Contacts of the helix formed by residues 1031 - 1047 (chain B) in PDB entry 3P8C
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 CYS1031 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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807B TYR* 4.0 13.7 - - - -
908B THR 4.3 3.4 - - - +
911B GLY* 3.3 30.3 - - - +
912B VAL* 3.7 19.7 - - - +
915B SER* 3.4 20.4 - - - -
1028B ASN* 2.9 19.7 + - - +
1030B HIS* 1.3 92.6 - - - +
1032B LEU* 1.3 62.0 + - - +
1033B ALA 3.2 0.7 - - - -
1034B LYS* 3.2 8.1 + - - +
1035B ALA 3.1 15.8 + - - -
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Residues in contact with LEU1032 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
904B LEU* 4.2 7.9 - - + +
907B MET* 3.6 21.1 - - + +
908B THR* 3.5 40.1 - - - +
1003B VAL* 5.7 2.2 - - + -
1007B LEU* 4.2 13.7 - - + -
1010B LEU* 3.8 29.4 - - + -
1028B ASN 4.2 0.2 + - - -
1029B ILE* 2.9 26.8 + - + +
1031B CYS* 1.3 75.9 - - - +
1033B ALA* 1.3 58.8 + - - +
1035B ALA* 4.1 3.6 - - + -
1036B ILE* 2.8 49.3 + - + +
1087B LEU* 4.5 6.3 - - + -
1091B ILE* 6.0 0.7 - - + -
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Residues in contact with ALA1033 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1029B ILE 4.3 0.2 + - - -
1030B HIS 3.2 15.2 + - - +
1032B LEU* 1.3 78.0 - - - +
1034B LYS* 1.3 59.9 + - - +
1036B ILE* 4.3 1.2 - - - +
1037B ASN* 3.4 25.1 + - - +
1087B LEU* 5.4 2.5 - - + +
1090B MET* 3.6 40.8 - - + +
1091B ILE* 3.7 19.7 - - + +
1094B GLU* 3.9 12.8 - - + +
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Residues in contact with LYS1034 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
807B TYR* 5.6 5.2 - - - -
911B GLY 4.7 3.4 - - - +
914B LEU* 3.5 34.7 - - + +
915B SER* 3.7 17.9 - - - +
918B SER* 3.0 25.6 + - - +
922B GLU* 5.4 1.2 + - - -
1030B HIS 4.4 0.4 + - - -
1031B CYS* 3.2 11.9 + - - +
1032B LEU 3.2 0.4 - - - -
1033B ALA* 1.3 76.5 - - - +
1035B ALA* 1.3 60.7 + - - +
1037B ASN* 4.1 0.4 - - - -
1038B GLN* 3.1 56.4 + - + +
1094B GLU* 3.2 40.9 + - - +
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Residues in contact with ALA1035 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
907B MET* 3.2 40.4 - - + +
910B ILE* 4.2 6.1 - - + -
911B GLY* 3.7 14.6 - - - +
914B LEU* 3.9 11.4 - - - -
1031B CYS 3.1 7.0 + - - +
1032B LEU* 3.1 8.7 + - + +
1034B LYS* 1.3 74.6 - - - +
1036B ILE* 1.3 64.9 + - - +
1039B ILE* 3.0 31.5 + - - +
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Residues in contact with ILE1036 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
907B MET* 3.8 20.6 - - + -
1000B MET* 4.8 7.1 - - - +
1003B VAL* 4.0 15.9 - - + -
1007B LEU* 4.8 5.8 - - + -
1032B LEU* 2.8 37.0 + - + +
1033B ALA* 4.3 2.9 - - - +
1035B ALA* 1.3 70.7 - - - +
1037B ASN* 1.3 62.6 + - - +
1039B ILE* 4.4 0.5 - - - +
1040B ALA* 3.2 26.2 + - - +
1055B LEU* 4.1 11.4 - - + -
1058B PHE* 3.6 47.6 - - + -
1091B ILE* 4.0 24.7 - - + -
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Residues in contact with ASN1037 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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970B GLU 5.2 5.9 + - - -
1033B ALA 3.4 17.7 + - - +
1034B LYS 4.1 2.0 - - - +
1035B ALA 3.3 0.4 - - - -
1036B ILE* 1.3 81.1 - - - +
1038B GLN* 1.3 69.0 + - - +
1040B ALA* 3.7 2.1 - - - +
1041B ALA* 2.9 26.9 + - - +
1055B LEU* 3.8 10.8 - - + +
1091B ILE* 5.3 2.0 - - + +
1094B GLU* 3.9 14.7 + - + +
1095B SER* 3.0 36.6 + - - +
1096B PRO* 3.7 19.9 - - - +
1097B PHE* 3.7 10.7 - - - -
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Residues in contact with GLN1038 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
914B LEU* 3.4 29.6 - - + +
917B ARG* 5.1 1.2 - - - +
918B SER* 4.6 4.0 + - - -
969B CYS 6.0 2.0 - - - +
970B GLU 5.5 5.2 - - - +
972B ASP* 3.3 36.3 + - + +
975B LEU* 3.4 9.2 - - + +
1034B LYS* 3.1 45.3 + - + +
1037B ASN* 1.3 85.8 - - - +
1039B ILE* 1.3 59.6 + - - +
1041B ALA* 3.5 6.5 + - - +
1042B ALA* 3.0 30.3 + - - +
1094B GLU* 5.4 0.5 - - - +
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Residues in contact with ILE1039 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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859B ILE* 4.1 8.5 - - + -
863B VAL* 3.9 27.4 - - + -
866B LEU* 6.3 0.2 - - + -
907B MET* 4.7 14.1 - - + -
910B ILE* 3.9 26.7 - - + -
914B LEU* 5.0 0.7 - - + -
975B LEU* 4.3 9.0 - - + -
979B LEU* 4.1 11.7 - - + -
999B LEU* 4.2 15.9 - - + -
1000B MET* 4.3 5.4 - - + -
1035B ALA* 3.0 22.3 + - - +
1036B ILE 4.4 0.9 - - - +
1038B GLN* 1.3 75.4 - - - +
1040B ALA* 1.3 59.3 + - - +
1042B ALA* 3.4 1.8 + - - +
1043B LEU* 2.9 52.2 + - + +
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Residues in contact with ALA1040 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1000B MET* 3.8 25.3 - - + +
1036B ILE 3.2 19.3 + - - +
1037B ASN 3.7 2.9 - - - +
1039B ILE* 1.3 76.7 - - - +
1041B ALA* 1.3 65.0 - - - +
1044B PHE* 3.0 39.1 + - + +
1051B ILE* 4.2 3.2 - - + +
1055B LEU* 3.8 26.2 - - + +
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Residues in contact with ALA1041 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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970B GLU 3.8 22.2 - - - +
971B ILE* 3.6 16.1 - - + +
972B ASP 5.5 1.1 - - - +
1037B ASN* 2.9 19.2 + - - +
1038B GLN* 3.7 7.4 - - - +
1039B ILE 3.4 0.2 - - - -
1040B ALA* 1.3 75.5 - - - +
1042B ALA* 1.3 58.4 + - - +
1045B THR* 2.6 32.7 + - - -
1051B ILE* 3.7 14.4 - - - +
1097B PHE* 4.2 10.8 - - + -
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Residues in contact with ALA1042 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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971B ILE* 4.5 1.1 - - - -
972B ASP 5.1 2.0 - - - +
975B LEU* 3.8 25.6 - - + -
976B VAL* 4.2 23.0 - - + +
979B LEU* 4.1 10.1 - - + -
1038B GLN 3.0 18.2 + - - +
1039B ILE 3.8 3.1 - - - +
1041B ALA* 1.3 76.0 - - - +
1043B LEU* 1.3 65.1 + - - +
1045B THR* 3.2 3.6 + - - -
1046B ILE* 3.1 29.8 + - + +
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Residues in contact with LEU1043 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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863B VAL* 5.0 5.2 - - + -
867B LYS* 4.7 20.9 - - - +
979B LEU* 3.9 28.0 - - + +
996B ALA* 4.1 25.4 - - + -
999B LEU* 4.1 17.3 - - + -
1000B MET* 4.5 4.3 - - + -
1039B ILE* 2.9 39.4 + - + +
1040B ALA 4.4 1.3 - - - +
1042B ALA* 1.3 75.8 - - - +
1044B PHE* 1.3 61.4 + - + +
1046B ILE* 3.3 6.0 + - + +
1047B HIS* 2.7 51.2 + - + +
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Residues in contact with PHE1044 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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993B TYR* 3.8 22.9 - + - -
996B ALA* 3.7 40.4 - - + -
997B CYS* 3.8 13.0 - - - -
1000B MET* 3.7 25.6 - - + -
1040B ALA* 3.0 30.3 + - + +
1041B ALA 4.2 0.9 - - - -
1043B LEU* 1.3 76.9 - - + +
1045B THR* 1.3 60.1 + - - +
1047B HIS* 4.1 2.2 - - - +
1048B LYS* 3.6 0.7 + - - -
1049B GLY* 3.0 36.0 + - - +
1051B ILE* 4.1 22.4 - - + +
1054B ARG* 3.6 46.7 - - + -
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Residues in contact with THR1045 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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952B MET* 5.4 9.2 - - + +
956B MET* 4.8 11.0 - - + -
971B ILE* 3.4 24.3 - - + +
976B VAL* 4.6 11.9 - - + -
1041B ALA 2.6 23.8 + - - -
1042B ALA 3.2 5.7 + - - -
1044B PHE* 1.3 76.3 - - - +
1046B ILE* 1.3 65.5 + - - +
1047B HIS 3.2 1.1 - - - -
1048B LYS* 3.2 19.1 + - - +
1051B ILE* 3.7 11.8 - - - +
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Residues in contact with ILE1046 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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976B VAL* 3.5 37.0 - - + +
979B LEU* 3.8 30.1 - - + +
980B SER* 3.9 21.3 - - - +
992B GLU* 5.8 0.9 - - - +
1042B ALA 3.1 20.3 + - - +
1043B LEU* 3.3 11.4 + - + +
1045B THR* 1.3 78.4 - - - +
1047B HIS* 1.3 74.4 + - + +
1048B LYS* 3.3 5.8 + - - +
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Residues in contact with HIS1047 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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867B LYS* 5.6 6.3 - - - -
989B PRO* 4.5 7.4 - - + +
992B GLU* 3.4 51.9 + - + +
993B TYR* 3.9 30.8 - - + -
996B ALA* 4.4 10.8 - - + +
1043B LEU* 2.7 44.8 + - + +
1044B PHE* 4.2 1.8 - - - -
1046B ILE* 1.3 91.2 - - + +
1048B LYS* 1.3 58.0 + - - +
1049B GLY* 2.8 17.3 + - - -
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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