Contacts of the helix formed by residues 792 - 807 (chain N) in PDB entry 6AH0
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 792 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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787N GLU 4.2 2.4 - - - +
791N GLY* 1.3 73.8 - - - +
793N LYS* 1.3 57.6 + - - +
794N ASN* 2.9 8.5 - - - +
795N ILE* 3.0 20.0 + - - +
796N ALA 3.6 5.2 + - - -
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Residues in contact with LYS 793 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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787N GLU 4.8 4.9 - - - -
788N TYR* 5.0 9.1 + - - +
791N GLY* 3.3 4.4 - - - -
792N LEU* 1.3 71.6 - - - +
794N ASN* 1.3 63.8 + - - +
795N ILE 3.2 0.2 - - - -
796N ALA* 3.1 15.6 + - - +
797N ASN* 3.2 9.9 + - - -
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Residues in contact with ASN 794 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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792N LEU* 2.9 4.7 - - - +
793N LYS* 1.3 78.1 - - - +
795N ILE* 1.3 59.8 + - - +
797N ASN* 3.3 13.2 + - - -
798N THR 4.0 1.7 + - - -
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Residues in contact with ILE 795 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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792N LEU* 3.0 10.7 + - - +
794N ASN* 1.3 71.0 - - - +
796N ALA* 1.3 57.7 + - - +
797N ASN 2.9 4.9 - - - -
798N THR* 2.7 21.6 + - - +
799N LEU* 2.9 10.4 + - - -
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Residues in contact with ALA 796 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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784N VAL* 5.8 9.9 - - - +
787N GLU* 5.7 6.4 + - - +
792N LEU 3.6 4.4 + - - -
793N LYS* 3.1 15.1 + - - +
795N ILE* 1.3 75.3 - - - +
797N ASN* 1.3 60.5 + - - +
798N THR 3.2 0.2 - - - -
799N LEU* 3.9 4.5 - - - +
800N MET* 3.3 17.3 + - - -
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Residues in contact with ASN 797 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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793N LYS 3.2 10.0 + - - -
794N ASN 3.3 7.3 + - - -
795N ILE 2.9 1.8 - - - -
796N ALA* 1.3 77.9 - - - +
798N THR* 1.3 58.8 + - - +
800N MET* 3.9 1.0 + - - -
801N ALA* 3.3 15.8 + - - -
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Residues in contact with THR 798 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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794N ASN 4.0 3.0 + - - -
795N ILE* 2.7 15.2 + - - +
797N ASN* 1.3 70.9 - - - +
799N LEU* 1.3 58.8 + - - +
800N MET 3.2 0.2 - - - -
801N ALA* 2.9 3.0 + - - +
802N LYS* 2.7 28.9 + - - -
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Residues in contact with LEU 799 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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784N VAL* 6.2 2.9 - - - +
795N ILE 2.9 12.8 + - - -
796N ALA* 4.3 2.9 - - - +
798N THR* 1.3 76.7 - - - +
800N MET* 1.3 60.0 + - - +
802N LYS* 4.1 1.1 - - - +
803N ALA* 3.0 21.0 + - - -
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Residues in contact with MET 800 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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796N ALA 3.3 15.7 + - - -
797N ASN 4.2 1.3 - - - -
798N THR 3.2 0.6 - - - -
799N LEU* 1.3 73.5 - - - +
801N ALA* 1.3 52.9 + - - +
803N ALA* 5.1 0.2 - - - +
804N LEU* 2.6 36.6 + - - -
813N LEU 6.1 1.3 - - - -
817N ALA* 6.5 0.9 - - - +
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Residues in contact with ALA 801 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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797N ASN 3.3 12.7 + - - -
798N THR* 2.9 8.8 + - - +
800N MET* 1.3 76.5 - - - +
802N LYS* 1.3 51.3 + - - +
804N LEU* 3.6 0.8 - - - +
805N GLN* 2.7 33.6 + - - -
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Residues in contact with LYS 802 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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798N THR 2.7 17.8 + - - -
799N LEU* 4.1 0.9 - - - +
801N ALA* 1.3 72.7 - - - +
803N ALA* 1.3 62.6 + - - +
805N GLN* 3.4 1.3 + - - +
806N GLU* 3.4 15.1 + - - -
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Residues in contact with ALA 803 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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780N TRP* 6.5 0.7 - - - +
799N LEU 3.0 16.7 + - - -
800N MET* 3.5 0.7 - - - +
802N LYS* 1.3 77.0 - - - +
804N LEU* 1.3 61.4 + - - +
806N GLU* 3.4 9.6 + - - +
807N CYS* 3.4 10.7 + - - -
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Residues in contact with LEU 804 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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800N MET 2.6 22.5 + - - -
801N ALA 3.6 0.7 - - - -
803N ALA* 1.3 71.9 - - - +
805N GLN* 1.3 64.2 + - - +
806N GLU 3.2 0.2 - - - -
808N PRO* 3.3 27.5 - - - +
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Residues in contact with GLN 805 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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801N ALA 2.7 20.2 + - - -
802N LYS* 3.4 3.1 + - - +
803N ALA 3.3 0.2 - - - -
804N LEU* 1.3 74.5 - - - +
806N GLU* 1.3 62.1 + - - +
808N PRO 4.5 1.7 - - - -
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Residues in contact with GLU 806 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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802N LYS 3.4 8.8 + - - -
803N ALA 3.4 6.7 + - - -
804N LEU 3.2 0.6 - - - -
805N GLN* 1.3 80.2 - - - +
807N CYS* 1.3 62.2 + - - +
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Residues in contact with CYS 807 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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803N ALA 3.4 12.6 + - - -
805N GLN 3.6 0.2 - - - -
806N GLU* 1.3 76.7 - - - +
808N PRO* 1.3 60.9 - - - +
809N ASN 3.4 5.5 + - - -
810N SER 4.7 2.6 + - - +
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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