Contacts of the helix formed by residues 742 - 757 (chain B) in PDB entry 5VOT
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 742 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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395B VAL* 4.6 26.7 - - + -
436B CYS* 6.2 3.4 - - + -
438B PHE* 5.8 13.2 - - + -
473B ASP* 5.8 4.5 - - + +
474B ILE* 6.1 5.8 - - + -
736B THR* 5.7 4.3 - - + -
740B SER* 3.6 9.9 + - - +
741B SER* 1.3 84.1 + - - +
743B GLY* 1.3 64.5 + - - +
744B ASN 3.0 1.0 + - - -
745B ALA* 3.2 9.9 + - + +
746B VAL* 3.0 36.8 + - + +
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Residues in contact with GLY 743 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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492B SER* 5.0 3.7 - - - -
736B THR* 4.4 24.4 - - - +
740B SER* 4.2 9.0 + - - -
741B SER 3.2 2.8 - - - -
742B LEU* 1.3 77.8 - - - +
744B ASN* 1.3 55.7 + - - +
746B VAL* 3.7 6.6 - - - +
747B ASN* 2.9 30.7 + - - +
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Residues in contact with ASN 744 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
740B SER 5.4 0.6 + - - -
741B SER 3.6 9.9 + - - +
742B LEU 3.0 0.8 + - - -
743B GLY* 1.3 76.0 - - - +
745B ALA* 1.3 65.9 + - - +
747B ASN* 3.1 10.3 + - - +
748B LEU* 2.9 36.7 + - - +
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Residues in contact with ALA 745 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436B CYS* 4.2 13.3 - - + -
741B SER 4.6 1.5 + - - +
742B LEU* 3.2 12.0 + - + +
744B ASN* 1.3 78.3 - - - +
746B VAL* 1.3 62.6 + - + +
748B LEU* 3.0 19.0 + - + +
749B ALA* 2.9 22.9 + - - +
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Residues in contact with VAL 746 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432B ILE* 3.9 22.8 - - + +
436B CYS* 4.1 21.5 - - + -
438B PHE* 5.4 4.3 - - + -
474B ILE* 4.7 12.6 - - + -
492B SER* 5.4 2.7 - - - -
734B ILE* 4.5 23.1 - - + -
736B THR* 5.8 1.6 - - + -
742B LEU* 3.0 35.5 + - + +
743B GLY* 3.7 7.4 - - - +
745B ALA* 1.3 77.2 - - + +
747B ASN* 1.3 63.1 + - - +
749B ALA* 3.1 4.5 + - - +
750B VAL* 2.9 36.7 + - + +
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Residues in contact with ASN 747 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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492B SER* 3.9 16.9 - - - +
493B LYS* 3.5 60.1 + - - +
743B GLY 2.9 15.1 + - - +
744B ASN* 3.3 13.1 + - - +
746B VAL* 1.3 75.1 - - - +
748B LEU* 1.3 64.0 + - + +
750B VAL* 3.2 5.7 + - - +
751B LEU* 2.9 34.3 + - - +
486C GLU* 5.5 2.0 + - - -
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Residues in contact with LEU 748 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
744B ASN* 2.9 30.8 + - - +
745B ALA* 3.0 23.3 + - + +
747B ASN* 1.3 77.2 - - + +
749B ALA* 1.3 63.3 + - - +
751B LEU* 3.1 11.5 + - + +
752B LYS* 2.9 21.4 + - - +
483C LEU* 3.7 23.1 - - + +
486C GLU* 5.1 11.2 - - + +
487C GLU* 5.7 6.3 - - + -
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Residues in contact with ALA 749 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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432B ILE* 4.6 9.4 - - + -
435B HIS* 3.8 30.2 - - + -
436B CYS* 4.3 11.4 - - - -
745B ALA 2.9 12.8 + - - +
746B VAL 3.7 6.1 - - - +
748B LEU* 1.3 76.0 - - - +
750B VAL* 1.3 63.4 + - - +
752B LYS* 3.1 13.0 + - + +
753B LEU* 2.9 28.9 + - - +
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Residues in contact with VAL 750 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428B LEU* 5.7 3.4 - - + -
432B ILE* 3.8 22.0 - - + -
492B SER* 4.7 9.0 - - - +
493B LYS 4.5 11.7 - - - +
495B PHE* 4.3 26.2 - - + -
734B ILE* 4.8 9.4 - - + -
746B VAL* 2.9 27.8 + - + +
747B ASN* 3.4 13.0 - - - +
749B ALA* 1.3 75.9 - - - +
751B LEU* 1.3 67.5 + - + +
753B LEU* 3.1 8.7 + - - +
754B ASN* 2.9 22.6 + - + +
759B LEU* 4.6 5.6 - - + +
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Residues in contact with LEU 751 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493B LYS* 4.3 17.5 - - + -
747B ASN* 2.9 38.9 + - - +
748B LEU* 3.5 9.6 - - + +
750B VAL* 1.3 78.7 - - + +
752B LYS* 1.3 63.4 + - - +
754B ASN* 3.1 14.6 + - + +
755B GLU* 2.9 26.5 + - - +
481C ILE* 5.4 8.7 - - + +
482C THR 5.8 0.4 - - - -
483C LEU* 3.6 26.2 - - + +
486C GLU* 3.5 35.7 - - + -
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Residues in contact with LYS 752 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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435B HIS* 4.5 21.8 + - + +
748B LEU 2.9 12.9 + - - +
749B ALA* 3.3 13.9 - - - +
751B LEU* 1.3 77.1 - - - +
753B LEU* 1.3 51.5 + - - +
755B GLU* 3.2 6.2 + - - +
756B GLN* 2.7 64.8 + - + +
483C LEU* 3.8 24.6 - - + +
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Residues in contact with LEU 753 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428B LEU* 5.1 2.5 - - + -
431B GLU* 3.8 34.3 - - + +
432B ILE* 4.1 18.6 - - + -
435B HIS* 3.4 24.2 - - + +
749B ALA 2.9 18.2 + - - +
750B VAL* 3.6 7.6 - - - +
752B LYS* 1.3 74.4 - - + +
754B ASN* 1.3 53.2 + - - +
756B GLN* 2.9 26.0 + - + +
757B GLY* 2.6 33.8 + - - -
758B LEU* 3.8 14.6 + - + -
759B LEU* 4.0 29.5 - - + +
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Residues in contact with ASN 754 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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494B PRO 5.2 6.3 + - - -
495B PHE* 5.1 12.8 + - + +
750B VAL* 2.9 16.0 + - + +
751B LEU* 3.1 19.0 + - + +
753B LEU* 1.3 76.3 - - - +
755B GLU* 1.3 63.3 + - + +
757B GLY* 3.2 13.3 + - - +
759B LEU* 4.0 15.6 - - + +
760B ASP* 5.3 4.7 - - - +
658C PHE* 6.1 0.5 - - - -
728C ASP* 5.6 4.9 - - - +
729C SER* 3.5 29.1 + - - +
730C LYS* 5.4 3.2 - - - +
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Residues in contact with GLU 755 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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751B LEU 2.9 12.6 + - - +
752B LYS* 3.6 6.5 - - - +
754B ASN* 1.3 75.7 - - + +
756B GLN* 1.3 62.5 + - + +
757B GLY* 3.3 1.4 + - - -
482C THR* 3.2 17.8 - - + -
483C LEU* 2.6 50.8 + - - +
484C VAL* 4.1 7.6 + - - +
658C PHE* 4.7 20.1 - - + -
661C ARG* 6.1 1.2 - - - +
730C LYS* 6.1 2.9 - - - +
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Residues in contact with GLN 756 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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435B HIS* 4.4 7.6 - - - -
752B LYS* 2.7 52.2 + - + +
753B LEU* 2.9 29.9 + - + +
755B GLU* 1.3 73.1 - - + +
757B GLY* 1.3 57.0 + - - +
758B LEU* 2.9 18.1 + - + +
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Residues in contact with GLY 757 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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753B LEU 2.6 13.3 + - - -
754B ASN* 3.2 10.2 + - - -
755B GLU 3.1 4.7 - - - -
756B GLN* 1.3 71.8 - - - +
758B LEU* 1.3 57.1 + - - -
759B LEU* 3.0 3.8 - - - -
760B ASP* 2.9 42.0 + - - +
761B LYS* 3.6 3.1 + - - +
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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