Contacts of the helix formed by residues 1028 - 1050 (chain H) in PDB entry 6X34
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 ASP1028 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1020H ARG* 4.6 16.6 - - + +
1025H ARG 5.2 0.2 + - - -
1026H LEU* 4.6 4.8 - - - -
1027H LEU* 1.3 76.6 - - - +
1029H GLU* 1.3 59.8 + - - +
1030H ALA* 4.7 0.7 - - + +
1031H THR* 3.7 24.9 - - - +
1032H LYS* 3.2 25.1 + - - +
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Residues in contact with GLU1029 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1026H LEU 4.8 2.6 + - - +
1027H LEU 4.0 2.8 + - - -
1028H ASP* 1.3 70.8 - - - +
1030H ALA* 1.3 61.4 + - - +
1032H LYS* 3.4 5.7 + - - +
1033H ARG* 2.9 30.0 + - - +
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Residues in contact with ALA1030 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1028H ASP* 3.5 1.7 - - + +
1029H GLU* 1.3 79.2 - - - +
1031H THR* 1.3 57.5 + - - +
1033H ARG* 3.3 6.9 + - - +
1034H SER* 2.9 29.1 + - - -
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Residues in contact with THR1031 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
993H HIS* 4.9 10.0 + - - -
1028H ASP* 3.7 23.2 + - - +
1029H GLU 3.3 0.6 - - - -
1030H ALA* 1.3 78.0 - - - +
1032H LYS* 1.3 58.1 + - - +
1034H SER* 3.3 6.0 + - - -
1035H ASN* 2.9 30.9 + - - +
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Residues in contact with LYS1032 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
993H HIS* 6.1 0.2 - - - -
1026H LEU* 5.9 5.2 - - - -
1028H ASP 3.2 18.1 + - - +
1029H GLU* 3.7 6.1 - - - +
1030H ALA 3.3 0.2 - - - -
1031H THR* 1.3 79.4 - - - +
1033H ARG* 1.3 56.7 + - - +
1035H ASN* 3.3 5.4 + - - +
1036H ARG* 2.9 31.1 + - - +
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Residues in contact with ARG1033 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1029H GLU 2.9 17.9 + - - +
1030H ALA* 3.7 6.7 - - - +
1032H LYS* 1.3 75.2 - - - +
1034H SER* 1.3 57.4 + - - +
1036H ARG* 3.3 5.6 + - - +
1037H ASP* 2.9 32.8 + - - +
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Residues in contact with SER1034 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1030H ALA 2.9 17.8 + - - -
1031H THR* 3.7 7.4 - - - -
1032H LYS 3.3 0.2 - - - -
1033H ARG* 1.3 77.5 - - - +
1035H ASN* 1.3 56.8 + - - +
1037H ASP* 4.5 3.4 - - - +
1038H SER* 2.9 38.7 + - - +
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Residues in contact with ASN1035 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
985H VAL 4.6 1.4 - - - +
989H ALA* 3.5 19.0 - - + +
993H HIS* 3.5 31.6 - - + +
1031H THR 2.9 18.1 + - - +
1032H LYS* 3.3 5.4 + - - +
1034H SER* 1.3 76.7 - - - +
1036H ARG* 1.3 58.2 + - - +
1039H LEU* 3.2 29.0 - - - +
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Residues in contact with ARG1036 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
982H THR* 5.6 2.2 - - - +
985H VAL* 4.8 2.5 - - - +
986H ASP* 5.0 21.1 - - + +
1032H LYS 2.9 17.7 + - - +
1033H ARG* 3.8 6.3 - - - +
1035H ASN* 1.3 79.0 - - - +
1037H ASP* 1.3 57.7 + - - +
1040H CYS* 3.3 23.2 - - - +
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Residues in contact with ASP1037 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1033H ARG 2.9 17.0 + - - +
1034H SER* 4.1 2.7 - - - +
1036H ARG* 1.3 79.4 - - - +
1038H SER* 1.3 61.6 + - - +
1039H LEU 3.4 0.2 - - - -
1040H CYS* 3.3 4.0 + - - +
1041H GLN* 2.9 29.3 + - - +
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Residues in contact with SER1038 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1034H SER* 2.9 20.6 + - - -
1037H ASP* 1.3 74.9 - - - +
1039H LEU* 1.3 58.2 + - - +
1041H GLN* 3.3 7.5 + - - +
1042H ALA* 2.9 29.8 + - - +
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Residues in contact with LEU1039 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
928H THR* 5.8 0.3 - - - +
985H VAL* 4.7 8.5 - - + +
988H LEU* 6.3 0.9 - - + -
989H ALA* 4.7 11.0 - - + +
1034H SER 4.1 0.4 + - - -
1035H ASN* 3.2 25.1 + - - +
1037H ASP 3.4 0.4 - - - -
1038H SER* 1.3 78.4 - - - +
1040H CYS* 1.3 56.3 + - - +
1042H ALA* 3.3 6.3 + - - +
1043H VAL* 2.9 29.9 + - - +
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Residues in contact with CYS1040 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
981H GLN 5.4 0.7 - - - +
982H THR* 5.3 7.2 - - - -
985H VAL* 3.7 24.1 - - + +
1036H ARG 3.3 22.4 + - - +
1037H ASP* 3.3 4.3 + - - +
1038H SER 3.3 0.6 - - - -
1039H LEU* 1.3 79.2 - - - +
1041H GLN* 1.3 57.1 + - - +
1043H VAL* 3.3 4.3 + - - +
1044H ARG* 2.9 30.2 + - - +
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Residues in contact with GLN1041 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1037H ASP 2.9 17.6 + - - +
1038H SER* 3.7 7.0 - - - +
1040H CYS* 1.3 77.9 - - - +
1042H ALA* 1.3 57.6 + - - +
1044H ARG* 3.3 6.3 + - - +
1045H THR* 2.9 29.5 + - - -
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Residues in contact with ALA1042 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
874H LEU* 5.4 4.3 - - + +
877H ASN* 5.7 4.7 - - + +
878H ILE* 6.0 9.2 - - + +
928H THR* 4.9 13.8 - - + +
1038H SER 2.9 18.0 + - - +
1039H LEU* 3.7 6.7 - - - +
1041H GLN* 1.3 75.7 - - - +
1043H VAL* 1.3 58.1 + - - +
1045H THR* 3.3 6.2 + - - -
1046H LEU* 2.9 30.3 + - - +
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Residues in contact with VAL1043 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
928H THR* 4.6 12.5 - - + +
932H LEU* 6.0 5.6 - - + -
985H VAL* 5.4 5.6 - - + -
1039H LEU 2.9 17.6 + - - +
1040H CYS* 3.7 7.2 - - - +
1042H ALA* 1.3 76.1 - - - +
1044H ARG* 1.3 58.7 + - - +
1046H LEU* 3.3 5.8 + - - +
1047H LEU* 2.9 30.5 + - - +
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Residues in contact with ARG1044 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1040H CYS 2.9 17.4 + - - +
1041H GLN* 3.7 6.3 - - - +
1043H VAL* 1.3 77.0 - - - +
1045H THR* 1.3 55.9 + - - +
1047H LEU* 3.3 5.6 + - - +
1048H GLY* 2.9 27.9 + - - -
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Residues in contact with THR1045 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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873H LYS 6.0 0.2 - - - -
877H ASN* 4.2 15.7 - - - -
969H PRO* 4.9 7.4 - - - -
971H ASP* 3.4 29.0 - - - +
1041H GLN 2.9 17.8 + - - -
1042H ALA* 3.8 5.8 - - - -
1044H ARG* 1.3 76.3 - - - +
1046H LEU* 1.3 61.2 + - - +
1048H GLY* 5.3 0.2 - - - -
1049H TYR* 3.2 26.7 + - - +
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Residues in contact with LEU1046 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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870H ILE* 4.3 17.5 - - + +
873H LYS 5.5 0.2 - - - -
874H LEU* 3.7 32.3 - - + +
928H THR* 4.8 7.4 - - + -
1042H ALA 2.9 18.1 + - - +
1043H VAL* 3.8 6.1 - - - +
1044H ARG 3.3 0.2 - - - -
1045H THR* 1.3 76.6 - - - +
1047H LEU* 1.3 63.7 + - - +
1049H TYR* 4.2 3.6 - - - +
1050H GLY 3.7 14.6 + - - -
1051H TYR 4.2 4.7 - - - +
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Residues in contact with LEU1047 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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946H ALA* 5.7 0.3 - - - +
1043H VAL 2.9 17.0 + - - +
1044H ARG* 3.9 5.6 - - - +
1046H LEU* 1.3 77.6 - - - +
1048H GLY* 1.3 62.1 + - - +
1049H TYR 3.5 0.7 + - - -
1050H GLY 4.0 2.6 - - - +
1051H TYR 3.5 12.1 - - - +
1052H ASN* 3.3 25.0 + - + +
1053H ILE* 4.3 24.0 - - + +
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Residues in contact with GLY1048 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
946H ALA* 3.3 25.9 - - - +
971H ASP 3.9 7.8 - - - +
1044H ARG 2.9 16.3 + - - -
1045H THR* 4.2 0.7 - - - -
1047H LEU* 1.3 75.3 - - - +
1049H TYR* 1.3 62.0 + - - +
1052H ASN* 5.8 0.7 - - - -
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Residues in contact with TYR1049 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
873H LYS* 3.7 27.8 - - + -
946H ALA 3.4 14.2 - - - +
947H GLU* 3.6 15.5 - - - +
971H ASP* 3.4 21.7 + - + +
1045H THR 3.2 19.6 + - - +
1046H LEU 4.2 2.7 - - - +
1047H LEU 3.3 0.6 - - - -
1048H GLY* 1.3 80.3 - - - +
1050H GLY* 1.3 61.4 + - - +
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Residues in contact with GLY1050 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
869H ARG* 5.4 4.0 - - - -
870H ILE* 4.8 11.7 - - - +
873H LYS* 5.2 0.4 - - - +
941H MET* 4.6 7.9 - - - +
942H ALA 5.0 1.0 + - - -
946H ALA* 4.1 13.2 - - - +
947H GLU* 5.9 1.3 - - - -
1046H LEU 3.7 7.2 + - - -
1047H LEU 4.0 2.9 - - - +
1049H TYR* 1.3 83.0 - - - +
1051H TYR* 1.3 61.7 + - - +
1052H ASN* 3.6 3.1 + - - +
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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) + - + + + + + -
------------------------------------------------------------
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