Contacts of the helix formed by residues 1041 - 1058 (chain A) in PDB entry 3H0G
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 ASN1041 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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974A PHE* 4.8 4.7 - - - +
976A LEU* 2.7 37.6 - - + +
982A THR* 5.5 0.4 - - - -
983A ASP* 4.5 25.3 + - + +
984A LEU* 3.6 6.5 - - - -
1040A LEU* 1.3 76.6 - - - +
1042A LYS* 1.3 69.6 + - - +
1043A VAL* 3.0 16.2 - - - +
1044A ALA* 2.6 41.2 + - - +
1045A PHE 3.0 7.9 + - - -
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Residues in contact with LYS1042 (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 ASP* 2.8 35.2 + - + +
984A LEU* 3.0 32.3 + - + +
985A LEU* 5.2 1.8 - - - +
988A ASP* 4.2 16.4 + - - +
1041A ASN* 1.3 69.6 - - - +
1043A VAL* 1.3 54.3 + - - +
1045A PHE* 4.1 1.3 - - - +
1046A GLU* 2.7 46.5 + - + +
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Residues in contact with VAL1043 (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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974A PHE* 3.9 32.1 - - + -
1041A ASN* 2.6 27.8 + - - +
1042A LYS* 1.3 74.8 - - - +
1044A ALA* 1.3 76.0 + - - +
1046A GLU* 3.7 5.0 - - - +
1047A TRP* 3.0 24.2 + - + +
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Residues in contact with ALA1044 (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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970A ALA* 5.7 1.8 - - + +
971A LEU* 6.1 1.3 - - + -
974A PHE* 3.6 30.7 - - + -
1040A LEU* 4.5 13.9 - - + -
1041A ASN* 2.6 31.0 + - - +
1043A VAL* 1.3 74.0 - - - +
1045A PHE* 1.3 51.4 + - - +
1047A TRP* 2.7 8.8 + - - +
1048A ILE* 2.7 40.2 + - + +
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Residues in contact with PHE1045 (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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984A LEU* 4.5 18.8 - - + -
988A ASP* 4.6 2.9 - - + -
989A ILE* 3.6 45.3 - - + -
992A GLY* 4.1 11.4 - - - -
1029A PHE* 4.3 22.2 - + + -
1034A VAL* 4.7 8.3 - - + -
1040A LEU* 4.0 19.8 - - + +
1041A ASN 3.0 13.1 + - - +
1042A LYS 4.1 2.7 - - - +
1044A ALA* 1.3 78.6 - - - +
1046A GLU* 1.3 73.5 + - + +
1047A TRP 3.0 1.0 + - - -
1048A ILE* 3.1 10.2 + - + +
1049A MET* 3.0 60.1 + - + +
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Residues in contact with GLU1046 (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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996A LEU* 5.8 3.3 - - - +
1042A LYS* 2.7 38.8 + - + +
1043A VAL* 3.7 6.5 - - - +
1045A PHE* 1.3 81.7 - - + +
1047A TRP* 1.3 58.0 + - - +
1049A MET* 4.3 4.7 + - - +
1050A GLY* 3.7 13.3 + - - -
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Residues in contact with TRP1047 (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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642A GLU* 6.1 0.7 - - - -
966A ILE* 3.9 24.0 - - + -
969A ASN* 4.8 7.0 - - - -
970A ALA* 4.5 7.9 - - + -
973A ILE* 5.3 13.8 - - + +
974A PHE* 4.3 25.4 - + + -
1043A VAL* 3.0 11.6 + - + +
1044A ALA 2.7 8.1 + - - +
1046A GLU* 1.3 78.9 - - - +
1048A ILE* 1.3 80.2 + - + +
1050A GLY* 3.0 10.1 + - - -
1051A GLU* 3.2 53.7 + - + +
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Residues in contact with ILE1048 (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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966A ILE* 3.6 29.5 - - + +
967A ILE* 4.1 16.6 - - + -
970A ALA* 4.3 16.8 - - + -
1029A PHE* 3.8 19.3 - - + -
1040A LEU* 3.3 39.3 - - + -
1044A ALA* 2.7 18.8 + - + +
1045A PHE* 3.5 8.3 - - + +
1047A TRP* 1.3 86.4 - - + +
1049A MET* 1.3 58.4 + - + +
1050A GLY 2.6 15.2 + - - -
1051A GLU* 3.0 14.4 + - - +
1052A VAL* 3.2 13.5 + - + +
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Residues in contact with MET1049 (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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992A GLY 3.2 28.7 - - - +
993A LEU* 3.8 25.1 - - + -
996A LEU* 3.3 43.8 - - + +
1025A LEU* 6.2 2.0 - - + -
1029A PHE* 5.1 11.4 - - - -
1045A PHE* 3.0 53.7 + - + +
1046A GLU* 4.4 4.9 - - - +
1048A ILE* 1.3 74.3 - - + +
1050A GLY* 1.3 62.0 + - - +
1052A VAL* 4.2 12.3 - - + +
1053A GLU* 3.6 19.3 + - - +
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Residues in contact with GLY1050 (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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996A LEU* 5.6 0.4 - - - -
1046A GLU 3.7 7.6 + - - -
1047A TRP* 3.0 11.8 + - - -
1048A ILE 2.6 8.1 + - - -
1049A MET* 1.3 75.9 - - - +
1051A GLU* 1.3 64.8 + - - -
1052A VAL 3.3 0.5 + - - -
1053A GLU* 3.4 5.9 + - - +
1054A ALA* 3.2 21.5 + - - +
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Residues in contact with GLU1051 (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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966A ILE* 4.6 13.2 - - + -
1047A TRP* 3.2 57.3 + - + +
1048A ILE 3.0 5.2 + - - +
1050A GLY* 1.3 74.9 - - - +
1052A VAL* 1.3 55.2 + - - +
1054A ALA* 3.1 7.9 + - - +
1055A ARG* 2.6 71.9 + - + +
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Residues in contact with VAL1052 (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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961A VAL* 4.1 22.6 - - + +
963A VAL* 5.0 0.9 - - + -
966A ILE* 3.1 36.5 - - + +
996A LEU 5.9 1.3 - - - +
1000A LEU* 5.5 3.6 - - + -
1021A PHE* 4.4 19.7 - - + -
1025A LEU* 4.4 17.7 - - + -
1029A PHE* 5.2 2.9 - - + -
1048A ILE* 3.2 17.5 - - + +
1049A MET* 4.2 10.8 - - + +
1051A GLU* 1.3 78.1 - - - +
1053A GLU* 1.3 67.8 + - - +
1055A ARG* 3.6 0.5 - - - +
1056A PHE* 2.8 21.9 + - + +
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Residues in contact with GLU1053 (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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996A LEU* 4.4 8.4 + - + +
999A LYS* 3.1 68.3 + - + +
1000A LEU* 4.1 16.4 - - + +
1049A MET 3.6 11.6 + - - +
1050A GLY* 3.4 11.4 + - - +
1052A VAL* 1.3 79.1 - - - +
1054A ALA* 1.3 72.4 + - - +
1056A PHE* 3.3 3.5 - - - +
1057A GLN* 3.2 32.8 + - - +
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Residues in contact with ALA1054 (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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1050A GLY 3.2 9.3 + - - +
1051A GLU* 3.1 12.7 + - - +
1052A VAL 2.9 4.0 + - - -
1053A GLU* 1.3 82.7 - - - +
1055A ARG* 1.3 64.9 + - + +
1056A PHE 3.1 1.8 - - - -
1057A GLN* 3.5 4.1 + - - +
1058A GLN* 3.1 42.1 + - - +
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Residues in contact with ARG1055 (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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641A LYS* 4.7 5.5 + - - +
642A GLU* 3.6 56.8 + - - +
643A LYS* 5.1 7.1 - - - +
961A VAL* 3.2 30.1 - - + +
966A ILE* 5.5 8.1 - - + +
1051A GLU* 2.6 51.3 + - + +
1052A VAL 3.8 0.2 - - - +
1054A ALA* 1.3 74.3 - - + +
1056A PHE* 1.3 62.4 + - - +
1058A GLN* 3.7 21.7 + - - +
1059A ALA* 3.4 15.8 + - - +
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Residues in contact with PHE1056 (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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879A LEU* 4.5 11.3 - - + +
960A PRO* 4.4 15.9 - - + -
961A VAL* 3.2 8.9 - - + +
1000A LEU* 3.3 44.4 - - + -
1002A ILE* 3.6 21.3 - - + -
1018A THR* 3.8 21.8 - - + -
1021A PHE* 3.6 44.2 - + + -
1052A VAL 2.8 12.2 + - - +
1053A GLU* 3.3 12.8 - - - +
1055A ARG* 1.3 73.9 - - - +
1057A GLN* 1.3 62.7 + - + +
1058A GLN 3.0 3.6 - - - -
1059A ALA* 2.6 32.5 + - - +
1060A VAL* 3.3 6.5 + - + -
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Residues in contact with GLN1057 (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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999A LYS 3.2 23.3 + - - +
1000A LEU* 3.7 2.2 - - - -
1001A THR* 2.9 32.3 + - - +
1004A ARG* 3.8 18.1 + - - +
1053A GLU* 3.2 25.9 + - - +
1054A ALA* 3.5 3.3 + - - +
1056A PHE* 1.3 82.5 - - + +
1058A GLN* 1.3 60.1 + - + +
1059A ALA 3.0 1.2 + - - -
1060A VAL* 3.5 30.4 + - - +
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Residues in contact with GLN1058 (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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883A LEU* 3.1 20.5 - - + +
1054A ALA* 3.1 34.8 + - - +
1055A ARG* 3.8 25.8 + - - +
1056A PHE 3.0 0.8 + - - -
1057A GLN* 1.3 78.2 - - + +
1059A ALA* 1.3 57.7 + - - +
1060A VAL 3.6 2.8 - - - +
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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