Contacts of the helix formed by residues 1029 - 1045 (chain D) in PDB entry 3GKL
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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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525B LYS* 4.8 2.7 - - - +
1028D THR* 1.3 90.0 + - - +
1030D GLU* 1.3 64.6 + - - +
1031D GLU* 3.4 20.0 + - - -
1032D GLU* 3.2 29.4 + - - +
1033D LEU* 3.2 7.8 + - - +
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Residues in contact with GLU1030 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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520B ARG* 2.8 42.0 + - - -
525B LYS* 3.7 28.6 + - + +
526B ALA 5.3 0.2 + - - -
528B LYS* 4.7 5.4 + - - -
540B SER* 4.5 4.0 + - - -
1029D SER* 1.3 76.3 - - - +
1031D GLU* 1.3 59.5 + - - +
1033D LEU* 4.0 12.1 - - - +
1034D ASP* 3.2 22.9 + - - +
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Residues in contact with GLU1031 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1029D SER* 3.4 20.1 + - - +
1030D GLU* 1.3 77.6 + - - +
1032D GLU* 1.3 69.8 + - + +
1034D ASP* 2.8 10.8 + - - +
1035D LYS* 2.7 46.8 + - + +
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Residues in contact with GLU1032 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1028D THR* 3.8 11.0 - - - +
1029D SER* 3.2 37.4 + - - +
1031D GLU* 1.3 74.9 - - + +
1033D LEU* 1.3 69.1 + - - +
1035D LYS* 2.7 26.0 + - + +
1036D LEU* 2.7 22.6 + - + +
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Residues in contact with LEU1033 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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520B ARG* 3.6 28.3 - - + +
525B LYS* 6.1 1.6 - - + +
528B LYS* 4.5 6.7 - - - +
1022D ILE* 3.6 34.8 - - + +
1025D ALA* 6.1 3.8 - - - -
1028D THR* 3.4 22.7 + - + +
1029D SER 3.2 8.7 + - - +
1030D GLU* 4.0 11.9 - - - +
1031D GLU 3.4 0.2 - - - -
1032D GLU* 1.3 76.9 - - - +
1034D ASP* 1.3 58.0 + - - +
1036D LEU* 3.2 6.9 + - + -
1037D ILE* 2.7 68.2 + - + +
1054D TYR* 3.9 11.4 - - - +
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Residues in contact with ASP1034 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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528B LYS* 4.4 6.0 + - - +
537B LYS* 4.1 31.9 - - + +
539B THR* 3.9 24.5 + - - +
1030D GLU 3.2 14.6 + - - +
1031D GLU* 2.8 16.7 + - - +
1033D LEU* 1.3 83.4 - - - +
1035D LYS* 1.3 57.9 + - - -
1037D ILE* 3.6 8.3 + - - +
1038D THR* 3.3 23.9 + - - -
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Residues in contact with LYS1035 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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537B LYS* 5.8 6.1 - - - +
1031D GLU* 2.7 25.1 + - + +
1032D GLU* 2.7 25.9 + - + +
1034D ASP* 1.3 70.3 - - - +
1036D LEU* 1.3 61.1 + - + +
1037D ILE 3.1 1.1 - - - -
1038D THR* 3.0 7.0 + - - +
1039D HIS* 2.8 29.5 + - - +
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Residues in contact with LEU1036 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1018D LEU* 4.0 21.6 - - + +
1021D THR* 3.9 27.6 - - + -
1022D ILE* 3.9 20.2 - - + +
1028D THR* 5.5 4.5 - - - +
1032D GLU* 2.7 30.1 + - + +
1033D LEU* 3.7 7.4 - - - +
1035D LYS* 1.3 74.6 - - + +
1037D ILE* 1.3 61.2 + - - +
1039D HIS* 3.2 11.6 + - + +
1040D PHE* 2.9 23.6 + - - +
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Residues in contact with ILE1037 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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528B LYS* 4.1 15.7 - - + +
1022D ILE* 4.5 7.2 - - + -
1033D LEU* 2.7 59.4 + - + +
1034D ASP* 3.9 7.0 - - - +
1036D LEU* 1.3 73.9 - - - +
1038D THR* 1.3 64.1 + - - +
1040D PHE* 3.3 11.9 + - + +
1041D GLY* 3.4 9.5 + - - -
1050D SER* 3.9 23.8 - - - -
1053D ILE* 5.3 6.3 - - + -
1054D TYR* 3.7 23.6 - - + +
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Residues in contact with THR1038 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1034D ASP* 3.3 18.0 + - - -
1035D LYS* 3.0 10.8 + - - -
1037D ILE* 1.3 77.1 - - - +
1039D HIS* 1.3 70.1 + - - +
1040D PHE 2.8 2.1 + - - -
1041D GLY* 3.2 3.1 + - - -
1042D GLU* 3.1 39.2 + - + +
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Residues in contact with HIS1039 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1004D LYS* 3.7 28.7 + - + +
1010D TYR* 3.1 39.4 + + - -
1018D LEU* 4.3 13.8 - - + +
1035D LYS 2.8 12.7 + - - +
1036D LEU* 3.4 16.9 - - + +
1038D THR* 1.3 78.1 - - - +
1040D PHE* 1.3 57.3 + - - +
1042D GLU* 3.0 15.5 + - - +
1043D MET* 2.9 52.9 + - + +
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Residues in contact with PHE1040 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1015D PHE* 3.9 24.5 - + - -
1018D LEU* 4.7 6.7 - - + -
1019D VAL* 3.9 21.3 - - + -
1022D ILE* 3.9 20.4 - - + -
1036D LEU 2.9 15.8 + - - +
1037D ILE* 3.9 7.4 - - + +
1038D THR 2.8 0.8 + - - -
1039D HIS* 1.3 78.1 - - - +
1041D GLY* 1.3 63.2 + - - +
1043D MET* 4.1 4.7 - - - +
1044D THR* 3.0 54.0 + - + +
1049D GLY 4.1 17.0 - - - -
1050D SER* 5.4 1.1 - - - -
1052D LEU* 5.1 7.6 - - + -
1053D ILE* 3.5 29.8 - - + -
1067D ILE* 4.2 16.2 - - + -
1071D VAL* 4.6 5.4 - - + -
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Residues in contact with GLY1041 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1037D ILE 3.4 8.3 + - - -
1038D THR 3.2 5.0 + - - -
1040D PHE* 1.3 83.0 - - - +
1042D GLU* 1.3 56.7 + - - +
1044D THR* 3.5 7.4 + - - -
1045D GLU* 3.0 25.8 + - - -
1046D HIS 4.3 2.7 + - - +
1049D GLY* 5.2 11.9 - - - -
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Residues in contact with GLU1042 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1038D THR* 3.1 31.7 + - + +
1039D HIS* 3.0 26.6 + - - +
1041D GLY* 1.3 75.2 - - - +
1043D MET* 1.3 79.3 + - + +
1044D THR 3.5 0.2 + - - -
1045D GLU* 3.5 16.1 + - - +
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Residues in contact with MET1043 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1004D LYS 4.4 2.7 - - - +
1005D HIS 4.3 14.6 - - - +
1006D SER* 3.7 31.0 - - - +
1007D ILE* 2.5 40.3 - - + +
1010D TYR* 4.2 13.0 - - + -
1015D PHE* 4.1 18.6 - - + -
1018D LEU* 5.3 0.4 - - + -
1039D HIS* 2.9 49.9 + - + +
1040D PHE* 4.1 2.7 - - - +
1042D GLU* 1.3 97.0 - - + +
1044D THR* 1.3 55.9 + - - +
1045D GLU* 3.6 2.4 - - - +
1075D ARG* 3.4 2.8 + - - -
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Residues in contact with THR1044 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1007D ILE* 3.9 5.2 - - - -
1015D PHE* 4.0 11.0 - - + -
1040D PHE* 3.0 50.8 + - + +
1041D GLY* 3.5 7.4 + - - -
1043D MET* 1.3 77.6 - - - +
1045D GLU* 1.3 63.0 + - - +
1046D HIS* 2.7 29.9 + - - +
1049D GLY* 5.6 1.2 - - - -
1052D LEU* 6.0 0.2 - - + -
1071D VAL* 4.0 23.1 - - + +
1074D TRP* 3.8 7.4 - - - -
1075D ARG* 2.8 17.8 + - - -
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Residues in contact with GLU1045 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1041D GLY 3.0 16.4 + - - -
1042D GLU* 3.6 9.8 - - - +
1043D MET 3.2 6.9 - - - +
1044D THR* 1.3 77.8 - - - +
1046D HIS* 1.3 62.0 + - - +
1047D PRO 3.6 1.0 - - - -
1074D TRP* 3.4 15.4 - - + -
1075D ARG* 3.4 19.3 + - - +
1080D LYS* 3.7 27.4 + - + +
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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