Contacts of the helix formed by residues 1036 - 1042 (chain A) in PDB entry 3SQD
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 CYS1036 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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981A THR* 4.4 11.0 - - - -
1026A LEU* 6.4 0.4 - - - -
1028A SER* 3.8 30.3 - - - -
1032A ASP 4.1 5.8 - - - -
1033A LEU* 2.9 6.9 + - - +
1035A LEU* 1.3 80.5 - - - +
1037A ARG* 1.3 64.0 + - - +
1038A GLU 3.3 2.7 - - - -
1039A TYR* 2.9 23.8 + - + +
1040A PHE* 2.9 37.2 + - + -
1046A VAL* 4.3 17.9 - - + -
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Residues in contact with ARG1037 (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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1033A LEU 3.4 3.1 + - - +
1034A HIS* 3.1 57.3 + - - +
1035A LEU 3.4 2.4 - - - -
1036A CYS* 1.3 78.6 - - - +
1038A GLU* 1.3 66.8 + - + +
1040A PHE* 3.2 11.2 + - + +
1041A ALA* 3.2 19.8 + - - +
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Residues in contact with GLU1038 (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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1009A PHE* 3.7 24.2 - - + -
1035A LEU 5.1 1.2 + - - +
1036A CYS 3.3 0.2 - - - -
1037A ARG* 1.3 80.5 - - + +
1039A TYR* 1.3 66.9 + - + +
1041A ALA* 3.4 10.0 + - - +
1042A ARG* 3.2 25.5 + - - +
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Residues in contact with TYR1039 (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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1006A GLN* 3.1 32.9 + - + +
1007A PRO* 2.5 31.5 + - + -
1008A SER* 4.2 4.0 - - - -
1009A PHE* 3.5 29.6 + + - -
1012A LEU* 3.6 24.2 - - + -
1026A LEU* 4.3 13.7 - - + -
1035A LEU 4.1 7.4 - - - -
1036A CYS* 2.9 29.6 + - + +
1038A GLU* 1.3 81.9 - - + +
1040A PHE* 1.3 61.4 + - - +
1042A ARG* 3.0 13.9 + - - +
1044A ILE* 3.1 30.1 + - + +
1046A VAL* 4.9 6.5 - - + -
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Residues in contact with PHE1040 (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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1033A LEU* 4.0 30.7 - - + -
1036A CYS* 2.9 43.5 + - + -
1037A ARG* 3.6 9.2 - - + +
1039A TYR* 1.3 75.7 - - - +
1041A ALA* 1.3 58.9 + - - +
1043A GLY* 2.9 19.4 + - - -
1044A ILE 4.0 9.6 - - - -
1046A VAL* 3.7 36.8 - - + -
1068A PHE* 4.0 18.8 - - + -
1069A ASN* 3.5 27.7 - - - +
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Residues in contact with ALA1041 (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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1037A ARG 3.2 12.2 + - - +
1038A GLU* 3.6 13.0 - - - +
1039A TYR 3.2 0.4 - - - -
1040A PHE* 1.3 78.2 - - - +
1042A ARG* 1.3 60.1 + - + +
1043A GLY 3.3 0.9 + - - -
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Residues in contact with ARG1042 (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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1009A PHE* 3.2 54.9 - - + +
1038A GLU 3.2 13.7 + - - +
1039A TYR 3.0 11.8 + - - +
1041A ALA* 1.3 76.6 - - + +
1043A GLY* 1.3 59.5 + - - +
1044A ILE* 3.8 16.9 - - + +
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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