Contacts of the helix formed by residues 1011 - 1023 (chain C) 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 THR1011 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1009C ASP 4.1 0.2 + - - -
1010C TYR* 1.3 72.1 - - - +
1012C GLU* 1.3 55.9 + - - +
1013C ALA* 3.6 9.5 + - - +
1014C GLU* 2.3 66.1 + - - +
1015C PHE 2.8 9.9 + - - -
1083C PHE* 4.1 1.3 - - - -
1084C LYS* 3.8 37.4 - - + +
1085C GLN* 4.3 9.6 - - + -
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Residues in contact with GLU1012 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1011C THR* 1.3 71.1 - - - +
1013C ALA* 1.3 62.1 + - - +
1015C PHE* 3.2 1.4 + - - +
1016C LEU* 2.9 25.9 + - + +
1068C VAL* 3.9 19.4 - - + +
1069C ASN* 5.2 1.4 + - - -
1072C LYS* 3.0 46.4 + - - +
1083C PHE* 3.7 33.3 - - + +
1084C LYS 4.4 1.8 + - - +
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Residues in contact with ALA1013 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1011C THR* 2.8 9.8 + - - +
1012C GLU* 1.3 79.6 - - - +
1014C GLU* 1.3 62.6 + - + +
1016C LEU* 3.6 11.4 - - - +
1017C GLN* 3.3 20.8 + - - +
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Residues in contact with GLU1014 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1009C ASP 4.1 4.5 - - - +
1010C TYR* 3.7 23.7 - - + -
1011C THR* 2.3 62.8 + - - +
1013C ALA* 1.3 69.9 - - + +
1015C PHE* 1.3 63.0 + - - +
1017C GLN* 3.4 7.9 + - - +
1018C LEU* 3.3 17.2 + - - +
1084C LYS* 4.1 6.0 + - - -
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Residues in contact with PHE1015 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1007C ILE* 4.7 6.3 - - + -
1010C TYR* 4.0 23.0 - + + -
1011C THR 2.8 4.8 + - - +
1012C GLU 3.8 3.4 - - - +
1014C GLU* 1.3 74.0 - - - +
1016C LEU* 1.3 65.2 + - - +
1018C LEU* 2.9 35.7 + - + +
1019C VAL* 2.9 23.9 + - + +
1040C PHE* 4.1 23.6 - + - -
1043C MET* 4.2 20.2 - - + -
1044C THR* 4.1 14.8 - - + -
1068C VAL* 3.9 14.8 - - + -
1071C VAL* 4.4 15.7 - - + -
1083C PHE* 3.3 41.7 - + + -
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Residues in contact with LEU1016 (chain C).
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* 5.3 4.5 - - - +
1012C GLU* 2.9 19.1 + - + +
1013C ALA* 3.6 11.0 - - - +
1015C PHE* 1.3 77.3 - - - +
1017C GLN* 1.3 64.3 + - - +
1019C VAL 3.0 1.0 + - - -
1020C ALA* 2.9 24.7 + - + +
1064C PRO* 3.8 10.5 - - + -
1065C SER* 3.7 39.5 - - - +
1068C VAL* 3.8 22.2 - - + +
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Residues in contact with GLN1017 (chain C).
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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1013C ALA 3.3 10.2 + - - +
1014C GLU* 3.7 10.1 - - - +
1015C PHE 3.3 0.4 - - - -
1016C LEU* 1.3 79.7 - - - +
1018C LEU* 1.3 61.3 + - - +
1020C ALA* 3.6 7.7 + - - +
1021C THR* 2.8 42.4 + - - +
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Residues in contact with LEU1018 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1010C TYR* 4.4 11.4 - - + +
1014C GLU 3.3 9.4 + - - +
1015C PHE* 2.9 37.3 + - + +
1017C GLN* 1.3 81.2 - - - +
1019C VAL* 1.3 63.5 + - - +
1021C THR* 3.1 13.6 + - - -
1022C ILE* 3.1 23.8 + - + +
1036C LEU* 4.2 30.3 - - + -
1039C HIS* 4.2 22.0 - - + +
1040C PHE* 4.9 13.7 - - + +
1043C MET* 5.5 0.2 - - + -
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Residues in contact with VAL1019 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1015C PHE* 2.9 21.7 + - + +
1016C LEU 3.7 5.2 - - - +
1018C LEU* 1.3 73.9 - - + +
1020C ALA* 1.3 67.0 + - - +
1021C THR 3.0 2.8 + - - -
1022C ILE* 3.2 10.2 + - + +
1023C CYS* 3.0 21.2 + - - +
1040C PHE* 3.7 33.0 - - + -
1053C ILE* 5.9 1.8 - - + -
1064C PRO* 3.7 31.6 - - + +
1067C ILE* 4.2 19.5 - - + -
1068C VAL* 4.1 15.0 - - + -
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Residues in contact with ALA1020 (chain C).
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* 5.8 5.4 - - + +
1016C LEU* 2.9 17.9 + - + +
1017C GLN* 4.1 9.2 - - - +
1019C VAL* 1.3 78.0 - - - +
1021C THR* 1.3 61.3 + - - +
1023C CYS* 3.4 4.3 + - - +
1024C ASP* 3.4 19.9 + - - +
1064C PRO* 3.7 27.8 - - + +
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Residues in contact with THR1021 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1017C GLN* 2.8 32.0 + - - +
1018C LEU* 3.1 12.5 + - - -
1019C VAL 3.0 1.0 - - - -
1020C ALA* 1.3 73.8 - - - +
1022C ILE* 1.3 68.7 + - - +
1023C CYS 2.7 2.5 + - - -
1024C ASP* 2.9 22.5 + - - +
1027C ALA* 4.2 8.5 - - + +
1028C THR* 3.9 23.8 - - + +
1036C LEU* 4.3 11.4 - - + -
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Residues in contact with ILE1022 (chain C).
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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520A ARG* 3.1 22.5 + - - -
1018C LEU* 3.1 18.2 + - + +
1019C VAL* 3.5 11.2 - - + +
1021C THR* 1.3 77.9 - - - +
1023C CYS* 1.3 58.8 + - - +
1024C ASP 3.2 2.0 + - - +
1028C THR* 5.5 0.7 - - - -
1033C LEU* 3.6 22.0 - - + +
1036C LEU* 3.7 35.9 - - + +
1037C ILE* 4.2 9.6 - - + +
1040C PHE* 3.9 37.7 - - + -
1053C ILE* 4.5 19.5 - - + -
1054C TYR* 4.2 7.5 + - - +
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Residues in contact with CYS1023 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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515A ARG* 3.2 25.8 + - - +
516A ASN* 3.2 29.8 + - - +
519A ASP* 3.2 6.1 - - - +
520A ARG* 4.9 3.8 - - - +
1019C VAL* 3.0 20.0 + - - +
1020C ALA* 3.8 9.2 - - - +
1021C THR 2.7 4.0 + - - -
1022C ILE* 1.3 75.8 - - - +
1024C ASP* 1.3 58.7 + - - +
1053C ILE* 4.1 11.7 - - - -
1062C ASP 5.0 0.4 - - - -
1064C PRO* 4.7 13.0 - - + -
1067C ILE* 3.9 26.0 - - - -
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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