Contacts of the helix formed by residues 1029 - 1045 (chain A) in PDB entry 3GJN
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 SER1029 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1027A ALA 4.4 0.2 + - - -
1028A THR* 1.3 89.3 + - - +
1030A GLU* 1.3 60.0 + - - +
1031A GLU* 3.7 11.8 + - - +
1032A GLU* 3.2 38.2 + - - +
1033A LEU* 3.1 13.2 + - - +
525B LYS* 4.4 2.2 + - - +
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Residues in contact with GLU1030 (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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1029A SER* 1.3 72.0 - - - +
1031A GLU* 1.3 68.3 + - + +
1033A LEU* 3.7 15.0 - - - +
1034A ASP* 3.0 32.2 + - - +
520B ARG* 2.8 32.9 + - - -
525B LYS* 3.7 32.3 + - + +
526B ALA 5.1 1.0 + - - -
528B LYS* 5.2 3.0 + - - -
540B SER* 5.6 1.6 + - - -
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Residues in contact with GLU1031 (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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1029A SER* 4.4 9.4 + - - +
1030A GLU* 1.3 79.0 - - + +
1032A GLU* 1.3 65.5 + - - +
1034A ASP* 3.6 12.7 + - - +
1035A LYS* 3.4 20.5 + - - +
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Residues in contact with GLU1032 (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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1027A ALA 4.1 4.7 - - - +
1028A THR* 3.8 14.4 - - + +
1029A SER* 3.2 39.0 + - - +
1031A GLU* 1.3 75.5 - - - +
1033A LEU* 1.3 61.9 + - - +
1035A LYS* 3.1 29.8 + - + +
1036A LEU* 3.1 20.7 + - + +
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Residues in contact with LEU1033 (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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1022A ILE* 4.0 33.0 - - + +
1025A ALA* 6.4 2.7 - - + -
1028A THR* 3.3 26.9 - - + +
1029A SER 3.1 11.0 + - - +
1030A GLU* 3.2 23.5 + - - +
1032A GLU* 1.3 73.1 - - - +
1034A ASP* 1.3 55.9 + - - +
1036A LEU* 3.2 3.7 + - + +
1037A ILE* 2.7 65.3 + - + +
1054A TYR* 3.5 19.5 - - - +
520B ARG* 4.1 15.7 - - + +
525B LYS* 6.0 2.0 - - + +
528B LYS* 4.2 6.3 - - - +
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Residues in contact with ASP1034 (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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1030A GLU* 3.0 21.5 + - - +
1031A GLU* 3.6 14.2 - - - +
1032A GLU 3.3 0.2 - - - -
1033A LEU* 1.3 74.8 - - - +
1035A LYS* 1.3 59.5 + - + +
1037A ILE* 3.5 7.6 + - - +
1038A THR* 2.8 32.1 + - - +
528B LYS* 4.0 6.6 + - - -
537B LYS* 4.4 34.0 - - + +
539B THR* 4.0 24.4 + - - +
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Residues in contact with LYS1035 (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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1031A GLU 3.4 11.6 + - - +
1032A GLU* 3.2 26.2 - - + +
1034A ASP* 1.3 79.2 - - + +
1036A LEU* 1.3 75.4 + - + +
1038A THR* 3.9 5.6 - - - -
1039A HIS* 3.0 25.3 + - - +
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Residues in contact with LEU1036 (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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1018A LEU* 3.7 22.4 - - + +
1021A THR* 4.3 14.1 - - + -
1022A ILE* 3.7 23.1 - - + +
1028A THR* 3.9 28.3 - - + -
1032A GLU* 3.1 21.0 + - + +
1033A LEU* 4.0 4.7 - - + +
1035A LYS* 1.3 83.3 - - + +
1037A ILE* 1.3 59.1 + - - +
1039A HIS* 3.4 10.2 + - + +
1040A PHE* 2.8 31.0 + - - +
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Residues in contact with ILE1037 (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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1022A ILE* 4.3 9.4 - - + -
1033A LEU* 2.7 56.0 + - + +
1034A ASP* 3.9 4.9 - - - +
1036A LEU* 1.3 74.8 - - - +
1038A THR* 1.4 62.1 + - - +
1040A PHE* 3.4 5.9 + - - +
1041A GLU* 3.2 25.9 + - + +
1050A SER* 3.5 32.1 - - - +
1053A ILE* 4.9 4.9 - - + -
1054A TYR* 3.6 20.4 - - + +
528B LYS* 3.6 25.6 - - + +
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Residues in contact with THR1038 (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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1034A ASP* 2.8 23.2 + - - +
1035A LYS* 3.9 6.1 - - - -
1036A LEU 3.3 0.2 - - - -
1037A ILE* 1.4 76.6 - - - +
1039A HIS* 1.3 66.2 + - - +
1041A GLU* 3.2 14.3 + - + +
1042A GLU* 3.1 40.4 + - + +
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Residues in contact with HIS1039 (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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1004A LYS* 3.4 31.1 + - + +
1010A TYR* 2.7 36.5 + + - -
1018A LEU* 4.0 16.5 - - + +
1035A LYS 3.0 18.6 + - - +
1036A LEU* 3.4 10.5 - - + +
1038A THR* 1.3 74.1 - - - +
1040A PHE* 1.4 51.9 + - - +
1042A GLU* 2.8 18.3 + - - +
1043A MET* 2.7 74.3 + - + +
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Residues in contact with PHE1040 (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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1015A PHE* 4.0 16.6 - + - -
1018A LEU* 4.7 8.0 - - + +
1019A VAL* 4.0 25.1 - - + -
1022A ILE* 3.8 15.5 - - + -
1036A LEU 2.8 20.9 + - - +
1037A ILE* 3.6 7.2 - - - +
1038A THR 3.3 0.2 - - - -
1039A HIS* 1.4 72.1 + - - +
1041A GLU* 1.3 63.2 + - + +
1043A MET* 3.3 5.2 + - - +
1044A THR* 2.7 65.1 + - + +
1049A GLY 3.8 17.5 - - - -
1050A SER* 5.0 0.4 - - - -
1052A LEU* 4.1 11.4 - - + -
1053A ILE* 3.6 29.8 - - + -
1067A ILE* 4.0 21.1 - - + -
1071A VAL* 4.3 1.6 - - + -
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Residues in contact with GLU1041 (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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1037A ILE* 3.2 17.0 + - - +
1038A THR* 3.4 16.5 - - + +
1040A PHE* 1.3 76.2 - - + +
1042A GLU* 1.3 61.3 + - + +
1044A THR* 3.4 6.9 + - - -
1045A GLU* 2.8 27.7 + - - -
1046A HIS 4.3 2.4 + - - +
1049A GLY* 3.1 39.9 - - - -
1050A SER* 3.2 13.4 + - - +
531B THR* 3.4 15.6 - - - +
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Residues in contact with GLU1042 (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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1038A THR* 3.1 31.4 + - + +
1039A HIS* 2.8 28.4 + - - +
1041A GLU* 1.3 76.2 - - + +
1043A MET* 1.3 73.0 + - + +
1045A GLU* 3.2 22.3 - - - +
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Residues in contact with MET1043 (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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1004A LYS 3.6 6.1 - - - +
1005A HIS 3.5 23.8 - - - +
1006A SER* 3.4 28.3 - - - +
1007A ILE* 3.1 44.1 - - + +
1010A TYR* 3.8 13.7 - - + -
1015A PHE* 4.1 11.4 - - + -
1018A LEU* 5.4 0.2 - - + -
1039A HIS* 2.7 57.0 + - + +
1040A PHE* 3.8 3.8 - - - +
1042A GLU* 1.3 87.8 - - + +
1044A THR* 1.3 59.5 + - - +
1045A GLU* 4.1 2.9 - - - +
1075A ARG* 3.6 1.9 + - - -
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Residues in contact with THR1044 (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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1007A ILE* 4.9 0.4 - - - -
1015A PHE* 3.7 21.5 - - + -
1040A PHE* 2.7 53.0 + - + +
1041A GLU* 3.4 8.3 + - - +
1043A MET* 1.3 77.5 - - - +
1045A GLU* 1.3 60.3 + - - +
1046A HIS* 2.8 31.1 + - - +
1049A GLY* 5.3 0.3 - - - -
1071A VAL* 4.1 16.2 - - + -
1074A TRP* 3.2 16.9 - - - -
1075A ARG* 3.3 15.7 + - - +
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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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1006A SER* 5.9 2.1 - - - -
1007A ILE* 5.0 3.8 - - - +
1041A GLU 2.8 17.2 + - - -
1042A GLU* 3.2 19.6 - - - +
1043A MET 4.1 4.0 - - - +
1044A THR* 1.3 75.9 - - - +
1046A HIS* 1.3 59.0 + - - +
1047A PRO* 3.8 1.6 - - - +
1074A TRP* 2.8 23.6 - - + -
1075A ARG* 4.0 13.1 + - - +
1080A LYS* 3.5 34.0 + - - +
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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