Contacts of the helix formed by residues 760 - 768 (chain x) in PDB entry 5Z58
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 760 (chain x).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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755x ILE 5.9 2.2 - - - +
758x THR 3.7 2.8 + - - +
759x SER* 1.3 72.5 - - - +
761x GLY* 1.3 64.5 + - - +
762x ASN 3.5 1.3 - - - -
763x VAL* 3.3 12.9 + - + +
764x VAL* 3.0 21.0 + - - +
784x PRO* 6.3 3.4 - - + -
788x THR* 4.1 15.7 - - - +
789x LEU* 5.0 4.3 - - + -
792x ALA* 3.4 22.8 - - + +
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Residues in contact with GLY 761 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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759x SER* 3.4 7.7 - - - -
760x LEU* 1.3 80.5 - - - +
762x ASN* 1.3 61.8 + - - +
764x VAL* 3.2 11.1 + - - +
765x LEU* 3.4 10.4 + - - +
792x ALA* 3.4 25.1 - - - +
795x GLN* 5.2 6.5 - - - -
796x LEU* 5.0 7.4 - - - +
822x PRO* 5.8 2.4 - - - +
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Residues in contact with ASN 762 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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759x SER* 5.1 2.4 + - - +
761x GLY* 1.3 72.9 - - - +
763x VAL* 1.3 65.7 + - - +
765x LEU* 3.3 9.7 + - - +
766x LEU* 3.0 23.7 + - - +
820x VAL 4.8 12.8 - - - +
821x ASP* 5.0 9.6 - - + -
822x PRO* 5.0 9.3 - - + +
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Residues in contact with VAL 763 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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759x SER 4.7 4.6 + - - +
760x LEU* 3.4 22.3 - - + +
761x GLY 3.2 0.8 - - - -
762x ASN* 1.3 79.3 - - - +
764x VAL* 1.3 56.5 + - - +
766x LEU* 3.3 7.2 + - - +
767x LEU* 2.9 28.6 + - - +
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Residues in contact with VAL 764 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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760x LEU 3.0 12.3 + - - +
761x GLY* 3.6 9.9 - - - +
762x ASN 3.2 0.2 - - - -
763x VAL* 1.3 74.7 - - - +
765x LEU* 1.3 57.8 + - - +
767x LEU* 2.9 5.6 + - - +
768x LYS* 2.6 40.3 + - + +
792x ALA* 5.2 9.2 - - + +
793x LEU* 5.3 8.5 - - + +
796x LEU* 5.8 4.3 - - + -
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Residues in contact with LEU 765 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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761x GLY 3.4 7.5 + - - +
762x ASN* 3.3 12.2 + - - +
764x VAL* 1.3 78.5 - - - +
766x LEU* 1.3 60.0 + - - +
768x LYS* 4.2 4.7 - - - +
769x SER* 3.4 20.6 + - - -
796x LEU* 5.7 8.8 - - + +
801x ALA* 6.2 4.0 - - + -
812x GLY 5.7 5.4 - - - +
816x ALA* 4.8 12.2 - - + +
822x PRO* 5.1 12.6 - - + -
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Residues in contact with LEU 766 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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502x LEU* 6.4 1.8 - - + -
506x LEU* 5.2 8.1 - - + +
762x ASN 3.0 16.3 + - - +
763x VAL* 3.7 7.4 - - - +
764x VAL 3.1 0.2 - - - -
765x LEU* 1.3 76.3 - - - +
767x LEU* 1.3 62.6 + - - +
769x SER* 3.5 7.4 - - - -
770x LEU* 3.5 16.6 + - - +
816x ALA* 6.1 1.6 - - - -
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Residues in contact with LEU 767 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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763x VAL 2.9 17.9 + - - +
764x VAL* 3.6 6.5 - - - +
766x LEU* 1.3 74.0 - - - +
768x LYS* 1.3 55.4 + - - +
769x SER 3.0 4.5 - - - -
770x LEU* 2.7 33.2 + - - +
771x GLY 3.4 3.3 + - - -
772x ILE* 3.8 17.5 + - + +
775x LEU* 6.2 4.3 - - + -
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Residues in contact with LYS 768 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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764x VAL* 2.6 23.6 + - + +
765x LEU* 4.7 4.0 - - - +
767x LEU* 1.3 71.7 - - - +
769x SER* 1.3 59.7 + - - +
770x LEU 3.3 0.2 - - - -
771x GLY* 3.7 9.3 + - - +
772x ILE 4.7 10.9 + - - +
806x GLY 5.6 6.1 - - - +
808x LEU* 6.2 4.5 - - + -
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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