Contacts of the helix formed by residues 1040 - 1056 (chain S) 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 S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1246J ARG* 5.5 1.8 - - - +
1038S ALA 3.5 4.2 + - - -
1039S ALA* 1.3 76.6 - - - +
1041S MET* 1.3 65.2 + - - +
1042S ARG* 3.9 9.4 - - - +
1043S GLU* 2.9 37.2 + - - +
1044S ARG* 3.0 20.1 + - - +
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Residues in contact with MET1041 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1243J GLU* 3.7 47.3 - - + +
1246J ARG* 3.6 52.3 - - + +
1247J MET* 3.9 24.7 - - + -
1250J GLN* 4.2 6.3 - - - +
982S SER* 5.6 0.7 - - - -
983S ALA* 4.5 10.8 - - + +
1039S ALA 3.5 1.8 + - - -
1040S SER* 1.3 70.4 - - - +
1042S ARG* 1.3 66.5 + - - +
1044S ARG* 2.9 12.8 + - - +
1045S ILE* 2.9 39.7 + - + +
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Residues in contact with ARG1042 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1250J GLN* 3.5 27.2 - - + +
1251J TYR* 5.7 7.5 - - - +
1252J ASN* 5.3 13.3 - - - +
1255J MET* 6.3 0.6 - - - +
1040S SER* 3.9 9.2 - - - +
1041S MET* 1.3 81.8 - - - +
1043S GLU* 1.3 63.7 + - - +
1045S ILE* 4.0 2.1 - - - +
1046S GLU* 3.2 38.9 + - + +
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Residues in contact with GLU1043 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1236E ASN* 5.2 6.3 + - - -
1009S SER 4.9 4.2 - - - +
1010S PHE* 3.9 35.3 - - + +
1035S VAL* 6.1 0.8 - - - +
1039S ALA* 3.7 21.7 - - + +
1040S SER* 2.9 29.0 + - - +
1041S MET 3.2 0.2 - - - -
1042S ARG* 1.3 79.8 - - - +
1044S ARG* 1.3 58.0 + - - +
1046S GLU* 3.6 6.8 + - - +
1047S PHE* 3.1 28.1 + - - +
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Residues in contact with ARG1044 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
982S SER* 4.3 18.8 + - - -
983S ALA* 4.2 16.7 - - + +
984S ALA 4.5 0.4 - - - +
1035S VAL* 3.1 30.2 + - + +
1036S ASN 2.7 34.6 + - - -
1037S GLU* 3.7 13.9 + - - +
1039S ALA* 3.8 16.4 + - + +
1040S SER 3.0 14.5 + - - +
1041S MET* 2.9 12.1 + - - +
1043S GLU* 1.3 75.1 - - - +
1045S ILE* 1.3 61.7 + - - +
1047S PHE* 3.7 10.9 + - + +
1048S LEU* 3.1 38.9 + - + +
1073S GLN 4.5 7.2 + - - -
1075S THR* 3.6 17.9 + - - +
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Residues in contact with ILE1045 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1247J MET* 4.5 3.8 - - + -
1250J GLN* 3.1 33.4 - - - +
1255J MET* 3.4 25.4 - - + +
983S ALA* 3.9 17.5 - - + -
987S TYR* 3.5 32.5 - - + +
1041S MET* 2.9 25.8 + - + +
1042S ARG* 4.0 3.6 - - - +
1044S ARG* 1.3 74.5 - - - +
1046S GLU* 1.3 66.8 + - - +
1048S LEU* 2.8 17.3 + - - +
1049S ASN* 2.8 30.3 + - - +
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Residues in contact with GLU1046 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1255J MET* 4.3 24.9 - - + -
1010S PHE* 4.3 18.6 - - + -
1042S ARG* 3.2 30.9 + - - +
1043S GLU* 3.7 6.4 - - - +
1045S ILE* 1.3 78.9 - - - +
1047S PHE* 1.3 62.0 + - - +
1049S ASN* 4.1 1.0 - - - +
1050S GLU* 3.2 25.6 + - - +
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Residues in contact with PHE1047 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15S 741 3.6 30.4 - + - -
1010S PHE* 3.3 41.0 - + + -
1033S LYS* 4.1 19.5 - - + -
1035S VAL* 3.7 27.4 - - + -
1043S GLU 3.1 15.7 + - - +
1044S ARG* 3.7 9.0 - - + +
1045S ILE 3.1 0.2 - - - -
1046S GLU* 1.3 79.0 - - - +
1048S LEU* 1.3 77.1 + - + +
1050S GLU* 3.8 3.0 + - - +
1051S ALA* 3.4 20.0 + - + +
1075S THR* 4.6 7.4 - - + -
1077S VAL* 3.0 37.2 - - + -
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Residues in contact with LEU1048 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
983S ALA* 4.2 7.2 - - + +
984S ALA* 3.7 31.9 - - + +
987S TYR* 4.2 18.9 - - + +
988S VAL* 4.0 25.4 - - + +
1044S ARG* 3.1 32.3 + - + +
1045S ILE* 2.8 5.9 + - - +
1047S PHE* 1.3 102.1 - - + +
1049S ASN* 1.3 60.2 + - - +
1051S ALA* 3.4 7.7 + - + +
1052S SER* 3.1 26.9 + - - -
1068S VAL* 5.1 2.2 - - + -
1075S THR* 4.5 10.3 - - + -
1077S VAL* 4.9 6.5 - - + -
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Residues in contact with ASN1049 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1254J LYS 4.5 9.2 + - - -
1255J MET* 3.6 26.3 - - + +
1261J GLU* 6.0 0.2 + - - -
987S TYR* 3.7 17.7 + - - -
1045S ILE* 2.8 38.1 + - - +
1046S GLU 4.1 2.9 - - - +
1048S LEU* 1.3 74.3 - - - +
1050S GLU* 1.3 65.6 + - - +
1051S ALA 3.2 0.7 - - - -
1052S SER* 3.1 21.3 + - - -
1053S VAL* 3.3 12.1 + - - +
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Residues in contact with GLU1050 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15S 741 3.3 34.6 - - + -
1009S SER* 5.1 0.7 + - - -
1010S PHE* 4.0 17.4 - - - -
1046S GLU 3.2 17.2 + - - +
1047S PHE 3.9 5.6 - - - +
1048S LEU 3.4 0.2 - - - -
1049S ASN* 1.3 76.7 - - - +
1051S ALA* 1.3 61.8 + - - +
1053S VAL* 3.4 24.2 + - + +
1054S MET* 3.6 11.2 - - + +
1153S ASP* 4.3 4.9 - - - +
1154S PHE 4.9 2.5 - - - +
1155S GLY* 3.5 36.5 + - - +
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Residues in contact with ALA1051 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15S 741 4.7 10.1 - - - +
1047S PHE* 3.4 12.9 + - + +
1048S LEU* 3.6 13.0 - - + +
1049S ASN 3.2 0.4 - - - -
1050S GLU* 1.3 79.0 - - - +
1052S SER* 1.3 62.4 + - - +
1054S MET* 3.1 28.4 - - - +
1055S LYS* 3.3 5.0 + - - +
1065S LEU* 3.5 22.7 - - + +
1068S VAL* 5.6 4.7 - - + -
1077S VAL* 5.0 12.8 - - + -
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Residues in contact with SER1052 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1261J GLU* 5.7 0.3 + - - -
987S TYR 3.8 15.9 + - - -
988S VAL* 5.9 0.5 - - - +
989S PRO* 5.0 8.7 - - - +
1048S LEU 3.1 14.3 + - - -
1049S ASN* 3.1 22.4 + - - -
1051S ALA* 1.3 78.2 - - - +
1053S VAL* 1.3 59.2 - - - +
1055S LYS* 3.3 21.7 - - - +
1056S GLU* 4.1 2.8 + - - +
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Residues in contact with VAL1053 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1049S ASN 3.3 9.5 + - - +
1050S GLU* 3.4 15.9 + - + +
1051S ALA 3.2 1.0 - - - -
1052S SER* 1.3 76.0 - - - +
1054S MET* 1.3 70.3 + - + +
1056S GLU* 3.8 7.8 - - + +
1057S PHE* 3.4 31.8 - - + -
1131S PHE* 3.9 32.3 - - + -
1154S PHE* 4.6 18.2 - - + +
1157S THR* 4.8 6.1 - - - +
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Residues in contact with MET1054 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15S 741 3.4 39.5 - - + -
1050S GLU* 3.6 14.6 - - + +
1051S ALA* 3.1 17.9 - - - +
1053S VAL* 1.3 74.8 - - - +
1055S LYS* 1.3 56.7 + - - +
1056S GLU 3.0 2.2 - - - -
1057S PHE* 2.4 44.0 + - - +
1063S VAL 5.1 3.8 - - - +
1065S LEU* 3.9 19.5 - - + +
1079S MET* 4.6 11.4 - - + -
1152S GLY 4.7 5.8 - - - +
1153S ASP* 5.5 0.4 - - - +
1154S PHE* 3.3 55.0 - - + +
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Residues in contact with LYS1055 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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992S TRP* 3.3 53.9 - - + +
1051S ALA 3.3 5.4 + - - +
1052S SER* 3.3 19.5 - - - +
1054S MET* 1.3 78.5 - - - +
1056S GLU* 1.3 63.4 + - - +
1057S PHE 3.1 6.1 + - - +
1058S ASN* 5.6 0.9 - - - +
1065S LEU* 4.9 4.0 - - + +
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Residues in contact with GLU1056 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1052S SER 4.1 2.6 + - - +
1053S VAL* 3.8 14.7 + - + +
1054S MET 2.7 3.6 + - - -
1055S LYS* 1.3 77.9 - - - +
1057S PHE* 1.3 70.5 + - + +
1058S ASN* 3.4 5.9 + - - +
1125S TYR* 3.5 7.1 + - - -
1129S ASN* 4.1 21.0 - - - +
1131S PHE* 3.3 26.4 - - + -
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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