Contacts of the helix formed by residues 1063 - 1072 (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 SER1063 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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482A ASN* 3.5 31.9 + - - +
483A LYS* 3.9 14.6 - - - +
486A ASP* 3.6 3.5 + - - -
1061D ASP* 2.6 24.4 + - - -
1062D ASP* 1.3 81.9 + - - +
1064D PRO* 1.3 71.0 - - - +
1065D SER* 4.5 1.6 - - - -
1066D GLY 2.8 26.9 + - - -
1067D ILE* 3.0 9.1 + - - +
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Residues in contact with PRO1064 (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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483A LYS* 5.1 5.8 - - + +
486A ASP* 3.4 26.9 - - + +
1016D LEU* 4.5 7.2 - - + +
1019D VAL* 3.8 22.1 - - + +
1020D ALA* 3.8 31.4 - - + +
1023D CYS* 4.3 14.8 - - + -
1062D ASP 4.0 1.3 - - - +
1063D SER* 1.3 83.2 - - - +
1065D SER* 1.3 56.7 + - - +
1067D ILE* 2.9 6.9 + - + +
1068D VAL* 2.8 31.4 + - - +
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Residues in contact with SER1065 (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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485A ARG* 6.3 1.1 - - - -
486A ASP* 2.8 28.6 + - - -
1016D LEU* 3.8 21.2 - - - +
1061D ASP* 4.7 0.9 - - - -
1063D SER* 3.3 2.2 - - - -
1064D PRO* 1.3 72.9 - - - +
1066D GLY* 1.3 66.1 + - - +
1067D ILE 3.0 1.3 - - - -
1068D VAL* 4.0 1.5 - - - +
1069D ASN* 3.1 23.4 + - - +
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Residues in contact with GLY1066 (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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1061D ASP* 3.3 39.4 + - - +
1063D SER* 2.8 16.3 + - - -
1065D SER* 1.3 78.9 - - - +
1067D ILE* 1.3 58.8 + - - +
1069D ASN* 3.7 5.2 - - - +
1070D THR* 3.0 27.4 + - - +
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Residues in contact with ILE1067 (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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516B ASN* 4.6 1.1 - - - +
1019D VAL* 4.0 14.1 - - + -
1023D CYS* 4.1 22.7 - - - -
1040D PHE* 4.2 24.5 - - + -
1052D LEU* 4.1 27.1 - - + +
1053D ILE* 4.2 13.0 - - + -
1061D ASP 4.4 1.3 - - - +
1062D ASP* 3.8 27.1 - - + +
1063D SER 3.0 8.6 + - - +
1064D PRO 2.9 8.1 + - - +
1066D GLY* 1.3 75.3 - - - +
1068D VAL* 1.3 69.6 + - - +
1070D THR* 2.8 23.8 + - - +
1071D VAL* 3.2 11.7 + - + +
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Residues in contact with VAL1068 (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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1012D GLU* 4.2 28.3 - - + +
1015D PHE* 3.9 11.9 - - + -
1016D LEU* 3.4 35.9 - - + -
1019D VAL* 3.8 22.4 - - + -
1064D PRO 2.8 13.4 + - - +
1065D SER 4.1 2.5 - - - +
1067D ILE* 1.3 76.4 - - - +
1069D ASN* 1.3 64.8 + - - +
1071D VAL* 3.1 7.7 + - - +
1072D LYS* 2.9 20.1 + - - -
1083D PHE* 4.5 12.7 - - + -
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Residues in contact with ASN1069 (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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1012D GLU* 5.9 1.0 + - - -
1065D SER 3.1 18.0 + - - +
1066D GLY* 3.7 7.0 - - - +
1068D VAL* 1.3 78.4 - - - +
1070D THR* 1.3 62.8 + - + +
1071D VAL 2.9 0.3 + - - -
1072D LYS* 3.1 10.7 + - - -
1073D GLN* 2.7 54.1 + - - +
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Residues in contact with THR1070 (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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1046D HIS* 5.0 3.8 + - - -
1052D LEU* 5.0 17.4 - - + +
1060D ASP* 4.5 23.8 - - + +
1061D ASP 5.4 3.5 + - - +
1066D GLY 3.0 13.8 + - - +
1067D ILE* 2.8 20.7 + - - +
1069D ASN* 1.3 80.4 - - + +
1071D VAL* 1.3 60.9 + - - +
1073D GLN* 4.0 6.0 - - - +
1074D TRP* 3.2 23.6 + - - +
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Residues in contact with VAL1071 (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* 5.2 2.2 - - + -
1015D PHE* 4.6 15.7 - - + -
1040D PHE* 4.6 11.2 - - + -
1044D THR* 4.0 32.8 - - + -
1046D HIS* 5.3 4.9 - - - +
1052D LEU* 4.8 12.6 - - + -
1067D ILE* 3.6 14.1 - - + +
1068D VAL* 3.1 8.3 + - - +
1069D ASN 2.9 0.2 - - - -
1070D THR* 1.3 78.2 - - - +
1072D LYS* 1.5 57.0 - - - +
1073D GLN 3.4 0.4 - - - -
1074D TRP* 2.8 26.7 + - + +
1075D ARG* 3.0 34.2 + - + +
1083D PHE* 5.1 6.5 - - + -
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Residues in contact with LYS1072 (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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1012D GLU* 4.8 13.5 - - - +
1068D VAL* 2.9 10.6 + - - -
1069D ASN* 3.3 16.6 + - - -
1071D VAL* 1.5 64.9 - - - +
1073D GLN* 2.5 38.6 + - - +
1074D TRP 4.3 0.2 - - - +
1075D ARG* 5.1 6.3 - - - +
1076D ALA* 5.3 7.6 - - - +
1083D PHE* 4.7 21.3 - - - -
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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