Contacts of the helix formed by residues 1011 - 1023 (chain D) 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 THR1011 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1009D ASP 4.1 0.2 + - - -
1010D TYR* 1.3 73.7 - - - +
1012D GLU* 1.3 66.3 + - - +
1013D ALA* 3.5 8.0 + - - +
1014D GLU* 2.8 39.5 + - - +
1015D PHE* 2.9 18.9 + - - -
1083D PHE* 4.0 1.3 - - - -
1084D LYS* 3.7 23.1 - - + +
1085D GLN* 4.1 31.9 - - - +
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Residues in contact with GLU1012 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1011D THR* 1.3 72.3 - - - +
1013D ALA* 1.3 58.7 + - - +
1015D PHE* 3.2 0.9 + - - +
1016D LEU* 2.8 33.8 + - + +
1068D VAL* 4.1 16.8 - - + +
1069D ASN* 5.8 0.2 - - - -
1072D LYS* 2.7 49.3 + - - +
1083D PHE* 3.6 36.4 - - + +
1084D LYS 4.5 1.0 + - - -
1085D GLN* 6.1 0.2 - - - +
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Residues in contact with ALA1013 (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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1011D THR* 3.2 7.1 + - - +
1012D GLU* 1.3 78.4 - - - +
1014D GLU* 1.3 61.5 + - - +
1016D LEU* 3.4 11.8 - - + +
1017D GLN* 3.1 22.5 + - - +
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Residues in contact with GLU1014 (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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1009D ASP 3.6 2.8 - - - +
1010D TYR* 3.5 23.1 - - + -
1011D THR* 2.8 40.6 + - - +
1013D ALA* 1.3 75.3 - - - +
1015D PHE* 1.3 62.4 + - - +
1017D GLN* 3.1 10.8 + - - +
1018D LEU* 3.0 19.1 + - - +
1084D LYS* 3.5 17.3 + - - -
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Residues in contact with PHE1015 (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* 4.2 7.0 - - + -
1010D TYR* 3.7 23.2 - + + -
1011D THR 2.9 12.1 + - - +
1012D GLU 3.9 3.1 - - - +
1014D GLU* 1.3 69.7 - - - +
1016D LEU* 1.3 66.7 + - - +
1018D LEU* 3.1 29.5 + - + +
1019D VAL* 2.9 44.0 + - + +
1040D PHE* 3.6 31.0 - + - -
1043D MET* 4.1 20.2 - - + -
1044D THR* 3.7 15.5 - - + -
1068D VAL* 3.8 17.5 - - + -
1071D VAL* 4.3 12.1 - - + -
1083D PHE* 3.7 30.1 - + + -
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Residues in contact with LEU1016 (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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486B ASP* 4.7 5.8 - - - +
1012D GLU* 2.8 19.8 + - + +
1013D ALA* 3.4 15.5 - - - +
1015D PHE* 1.3 72.8 - - - +
1017D GLN* 1.3 62.8 + - - +
1019D VAL* 3.1 5.2 + - - +
1020D THR* 2.9 30.9 + - - +
1064D PRO* 4.0 4.0 - - + -
1065D SER* 3.7 37.7 - - - +
1068D VAL* 3.5 28.8 - - + +
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Residues in contact with GLN1017 (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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1013D ALA 3.1 13.3 + - - +
1014D GLU* 3.1 10.7 + - - +
1016D LEU* 1.3 75.2 - - - +
1018D LEU* 1.3 68.1 + - - +
1020D THR* 3.3 12.8 + - - +
1021D THR* 3.1 29.8 + - - +
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Residues in contact with LEU1018 (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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1010D TYR* 4.2 20.9 - - + +
1014D GLU 3.0 12.1 + - - +
1015D PHE* 3.1 42.3 + - + +
1017D GLN* 1.3 82.3 - - - +
1019D VAL* 1.4 61.7 + - - +
1021D THR* 3.2 4.9 + - - -
1022D ILE* 3.2 25.2 + - + +
1036D LEU* 3.9 39.5 - - + -
1039D HIS* 4.7 11.4 - - - +
1040D PHE* 4.9 12.3 - - + -
1043D MET* 5.4 0.2 - - + -
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Residues in contact with VAL1019 (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* 2.9 37.7 + - + +
1016D LEU 3.7 5.2 - - - +
1018D LEU* 1.4 70.1 - - + +
1020D THR* 1.3 64.0 + - - +
1022D ILE* 3.4 8.9 + - + +
1023D CYS* 3.0 33.8 + - - -
1040D PHE* 4.2 11.4 - - + -
1053D ILE* 5.2 2.7 - - + -
1064D PRO* 3.9 16.2 - - + +
1067D ILE* 3.8 38.1 - - + -
1068D VAL* 3.6 19.1 - - + +
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Residues in contact with THR1020 (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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486B ASP* 4.8 16.1 + - - +
1016D LEU* 2.9 21.6 + - - +
1017D GLN* 3.8 13.7 - - - +
1019D VAL* 1.3 77.1 - - - +
1021D THR* 1.3 64.5 + - - +
1023D CYS* 3.8 2.6 + - - +
1024D ASP* 3.5 17.9 + - + +
1064D PRO* 3.2 30.6 - - + +
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Residues in contact with THR1021 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1017D GLN* 3.1 22.4 + - - +
1018D LEU* 3.7 9.0 - - - -
1020D THR* 1.3 77.3 - - - +
1022D ILE* 1.3 68.3 + - - +
1024D ASP* 2.9 24.2 + - - +
1027D ALA* 3.9 15.3 - - + +
1028D THR* 3.6 26.4 - - + +
1036D LEU* 4.6 7.9 - - + -
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Residues in contact with ILE1022 (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* 3.2 20.2 + - + +
1019D VAL* 3.6 10.3 - - - +
1021D THR* 1.3 77.6 - - - +
1023D CYS* 1.3 59.0 + - - +
1024D ASP 3.1 9.2 + - - +
1025D ALA* 4.3 1.4 + - - -
1028D THR* 5.2 0.3 + - - -
1033D LEU* 3.8 25.2 - - + +
1036D LEU* 3.7 44.2 - - + +
1037D ILE* 4.5 5.2 - - + +
1040D PHE* 3.7 26.5 - - + -
1053D ILE* 3.8 30.1 - - + -
1054D TYR* 3.9 19.7 + - - +
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Residues in contact with CYS1023 (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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515C ARG* 2.4 33.1 + - - +
516C ASN* 3.5 32.8 + - - +
519C ASP* 3.1 4.0 - - - +
1019D VAL* 3.0 25.6 + - - +
1020D THR 4.0 4.5 - - - +
1021D THR 3.2 0.2 - - - -
1022D ILE* 1.3 74.8 - - - +
1024D ASP* 1.3 55.9 + - - +
1025D ALA 3.8 1.1 - - - -
1053D ILE* 3.9 12.8 - - - -
1054D TYR* 5.7 0.9 - - - -
1064D PRO* 4.4 18.4 - - + -
1067D ILE* 3.7 23.1 - - - -
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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
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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