Contacts of the helix formed by residues 924 - 931 (chain A) in PDB entry 4ASE
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 LEU 924 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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922A GLY 3.6 1.7 + - - -
923A ASN* 1.3 71.2 - - - +
925A SER* 1.3 60.3 + - - +
927A TYR* 3.6 12.5 - - + +
928A LEU* 2.8 56.1 + - + +
1008A TYR* 4.0 28.3 - - + -
1012A VAL* 5.5 1.1 - - + -
1031A ALA* 3.5 8.7 + - + +
1034A ILE* 2.8 41.9 + - + +
1036A LEU* 4.7 8.5 - - + -
1042A VAL* 4.4 13.0 - - + -
1094A LEU* 5.2 2.7 - - + -
1098A ILE* 4.1 30.1 - - + -
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Residues in contact with SER 925 (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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923A ASN* 2.9 9.7 + - - -
924A LEU* 1.3 81.0 - - - +
926A THR* 1.3 63.3 + - - +
928A LEU* 3.4 1.5 + - - -
929A ARG* 3.0 42.2 + - - +
1031A ALA* 3.8 27.2 + - - +
1032A ARG* 4.4 5.2 - - - -
1097A GLU* 4.6 6.4 + - - -
1102A GLY* 3.7 18.6 + - - -
1103A ALA 5.1 0.9 + - - -
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Residues in contact with THR 926 (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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921A PHE 6.2 0.2 - - - -
923A ASN* 2.8 33.5 + - - -
925A SER* 1.3 75.5 - - - +
927A TYR* 1.3 64.1 + - - +
929A ARG* 3.3 27.8 + - - +
930A SER* 3.2 22.7 + - - -
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Residues in contact with TYR 927 (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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921A PHE* 4.0 38.3 + + + +
923A ASN 3.2 15.7 + - - +
924A LEU* 3.6 9.9 - - + +
926A THR* 1.3 79.8 - - - +
928A LEU* 1.3 72.6 + - + +
930A SER* 2.7 28.5 + - - -
931A LYS* 3.3 47.6 + - + +
998A ASP 5.2 0.3 + - - -
1000A LEU* 4.5 10.3 - - + +
1008A TYR* 4.1 12.6 + - - -
1036A LEU* 3.4 36.0 - - + +
1040A ASN* 5.1 3.5 + - - -
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Residues in contact with LEU 928 (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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924A LEU* 2.8 40.1 + - + +
925A SER* 3.9 3.1 - - - +
927A TYR* 1.3 80.2 - - + +
929A ARG* 1.3 62.1 + - - +
931A LYS* 3.2 13.7 + - - +
932A ARG* 3.4 10.7 + - - +
1000A LEU* 3.6 25.6 - - + -
1005A LEU* 4.2 4.3 - - + -
1008A TYR* 4.1 21.1 - - + -
1031A ALA* 6.1 1.3 - - + -
1097A GLU 4.3 0.7 - - - +
1098A ILE* 3.7 39.5 - - + +
1101A LEU* 3.5 30.5 - - + +
1102A GLY* 4.3 6.3 - - - +
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Residues in contact with ARG 929 (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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925A SER* 3.0 35.2 + - - +
926A THR* 3.7 31.6 + - - +
927A TYR 3.2 0.8 - - - -
928A LEU* 1.3 71.9 - - - +
930A SER* 1.3 60.1 + - - +
931A LYS 3.0 9.3 + - - -
932A ARG* 3.2 40.8 + - - +
933A ASN 4.9 0.2 + - - -
1101A LEU 3.3 17.0 - - - +
1102A GLY 3.1 19.1 + - - +
1103A ALA* 5.2 0.4 - - - +
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Residues in contact with SER 930 (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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926A THR* 3.2 13.2 + - - -
927A TYR* 2.7 30.5 + - - -
929A ARG* 1.3 75.5 - - - +
931A LYS* 1.3 63.2 + - - +
932A ARG 3.5 0.2 - - - -
933A ASN* 4.7 5.7 + - - +
934A GLU* 3.5 16.5 - - - +
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Residues in contact with LYS 931 (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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927A TYR* 3.3 50.6 + - + +
928A LEU 3.2 6.0 + - - +
929A ARG 3.0 1.4 - - - -
930A SER* 1.3 82.5 - - - +
932A ARG* 1.3 57.9 + - - +
933A ASN 3.0 2.9 - - - -
934A GLU* 2.8 63.9 + - + +
935A PHE* 3.2 6.2 + - - +
998A ASP* 2.6 35.2 + - - +
1000A LEU* 3.4 28.5 - - + -
1101A LEU* 4.9 0.9 - - - -
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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