Contacts of the helix formed by residues 1041 - 1058 (chain A) in PDB entry 6A5T
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 ARG1041 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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982A ASP* 2.1 66.3 + - - +
983A LEU* 4.1 5.3 - - + +
984A THR* 4.0 8.3 - - - +
987A GLU* 2.6 38.6 + - - +
1040A ASN* 1.3 78.2 - - - +
1042A ASP* 1.3 71.1 + - - +
1044A PHE* 3.3 3.2 + - + +
1045A GLU* 2.9 39.2 + - + +
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Residues in contact with ASP1042 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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973A PHE* 4.6 19.8 - - + -
1040A ASN* 2.7 20.7 + - - +
1041A ARG* 1.3 75.8 - - - +
1043A ALA* 1.3 63.4 + - - +
1045A GLU* 2.9 22.9 + - - +
1046A TRP* 2.9 12.4 + - - +
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Residues in contact with ALA1043 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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969A ALA* 4.6 13.2 - - + +
973A PHE* 3.6 32.0 - - + -
975A LEU* 3.7 21.8 - - + -
1039A LEU* 4.7 5.2 - - + -
1040A ASN* 2.3 29.2 + - - +
1042A ASP* 1.3 70.5 - - - +
1044A PHE* 1.3 55.5 + - - +
1046A TRP* 3.2 3.5 + - - +
1047A VAL* 2.9 33.6 + - - +
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Residues in contact with PHE1044 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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983A LEU* 4.7 10.8 - - + -
987A GLU* 4.6 15.5 - - + -
988A ILE* 4.5 23.8 - - + -
991A GLY* 5.0 1.6 - - - -
992A VAL* 4.9 8.3 - - + -
1028A LEU* 4.8 11.2 - - + -
1033A ILE* 4.0 24.5 - - + -
1039A LEU* 4.2 22.4 - - + -
1040A ASN* 3.0 24.3 + - - +
1041A ARG* 3.3 5.3 + - + +
1042A ASP 3.0 0.6 - - - -
1043A ALA* 1.3 77.4 - - - +
1045A GLU* 1.3 73.7 - - + +
1047A VAL* 3.1 7.0 + - + +
1048A LEU* 3.0 52.7 + - + +
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Residues in contact with GLU1045 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1041A ARG* 2.9 30.9 + - + +
1042A ASP* 2.9 13.4 + - - +
1044A PHE* 1.3 83.7 - - + +
1046A TRP* 1.3 62.7 + - - +
1048A LEU* 3.3 7.8 + - + +
1049A GLY* 3.0 20.1 + - - -
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Residues in contact with TRP1046 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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965A ILE* 4.5 11.9 - - + -
968A ASN* 4.6 8.5 - - + -
969A ALA* 4.1 35.7 - - + -
972A ILE* 4.2 22.4 - - + -
973A PHE* 4.4 19.5 - + + -
1042A ASP 2.9 11.0 + - - +
1043A ALA* 3.4 11.9 - - - +
1044A PHE 3.0 0.2 - - - -
1045A GLU* 1.3 78.0 - - - +
1047A VAL* 1.3 67.7 + - + +
1049A GLY* 3.2 3.4 + - - +
1050A THR* 2.9 42.9 + - + -
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Residues in contact with VAL1047 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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965A ILE* 4.0 14.4 - - + +
966A ILE* 4.6 13.9 - - + -
969A ALA* 3.5 27.8 - - + -
1028A LEU* 4.6 11.0 - - + -
1039A LEU* 4.4 13.7 - - + -
1043A ALA 2.9 17.4 + - - +
1044A PHE* 3.1 8.7 + - + +
1046A TRP* 1.3 81.7 - - + +
1048A LEU* 1.3 64.6 + - + +
1050A THR* 3.3 3.4 + - - +
1051A ILE* 2.9 44.6 + - + +
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Residues in contact with LEU1048 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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991A GLY* 4.3 23.1 - - - +
992A VAL* 4.9 3.1 - - + +
995A LEU* 3.8 38.1 - - + +
1028A LEU* 5.1 10.1 - - + -
1044A PHE* 3.0 45.7 + - + +
1045A GLU* 3.7 10.1 - - + +
1047A VAL* 1.3 78.2 - - + +
1049A GLY* 1.3 65.0 + - - +
1050A THR 3.2 0.2 + - - -
1051A ILE* 3.2 8.0 + - + -
1052A GLU* 3.0 25.9 + - - +
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Residues in contact with GLY1049 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1045A GLU 3.0 14.8 + - - -
1046A TRP* 3.7 3.1 - - - -
1048A LEU* 1.3 76.2 - - - +
1050A THR* 1.3 62.4 + - - +
1052A GLU* 3.3 13.5 - - - +
1053A ALA* 3.0 22.8 + - - +
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Residues in contact with THR1050 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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965A ILE* 3.5 32.8 - - + -
1046A TRP* 2.9 42.2 + - + -
1047A VAL* 3.9 3.8 - - - -
1049A GLY* 1.3 74.2 - - - +
1051A ILE* 1.3 66.8 + - - +
1053A ALA* 3.1 6.9 + - + +
1054A GLN* 2.9 37.6 + - + +
1057A ARG* 5.8 0.7 - - - +
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Residues in contact with ILE1051 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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960A VAL* 4.8 9.9 - - + -
962A LEU* 3.4 32.3 - - + -
965A ILE* 4.0 21.1 - - + -
966A ILE* 6.0 0.9 - - + -
995A LEU* 5.0 13.5 - - + -
999A LEU* 4.9 2.4 - - + +
1020A PHE* 4.6 19.1 - - + -
1024A VAL* 4.9 7.6 - - + -
1028A LEU* 4.6 12.8 - - + -
1047A VAL* 2.9 36.6 + - + +
1048A LEU* 4.2 6.3 - - + +
1050A THR* 1.3 74.7 - - - +
1052A GLU* 1.3 64.5 + - - +
1054A GLN 4.6 0.2 - - - +
1055A PHE* 3.0 23.6 + - + +
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Residues in contact with GLU1052 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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995A LEU* 4.9 11.6 - - + +
998A LYS* 3.3 46.0 + - + +
999A LEU* 5.0 10.6 - - - +
1048A LEU 3.0 13.4 + - - +
1049A GLY* 3.3 15.8 - - - +
1051A ILE* 1.3 81.0 - - - +
1053A ALA* 1.3 67.0 + - - +
1055A PHE* 3.2 2.3 + - - +
1056A GLN* 3.0 24.9 + - + +
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Residues in contact with ALA1053 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1049A GLY 3.0 13.6 + - - +
1050A THR* 3.1 6.7 + - + +
1052A GLU* 1.3 83.4 - - + +
1054A GLN* 1.3 59.7 + - - +
1056A GLN* 3.1 12.3 + - - +
1057A ARG* 3.0 47.8 + - - +
84F TYR* 6.1 0.2 - - - -
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Residues in contact with GLN1054 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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636A ARG* 4.4 25.1 + - - +
637A GLU* 6.0 0.2 + - - -
960A VAL* 3.0 38.9 - - + +
961A ASN 5.1 0.2 + - - -
965A ILE* 4.0 7.2 - - - +
1050A THR* 2.9 29.3 + - + +
1053A ALA* 1.3 74.2 - - - +
1055A PHE* 1.3 67.5 + - - +
1056A GLN 3.0 0.9 - - - -
1057A ARG* 3.1 39.3 + - + +
1058A SER* 3.1 14.2 + - - -
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Residues in contact with PHE1055 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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872A ASP 5.9 0.2 - - - -
874A LEU* 3.5 30.5 - - + -
959A PRO* 3.9 20.0 - - + -
960A VAL* 3.4 6.7 - - + +
999A LEU* 3.5 45.3 - - + -
1000A PHE 4.7 3.1 - - - -
1001A VAL* 3.8 30.3 - - + -
1017A THR* 4.3 11.9 - - + -
1020A PHE* 3.8 28.9 - + + -
1051A ILE 3.0 19.5 + - - +
1052A GLU 3.9 0.4 - - - +
1054A GLN* 1.3 75.8 - - - +
1056A GLN* 1.3 66.4 + - - +
1058A SER* 3.4 9.3 + - - -
1059A LEU* 4.0 12.2 - - + +
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Residues in contact with GLN1056 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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998A LYS 5.0 4.7 + - - +
1000A PHE* 3.9 26.9 + - - +
1003A ARG* 3.3 27.7 + - - +
1052A GLU* 3.0 19.5 + - + +
1053A ALA* 3.1 13.5 - - - +
1054A GLN 3.0 1.0 - - - -
1055A PHE* 1.3 80.5 + - - +
1057A ARG* 1.3 60.6 + - + +
1058A SER 2.7 7.6 + - - -
1059A LEU* 3.1 32.1 + - - +
82F THR* 5.6 1.0 + - - -
83F PRO* 5.7 1.2 - - - +
84F TYR* 3.1 48.3 - - + +
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Residues in contact with ARG1057 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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878A GLN* 4.4 10.2 - - - +
1050A THR* 5.8 1.0 - - - +
1053A ALA* 3.0 34.3 + - - +
1054A GLN* 3.1 39.6 + - + +
1056A GLN* 1.3 76.4 - - + +
1058A SER* 1.3 57.0 + - - +
1059A LEU 3.4 3.0 + - - +
1061A HIS* 4.5 13.4 + - - -
84F TYR* 5.7 7.0 - - + -
154F ASP* 3.0 37.4 + - - +
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Residues in contact with SER1058 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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636A ARG* 5.8 1.6 - - - -
874A LEU* 3.3 25.7 - - - +
875A ASP* 3.2 20.5 + - - -
878A GLN* 3.5 35.0 - - - -
959A PRO* 4.3 1.5 - - - +
960A VAL* 4.2 7.4 - - - +
1054A GLN 3.1 14.9 + - - -
1055A PHE* 3.4 11.8 + - - -
1056A GLN 2.7 5.4 + - - -
1057A ARG* 1.3 74.3 - - - +
1059A LEU* 1.3 59.5 + - - -
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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
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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