4.0 24.0 - - - +
1252I ASN* 5.7 9.5 - - - +
1255I MET* 5.9 5.5 - - + +
1040J SER* 3.0 10.9 - - - +
1041J MET* 1.3 82.0 - - - +
1043J GLU* 1.3 74.2 + - - +
1045J ILE* 3.3 3.7 + - - +
1046J GLU* 3.1 48.1 + - - +
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Residues in contact with GLU1043 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1009J SER 5.4 1.0 - - - +
1010J PHE* 3.6 28.9 - - + -
1035J VAL* 6.0 0.7 - - - -
1039J ALA* 4.9 6.5 - - + -
1040J SER* 3.0 31.0 + - - +
1042J ARG* 1.3 95.1 + - + +
1044J ARG* 1.3 56.9 + - - +
1046J GLU* 3.2 24.0 - - - +
1047J PHE* 3.0 28.6 + - - +
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Residues in contact with ARG1044 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
982J SER* 4.9 9.0 + - - -
983J ALA* 4.0 21.8 - - + +
984J ALA* 4.3 7.9 - - - +
1035J VAL* 3.3 42.0 + - + +
1036J ASN 4.0 0.6 - - - -
1037J GLU* 3.4 24.4 + - - +
1039J ALA* 3.6 22.6 + - + +
1040J SER 3.0 12.8 + - - +
1041J MET* 4.0 7.3 - - - +
1043J GLU* 1.3 75.2 - - - +
1045J ILE* 1.3 58.9 + - - +
1047J PHE* 3.4 9.5 - - + +
1048J LEU* 2.9 40.1 + - + +
1073J GLN 4.3 6.7 + - - -
1075J THR* 3.3 23.6 + - - +
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Residues in contact with ILE1045 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1247I MET* 4.9 1.6 - - - -
1250I GLN* 3.5 31.6 - - + +
1255I MET* 3.6 34.8 - - + +
983J ALA* 3.9 11.7 - - + -
987J TYR* 3.6 44.0 - - + +
1041J MET* 3.0 31.2 + - + +
1042J ARG* 3.8 3.1 - - - +
1044J ARG* 1.3 73.8 - - - +
1046J GLU* 1.3 57.7 + - - +
1047J PHE 3.0 1.1 - - - -
1048J LEU* 2.9 8.5 + - - +
1049J ASN* 2.8 34.6 + - - +
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Residues in contact with GLU1046 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1255I MET* 4.3 20.2 - - + +
1010J PHE* 3.9 19.7 - - + -
1042J ARG* 3.1 32.6 + - + +
1043J GLU* 3.2 24.1 - - - +
1045J ILE* 1.3 79.7 - - - +
1047J PHE* 1.3 58.0 + - - +
1049J ASN* 3.5 2.4 + - - +
1050J GLU* 3.1 31.2 + - - +
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Residues in contact with PHE1047 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10J 741 3.6 30.7 - + - -
1010J PHE* 3.3 40.1 - + + -
1033J LYS* 4.2 12.3 - - + -
1035J VAL* 3.3 30.7 - - + -
1043J GLU 3.0 19.0 + - - +
1044J ARG* 3.4 10.5 - - + +
1045J ILE 3.0 0.2 - - - -
1046J GLU* 1.3 77.8 - - - +
1048J LEU* 1.3 82.5 + - + +
1050J GLU* 3.4 3.7 + - - +
1051J ALA* 3.2 21.0 + - + +
1075J THR* 4.3 6.5 - - + -
1077J VAL* 3.1 37.7 - - + -
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Residues in contact with LEU1048 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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983J ALA* 4.0 3.1 - - + -
984J ALA* 3.4 38.6 - - + +
987J TYR* 4.0 25.3 - - + +
988J VAL* 3.8 24.1 - - + +
1044J ARG* 2.9 24.2 + - + +
1045J ILE 2.9 4.9 + - - +
1047J PHE* 1.3 105.2 - - + +
1049J ASN* 1.3 57.6 + - - +
1051J ALA* 3.5 6.7 + - + +
1052J SER* 3.1 28.6 + - - -
1068J VAL* 5.3 0.9 - - + -
1075J THR* 4.3 11.9 - - + -
1077J VAL* 5.0 5.2 - - + -
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Residues in contact with ASN1049 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1254I LYS 4.2 8.3 - - - +
1255I MET* 3.3 35.4 - - + +
1261I GLU* 5.5 2.4 + - - -
987J TYR* 4.0 23.4 + - - -
1045J ILE* 2.8 25.3 + - - +
1046J GLU 4.0 3.4 - - - +
1048J LEU* 1.3 75.5 + - - +
1050J GLU* 1.3 66.4 + - - +
1052J SER* 3.1 22.7 + - - -
1053J VAL* 3.2 18.0 + - - +
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Residues in contact with GLU1050 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10J 741 3.3 33.5 - - + -
1009J SER* 5.1 1.2 + - - -
1010J PHE* 3.6 20.6 - - - -
1046J GLU* 3.1 20.0 + - - +
1047J PHE* 3.6 6.1 - - - +
1049J ASN* 1.3 78.8 - - - +
1051J ALA* 1.3 59.4 + - - +
1053J VAL* 3.5 20.4 + - - +
1054J MET* 3.7 10.4 + - + +
1153J ASP* 4.3 5.4 - - - +
1154J PHE* 4.5 10.4 + - + +
1155J GLY* 3.6 35.4 + - - +
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Residues in contact with ALA1051 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10J 741 4.4 11.8 - - + +
1047J PHE* 3.2 14.1 + - + +
1048J LEU* 3.9 8.1 - - + +
1050J GLU* 1.3 74.3 - - - +
1052J SER* 1.3 61.3 + - - +
1053J VAL 3.1 2.2 - - - -
1054J MET* 3.1 29.4 - - - +
1055J LYS* 3.2 6.1 + - - +
1065J LEU* 3.4 23.4 - - + +
1068J VAL* 5.9 3.8 - - + -
1077J VAL* 4.8 14.1 - - + -
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Residues in contact with SER1052 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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987J TYR 3.7 16.1 + - - -
988J VAL* 5.2 2.3 - - - +
989J PRO* 4.8 9.4 - - - +
1048J LEU 3.1 19.5 + - - -
1049J ASN* 3.1 16.8 + - - -
1051J ALA* 1.3 75.0 - - - +
1053J VAL* 1.3 64.3 + - - +
1055J LYS* 3.6 18.7 - - - +
1056J GLU* 4.3 2.3 + - - +
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Residues in contact with VAL1053 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1049J ASN 3.2 18.4 - - - +
1050J GLU* 3.7 11.4 - - + +
1051J ALA 3.1 0.4 - - - -
1052J SER* 1.3 77.6 - - - +
1054J MET* 1.3 69.0 + - - +
1056J GLU* 3.2 21.5 + - + +
1057J PHE* 3.9 17.9 - - + -
1131J PHE* 3.8 32.3 - - + -
1154J PHE* 5.7 9.0 - - + +
1157J THR* 5.2 5.4 - - - +
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Residues in contact with MET1054 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10J 741 3.3 31.4 - - + +
1050J GLU* 3.8 5.2 - - + +
1051J ALA* 3.1 24.2 - - - +
1053J VAL* 1.3 76.1 - - - +
1055J LYS* 1.3 68.4 + - - +
1057J PHE* 2.7 36.0 + - - +
1063J VAL 4.2 7.0 - - - +
1065J LEU* 3.6 21.5 + - + +
1079J MET* 4.1 21.1 - - + -
1152J GLY 4.1 13.5 - - - +
1153J ASP* 5.2 0.4 - - - -
1154J PHE* 3.7 42.3 - - + +
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Residues in contact with LYS1055 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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989J PRO* 6.2 0.4 - - + -
992J TRP* 3.4 53.7 - - + +
1051J ALA 3.2 6.6 + - - +
1052J SER* 3.6 16.8 - - - +
1054J MET* 1.3 78.1 - - - +
1056J GLU* 1.3 65.8 + - - +
1057J PHE 3.3 6.8 + - - +
1058J ASN* 5.4 1.4 - - - +
1065J LEU* 4.6 6.7 - - + +
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Residues in contact with GLU1056 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1052J SER 4.3 2.1 + - - +
1053J VAL* 3.2 15.1 + - - +
1054J MET 2.8 2.6 + - - -
1055J LYS* 1.3 78.0 - - - +
1057J PHE* 1.3 78.4 + - + +
1058J ASN* 3.4 6.1 + - - +
1125J TYR* 3.8 4.3 + - - -
1129J ASN* 4.2 20.9 - - - +
1131J PHE* 4.2 17.6 - - + -
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Residues in contact with PHE1057 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1053J VAL* 3.9 32.5 - - + -
1054J MET* 2.7 27.1 + - - +
1055J LYS 3.5 5.7 - - - +
1056J GLU* 1.3 78.3 - - + +
1058J ASN* 1.3 60.5 + - - +
1059J CYS 3.9 0.7 - - - -
1062J VAL* 4.3 13.2 - - + -
1064J ARG* 4.5 12.8 - - - +
1065J LEU 5.5 1.0 + - - -
1125J TYR* 3.4 21.3 - + + -
1126J LEU* 3.8 27.1 - - + -
1129J ASN* 5.2 4.3 - - + -
1131J PHE* 3.7 35.7 - + - -
1154J PHE* 3.8 42.6 - + - -
1157J THR* 5.1 0.7 - - - -
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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
------------------------------------------------------------
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