Contacts of the helix formed by residues 737 - 743 (chain A) in PDB entry 6VSB
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 ASP 737 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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736A VAL* 1.3 69.6 - - - +
738A CYS* 1.3 60.2 + - - +
739A THR* 3.1 22.3 + - - +
740A MET* 3.2 26.4 + - + +
741A TYR* 2.8 29.5 + - - +
764A ASN* 5.5 5.7 + - - +
857A GLY* 2.9 18.5 + - - +
314C GLN* 5.6 7.3 + - - +
317C ASN* 3.4 41.2 + - - +
319C ARG* 5.1 1.6 + - - -
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Residues in contact with CYS 738 (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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736A VAL* 3.6 6.3 + - + +
737A ASP* 1.3 74.1 + - - +
739A THR* 1.3 63.7 + - - +
741A TYR* 3.0 5.8 + - - -
742A ILE* 2.9 48.7 + - - +
753A LEU* 3.8 2.5 - - - -
760A CYS* 2.0 62.6 - - + +
763A LEU* 5.9 2.7 - - + -
764A ASN* 5.6 4.3 - - + +
1001A LEU* 6.3 0.2 - - - -
1004A LEU* 4.4 15.5 - - + -
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Residues in contact with THR 739 (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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737A ASP* 3.1 22.6 + - - +
738A CYS* 1.3 79.8 - - - +
740A MET* 1.3 58.0 + - + +
743A CYS* 3.3 10.2 + - - +
744A GLY* 2.9 18.9 + - - -
750A SER* 4.2 18.7 - - - -
753A LEU* 4.1 17.9 - - - +
760A CYS* 5.4 1.1 - - - -
317C ASN* 5.8 2.0 - - + -
319C ARG* 6.1 1.8 - - - +
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Residues in contact with MET 740 (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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737A ASP* 3.2 26.0 + - + +
738A CYS 3.1 0.4 - - - -
739A THR* 1.3 81.9 - - + +
741A TYR* 1.3 64.8 + - - +
742A ILE 3.3 0.2 - - - -
743A CYS 3.6 2.1 - - - +
744A GLY* 3.3 29.0 + - - -
745A ASP* 5.3 6.3 - - - +
855A PHE 5.0 0.2 - - - +
856A ASN* 3.7 14.4 - - + +
857A GLY* 3.3 27.8 - - - +
317C ASN* 5.0 1.3 - - - +
319C ARG* 4.3 18.2 - - - +
592C PHE* 3.4 42.6 - - + -
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Residues in contact with TYR 741 (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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736A VAL* 4.2 11.7 - - + -
737A ASP 2.8 21.8 + - - +
738A CYS* 3.7 6.3 - - - +
740A MET* 1.3 75.4 - - - +
742A ILE* 1.3 68.3 + - + +
856A ASN* 4.3 9.8 + - - +
857A GLY* 5.0 0.2 - - - -
858A LEU* 3.8 24.0 - - + -
962A LEU* 2.8 47.8 + - + +
963A VAL* 5.1 0.2 - - - -
965A GLN* 4.2 3.8 - - - +
966A LEU* 3.4 36.7 + - + +
1000A ARG* 4.0 27.3 + - + +
1003A SER* 3.5 18.2 + - - -
1004A LEU* 3.8 24.7 - - + -
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Residues in contact with ILE 742 (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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738A CYS* 2.9 38.8 + - - +
741A TYR* 1.3 88.8 - - + +
743A CYS* 1.3 66.7 + - - +
749A CYS* 4.6 1.4 - - - -
753A LEU* 3.7 19.1 - - + -
977A LEU* 4.5 1.4 - - - +
997A ILE* 3.9 39.6 - - + +
1000A ARG* 2.7 41.2 + - + +
1001A LEU* 4.3 29.2 - - + +
1004A LEU* 4.8 4.9 - - + -
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Residues in contact with CYS 743 (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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739A THR 3.3 9.3 + - - +
740A MET 3.6 3.6 - - - +
742A ILE* 1.3 92.1 - - - +
744A GLY* 1.3 70.8 - - - +
746A SER* 4.4 6.1 - - - +
749A CYS* 2.0 61.2 - - + -
750A SER* 3.5 12.6 - - - +
753A LEU* 4.7 6.3 - - - -
977A LEU* 3.5 17.7 - - + +
997A ILE* 4.6 2.5 - - - -
1000A ARG* 5.0 2.1 + - - -
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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