Contacts of the helix formed by residues 1050 - 1055 (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 SER1050 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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528A LYS* 5.9 1.7 - - - +
529A THR 5.5 2.6 + - - -
531A THR* 4.1 20.3 + - - +
1037C ILE* 3.8 28.8 - - - +
1040C PHE* 5.7 0.7 - - - -
1048C SER 3.1 1.2 + - - -
1049C GLY* 1.3 70.3 - - - -
1051C ASP* 1.3 62.7 + - - +
1052C LEU 2.9 1.1 - - - +
1053C ILE* 2.9 31.3 + - - +
1054C TYR* 3.0 29.3 + - - +
1055C TYR* 5.6 0.4 - - - -
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Residues in contact with ASP1051 (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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529A THR 4.8 0.3 - - - +
530A ARG* 3.7 28.1 + - - +
531A THR* 3.2 35.2 + - - -
532A GLN* 4.7 6.1 - - - +
1048C SER* 3.5 20.6 + - - +
1050C SER* 1.3 76.7 + - - +
1052C LEU* 1.3 58.5 + - - +
1055C TYR* 2.8 52.2 + - + +
1056C PRO* 3.8 0.2 - - - +
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Residues in contact with LEU1052 (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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1040C PHE* 4.6 7.6 - - + -
1046C HIS* 3.9 35.0 - - + +
1048C SER* 3.8 23.5 + - - +
1049C GLY 3.3 17.6 + - - +
1050C SER 2.9 0.6 - - - -
1051C ASP* 1.3 79.7 - - - +
1053C ILE* 1.3 61.7 + - + +
1056C PRO* 4.0 16.7 - - + +
1060C ASP* 5.7 4.5 - - - +
1062C ASP* 5.2 1.6 - - - +
1067C ILE* 4.3 23.5 - - + +
1070C THR* 5.4 13.2 - - - +
1071C VAL* 4.2 22.7 - - + +
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Residues in contact with ILE1053 (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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514A SER* 4.7 0.2 + - - -
516A ASN* 2.6 39.4 - - + +
1019C VAL* 5.9 1.6 - - + -
1022C ILE* 4.5 18.8 - - + -
1023C CYS* 4.1 14.6 - - - -
1037C ILE* 5.4 3.1 - - + -
1040C PHE* 3.6 45.1 - - + -
1050C SER* 2.9 24.1 + - - +
1052C LEU* 1.3 80.1 - - - +
1054C TYR* 1.3 83.0 + - + +
1056C PRO* 4.4 4.0 - - - +
1062C ASP* 5.3 0.3 - - - +
1067C ILE* 4.3 15.4 - - + +
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Residues in contact with TYR1054 (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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514A SER* 3.1 24.1 + - - -
516A ASN* 3.6 26.5 - - + -
517A ASN* 3.5 22.2 + - - +
520A ARG* 3.0 40.5 + - - -
528A LYS* 3.6 27.4 - - + -
529A THR 5.8 0.4 - - - -
1022C ILE* 4.2 3.3 + - - +
1033C LEU* 3.9 2.6 - - - +
1037C ILE* 3.6 26.7 - - + +
1050C SER* 3.0 23.7 + - - -
1053C ILE* 1.3 90.6 - - + +
1055C TYR* 1.3 89.4 + - + +
1056C PRO* 3.2 5.6 - - - -
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Residues in contact with TYR1055 (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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513A PHE* 5.7 3.4 - + - -
517A ASN* 3.8 8.3 + - - -
527A PRO* 5.1 0.2 - - - +
528A LYS 2.3 34.7 + - - -
529A THR* 3.4 18.7 - - - -
530A ARG* 3.5 60.2 + - + +
541A PHE* 3.8 12.5 - + - -
1050C SER 5.6 0.2 - - - -
1051C ASP* 2.8 30.6 + - - +
1054C TYR* 1.3 95.7 - - + +
1056C PRO* 1.3 64.2 - - - +
1057C GLU* 3.7 6.9 + - - +
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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