Contacts of the helix formed by residues 791 - 805 (chain N) in PDB entry 5A31
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 ASP 791 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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429N ARG* 5.6 7.3 + - - -
509N TYR 4.7 17.2 - - - +
510N GLY 5.8 0.4 - - - +
511N SER* 5.1 3.6 - - - +
774N TYR* 4.0 9.4 - - - +
790N ILE* 1.3 75.6 - - - +
792N LEU* 1.3 65.4 + - - +
793N GLN* 4.1 11.1 - - - +
794N GLU* 3.0 27.7 + - - +
795N LEU* 3.0 18.9 + - - +
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Residues in contact with LEU 792 (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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770N LEU* 3.8 31.4 - - + +
771N ASP* 5.0 11.4 - - - +
774N TYR* 3.7 49.1 + - + -
791N ASP* 1.3 75.0 - - - +
793N GLN* 1.3 58.5 + - - +
795N LEU* 3.1 5.0 + - + +
796N GLN* 2.9 28.6 + - + +
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Residues in contact with GLN 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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426N ARG* 2.7 45.4 + - - +
429N ARG* 4.1 5.2 + - - -
791N ASP* 3.3 10.2 + - - +
792N LEU* 1.3 78.4 - - - +
794N GLU* 1.3 64.0 + - - +
796N GLN* 3.2 9.1 + - - +
797N GLY* 2.9 21.1 + - - -
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Residues in contact with GLU 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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751N LEU* 5.8 3.6 - - - +
754N PHE* 5.7 0.3 - - - -
789N GLU 4.4 3.3 - - - +
790N ILE* 3.2 30.0 - - + +
791N ASP* 3.0 19.5 + - - +
793N GLN* 1.3 78.6 - - - +
795N LEU* 1.3 64.7 + - - +
797N GLY* 3.4 2.2 + - - -
798N TYR* 2.9 25.4 + - + +
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Residues in contact with LEU 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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754N PHE* 6.0 0.4 - - + -
758N ILE* 4.3 6.5 - - + -
770N LEU* 3.8 11.4 - - + -
773N ILE* 4.1 5.8 - - + -
774N TYR* 3.5 48.9 - - + +
777N LEU* 3.7 23.8 - - + -
790N ILE* 3.8 18.1 - - + +
791N ASP 3.0 13.1 + - - +
792N LEU* 3.1 9.2 + - - +
794N GLU* 1.3 78.1 - - - +
796N GLN* 1.3 63.0 + - - +
798N TYR* 3.2 8.8 + - + +
799N LEU* 2.9 46.1 + - + +
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Residues in contact with GLN 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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770N LEU* 3.7 35.2 - - + +
792N LEU* 2.9 16.4 + - + +
793N GLN* 3.2 7.3 + - - +
795N LEU* 1.3 77.9 - - - +
797N GLY* 1.3 61.7 + - - +
799N LEU* 3.2 3.2 + - - +
800N GLN* 2.9 54.9 + - + +
815N TYR* 4.3 10.1 + - - +
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Residues in contact with GLY 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 GLN 2.9 14.1 + - - -
794N GLU* 3.8 2.9 - - - -
796N GLN* 1.3 77.4 - - - +
798N TYR* 1.3 54.7 + - - +
800N GLN* 3.3 14.8 + - - +
801N LYS* 2.9 28.6 + - - +
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Residues in contact with TYR 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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751N LEU* 3.3 40.2 + - + -
752N LEU* 4.7 4.9 + - - +
754N PHE* 5.1 3.6 - - + -
755N TRP* 3.3 16.3 - + + +
758N ILE* 4.4 22.2 - - + -
790N ILE* 5.7 1.8 - - + -
794N GLU 2.9 18.0 + - - +
795N LEU* 3.4 11.4 - - + +
797N GLY* 1.3 73.6 - - - +
799N LEU* 1.3 68.1 + - + +
801N LYS* 3.3 8.7 + - + +
802N LYS* 2.8 67.2 + - + +
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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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758N ILE* 3.9 32.5 - - + -
770N LEU* 3.5 31.9 - - + -
773N ILE* 4.0 18.4 - - + -
795N LEU* 2.9 30.4 + - + +
796N GLN 3.9 1.6 - - - +
798N TYR* 1.3 74.9 - - + +
800N GLN* 1.3 57.5 + - - +
802N LYS* 3.2 5.0 + - + +
803N VAL* 2.9 31.2 + - - +
808N LEU* 3.7 22.6 - - + +
815N TYR* 3.6 33.7 - - + +
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Residues in contact with GLN 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 GLN* 2.9 53.4 + - + +
797N GLY* 3.5 13.3 + - - +
799N LEU* 1.3 75.7 - - - +
801N LYS* 1.3 59.6 + - - +
803N VAL* 3.2 9.1 + - - +
804N ARG* 2.9 28.2 + - - +
815N TYR* 4.4 8.6 + - - +
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Residues in contact with LYS 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 GLY 2.9 17.0 + - - +
798N TYR* 3.3 9.6 + - + +
800N GLN* 1.3 76.4 - - - +
802N LYS* 1.3 63.0 + - + +
804N ARG* 3.3 7.3 + - - +
805N ASP* 3.0 35.7 + - - +
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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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752N LEU* 5.7 2.2 - - - +
755N TRP* 3.5 45.4 - - + -
798N TYR* 2.8 59.1 + - + +
799N LEU* 3.4 8.7 - - + +
801N LYS* 1.3 79.2 - - + +
803N VAL* 1.3 60.1 + - - +
805N ASP* 3.4 2.8 + - - +
806N GLN 3.1 2.8 + - - -
807N GLN* 2.9 56.3 + - + +
808N LEU* 3.2 23.2 + - + -
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Residues in contact with VAL 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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799N LEU 2.9 16.6 + - - +
800N GLN* 3.2 9.6 + - - +
802N LYS* 1.3 73.9 - - - +
804N ARG* 1.3 66.9 + - - +
806N GLN* 3.1 16.5 + - - +
808N LEU* 3.3 32.9 - - + +
809N VAL* 4.0 0.7 - - - -
810N TYR* 3.9 34.1 - - + +
815N TYR* 4.0 10.3 - - + -
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Residues in contact with ARG 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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146I PRO* 4.5 27.0 - - + +
800N GLN 2.9 13.6 + - - +
801N LYS* 3.3 12.3 + - - +
803N VAL* 1.3 78.4 - - - +
805N ASP* 1.3 64.6 + - - +
806N GLN* 3.2 10.8 + - - +
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Residues in contact with ASP 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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146I PRO 4.8 6.4 - - - +
148I ASN* 5.1 9.0 - - - +
801N LYS* 3.0 25.9 + - - +
802N LYS* 5.5 0.9 - - - +
804N ARG* 1.3 82.1 - - - +
806N GLN* 1.3 69.0 + - - +
807N GLN* 3.1 27.7 + - + +
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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