Contacts of the helix formed by residues 746 - 754 (chain A) in PDB entry 6VXX
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 SER 746 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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743A CYS 3.4 7.2 + - - +
744A GLY 3.2 2.6 - - - -
745A ASP* 1.3 78.7 - - - +
747A THR* 1.3 59.3 + - - +
748A GLU* 3.4 2.5 + - - -
749A CYS* 3.2 19.3 + - - +
750A SER* 3.0 28.5 + - - -
977A LEU* 3.6 26.7 - - - -
978A ASN* 5.2 2.9 - - - -
981A LEU* 3.3 25.3 - - - +
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Residues in contact with THR 747 (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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745A ASP 4.2 0.8 + - - -
746A SER* 1.3 69.9 - - - +
748A GLU* 1.3 76.5 + - + +
750A SER* 3.8 5.2 - - - -
751A ASN* 3.1 41.0 + - - +
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Residues in contact with GLU 748 (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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746A SER* 3.4 11.3 + - - -
747A THR* 1.3 86.5 + - + +
749A CYS* 1.3 61.2 + - - +
751A ASN* 3.6 6.8 + - - +
752A LEU* 3.4 25.6 + - - +
981A LEU* 3.8 34.0 - - + +
986A PRO* 6.2 4.5 - - + -
990A GLU* 5.8 3.4 - - + +
993A ILE* 4.8 3.1 - - + -
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Residues in contact with CYS 749 (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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742A ILE 4.0 3.6 - - - -
743A CYS* 2.0 58.4 - - + -
746A SER* 3.2 16.3 + - - +
748A GLU* 1.3 76.7 - - - +
750A SER* 1.4 59.1 + - - +
752A LEU* 3.1 6.6 + - - +
753A LEU 2.9 23.7 + - - -
977A LEU* 3.7 16.4 - - + -
993A ILE* 3.6 33.4 - - + +
996A LEU* 6.3 0.4 - - - -
997A ILE* 3.7 8.6 - - - +
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Residues in contact with SER 750 (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* 4.3 16.0 - - - +
743A CYS* 3.6 13.0 - - - -
746A SER 3.0 18.4 + - - -
747A THR* 3.4 7.8 + - - -
749A CYS* 1.4 74.5 - - - +
751A ASN* 1.3 67.2 + - - +
753A LEU* 3.0 7.6 + - - +
754A LEU* 3.0 31.1 + - - +
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Residues in contact with ASN 751 (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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747A THR* 3.1 33.3 + - - +
748A GLU* 3.9 6.9 - - - +
749A CYS 3.3 0.2 - - - -
750A SER* 1.3 79.9 + - - +
752A LEU* 1.3 62.5 + - - +
754A LEU* 3.4 30.7 + - + +
755A GLN* 4.0 9.6 + - - +
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Residues in contact with LEU 752 (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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748A GLU 3.4 15.2 + - - +
749A CYS 3.1 7.0 + - - +
751A ASN* 1.3 76.0 - - + +
753A LEU* 1.3 66.3 + - - +
755A GLN* 3.1 41.8 + - - +
756A TYR* 3.6 8.8 - - - -
990A GLU* 4.0 39.7 - - + +
993A ILE* 3.6 36.1 - - + -
994A ASP* 3.7 22.7 - - - +
997A ILE* 3.7 10.1 - - + -
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Residues in contact with LEU 753 (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* 4.0 34.5 - - + +
742A ILE* 3.8 22.0 - - + -
743A CYS* 4.1 16.4 - - - -
749A CYS 2.9 12.8 + - - +
750A SER* 3.0 10.7 + - - +
752A LEU* 1.3 77.6 - - - +
754A LEU* 1.3 62.7 + - + +
756A TYR* 3.0 29.8 + - + +
757A GLY 4.3 1.7 + - - +
760A CYS* 4.0 23.7 - - + +
997A ILE* 3.8 26.4 - - + +
1001A LEU* 4.8 7.4 - - + -
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Residues in contact with LEU 754 (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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750A SER* 3.0 21.5 + - - +
751A ASN* 3.6 29.2 - - - +
752A LEU 3.2 0.6 - - - -
753A LEU* 1.3 77.0 - - + +
755A GLN* 1.3 60.1 + - + +
756A TYR 3.0 2.4 + - - -
757A GLY* 3.2 19.1 + - - +
52C GLN* 6.0 2.0 - - - +
968C SER* 5.2 0.2 + - - -
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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