Contacts of the helix formed by residues 940 - 945 (chain A) in PDB entry 5G04
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 THR 940 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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938A GLY 3.6 11.8 + - - +
939A PHE* 1.3 82.6 - - - +
941A LEU* 1.3 66.5 + - - +
942A ARG* 4.3 3.7 + - - +
943A ASP* 3.2 21.6 + - - +
944A LEU* 3.1 20.4 + - - +
977A LEU* 4.3 6.3 - - - -
565O GLN* 3.8 12.2 + - - +
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Residues in contact with LEU 941 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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940A THR* 1.3 74.1 - - - +
942A ARG* 1.3 93.6 + - - +
944A LEU* 3.4 20.5 - - + +
945A GLU* 3.8 3.6 + - - +
959A ILE* 5.8 2.2 - - + -
976A LEU 3.5 22.0 - - - +
977A LEU* 3.1 42.7 - - + +
978A ILE 4.4 7.0 - - - +
979A GLY* 4.7 4.9 - - - +
981A GLN* 6.3 0.7 - - - +
1785A GLU* 4.0 26.1 - - + +
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Residues in contact with ARG 942 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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940A THR* 3.2 4.3 + - - +
941A LEU* 1.3 103.3 - - - +
943A ASP* 1.3 56.2 + - - +
945A GLU* 3.0 28.2 + - - +
561O HIS* 4.5 0.4 - - - +
565O GLN* 3.2 36.0 + - + +
568O LEU* 3.8 20.2 - - + +
584O LEU* 5.6 0.2 - - - +
587O VAL* 5.3 0.4 - - + -
591O TYR* 3.6 3.8 + - - +
603O MET* 3.4 44.0 - - + -
606O GLN* 5.2 9.7 + - - +
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Residues in contact with ASP 943 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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869A ARG* 3.5 27.9 + - - -
939A PHE* 4.2 14.9 - - + -
940A THR* 3.2 25.0 + - - +
942A ARG* 1.3 71.8 - - - +
944A LEU* 1.3 61.1 + - - +
945A GLU 3.0 4.9 - - - -
946A THR* 2.9 29.7 + - - -
947A LEU* 4.0 2.3 + - - +
561O HIS* 4.4 9.0 + - - -
562O LYS* 4.3 19.2 - - - +
565O GLN* 3.1 21.8 - - - +
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Residues in contact with LEU 944 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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939A PHE* 3.4 38.7 - - + -
940A THR 3.1 7.8 + - - +
941A LEU* 3.4 15.3 - - + +
943A ASP* 1.3 74.0 - - - +
945A GLU* 1.3 61.6 - - - +
946A THR 3.5 0.2 + - - -
947A LEU* 3.6 23.9 + - + +
952A ALA* 4.8 6.8 - - + +
955A ILE* 3.9 19.5 - - + -
956A ARG* 3.3 35.8 + - + +
959A ILE* 3.7 30.7 - - + -
977A LEU* 4.3 7.0 - - + -
1785A GLU* 4.8 4.3 - - - +
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Residues in contact with GLU 945 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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941A LEU 3.8 3.7 + - - +
942A ARG* 3.0 21.8 + - - +
944A LEU* 1.3 78.9 - - - +
946A THR* 1.3 58.6 + - - +
947A LEU 3.6 3.5 - - - +
956A ARG* 3.9 15.3 + - - +
1785A GLU* 3.7 18.3 - - - +
1788A PRO* 4.1 14.0 - - - +
591O TYR* 3.5 18.4 - - + +
599O ILE* 2.9 50.5 - - + +
602O PRO* 3.2 24.8 - - - +
603O MET* 3.8 14.1 - - - +
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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