Contacts of the helix formed by residues 794 - 802 (chain A) in PDB entry 5LPI
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 794 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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790A VAL* 5.7 0.9 - - - -
791A GLU* 3.0 30.5 + - - -
792A ILE 3.0 0.8 - - - -
793A SER* 1.3 81.3 + - - +
795A LEU* 1.3 59.3 + - - +
796A THR 3.4 2.5 - - - -
797A GLU* 3.3 23.8 + - - +
798A HIS* 2.9 27.3 + - - +
802A GLU* 6.2 0.2 - - - -
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Residues in contact with LEU 795 (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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781A THR* 4.4 10.1 - - + -
783A CYS* 4.9 7.6 - - + -
790A VAL* 3.7 22.0 - - + -
791A GLU 3.2 7.9 + - - +
792A ILE* 3.0 18.6 + - - +
793A SER 3.6 0.8 - - - -
794A SER* 1.3 78.3 - - - +
796A THR* 1.3 58.4 + - - +
798A HIS* 3.1 12.9 + - + +
799A LEU* 2.8 55.3 + - + +
846A PRO* 3.7 18.4 - - + +
847A LEU* 3.8 29.6 - - + -
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Residues in contact with THR 796 (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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793A SER 5.5 0.4 + - - -
794A SER 3.4 0.4 - - - -
795A LEU* 1.3 76.3 - - - +
797A GLU* 1.3 64.5 + - - +
799A LEU* 3.1 10.2 + - - +
800A LEU* 3.0 39.8 + - + +
816A SER* 3.5 26.7 + - - +
817A GLU* 4.4 9.9 - - - +
818A ALA 4.1 10.3 + - - +
844A ARG* 5.9 1.4 - - - +
846A PRO* 3.5 23.7 - - - +
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Residues in contact with GLU 797 (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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794A SER* 3.3 24.6 + - - +
795A LEU 3.3 0.4 - - - -
796A THR* 1.3 79.7 - - - +
798A HIS* 1.3 60.0 + - - +
800A LEU* 4.8 4.3 - - - -
801A THR* 2.7 36.9 + - + +
802A GLU* 3.5 9.0 - - - +
786D CYS* 6.2 0.9 - - - -
804D ASP* 3.6 41.5 - - - +
805D LYS* 2.7 35.8 + - - +
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Residues in contact with HIS 798 (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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783A CYS* 3.6 11.3 - - - +
786A CYS* 3.5 8.5 - - - -
788A GLN* 4.5 8.3 - - - -
790A VAL* 3.6 32.2 - - + +
794A SER 2.9 15.0 + - - +
795A LEU* 3.3 15.7 - - + +
797A GLU* 1.3 77.1 - - - +
799A LEU* 1.3 62.6 + - + +
802A GLU* 2.9 30.2 + - + +
803A CYS* 2.7 48.1 + - + +
903A ZN 2.1 37.3 - - - -
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Residues in contact with LEU 799 (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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783A CYS* 3.9 17.0 - - - -
785A HIS* 3.6 32.3 - - + +
795A LEU* 2.8 44.2 + - + +
796A THR* 3.1 6.3 + - - +
798A HIS* 1.3 77.3 - - + +
800A LEU* 1.3 58.3 + - - +
803A CYS* 4.0 5.6 - - - -
806A LYS* 3.2 27.7 - - - +
809A PHE* 3.3 23.1 - - + -
818A ALA* 3.8 27.6 - - + +
846A PRO* 5.8 2.5 - - + -
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Residues in contact with LEU 800 (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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796A THR* 3.0 35.7 + - + +
797A GLU* 4.1 1.8 - - - +
799A LEU* 1.3 78.8 - - - +
801A THR* 1.3 69.4 + - + +
806A LYS* 3.9 15.5 - - - +
809A PHE* 4.4 7.9 - - + +
810A GLY* 3.8 24.7 - - - +
811A LYS* 4.0 31.0 - - + +
816A SER 4.6 0.2 - - - +
818A ALA* 3.7 24.0 - - + +
786D CYS 5.3 2.5 - - - +
787D LYS* 4.2 25.8 - - + -
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Residues in contact with THR 801 (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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797A GLU* 2.7 25.8 + - + +
800A LEU* 1.3 91.2 - - + +
802A GLU* 1.3 62.5 + - - +
806A LYS* 3.3 26.2 + - - +
785D HIS 3.4 22.9 - - - +
786D CYS* 4.6 5.2 - - - +
787D LYS* 4.2 16.6 - - + +
805D LYS* 2.8 31.1 + - - -
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Residues in contact with GLU 802 (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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794A SER* 6.2 0.2 - - - -
797A GLU* 3.5 16.5 - - - +
798A HIS* 2.9 26.6 + - + +
801A THR* 1.3 88.7 - - - +
803A CYS* 1.3 72.5 + - - +
804A ASP* 3.5 1.6 + - - -
806A LYS* 3.8 3.0 - - - +
805D LYS* 3.2 22.1 + - - +
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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